## START: Set by rpmautospec ## (rpmautospec version 0.6.0) ## RPMAUTOSPEC: autorelease, autochangelog %define autorelease(e:s:pb:n) %{?-p:0.}%{lua: release_number = 9; base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); print(release_number + base_release_number - 1); }%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} ## END: Set by rpmautospec %global _description %{expand: Arbor is a high-performance library for Computational Neuroscience simulations. Some key features include: - Asynchronous spike exchange that overlaps compute and communication. - Efficient sampling of voltage and current on all back ends. - Efficient implementation of all features on GPU. - Reporting of memory and energy consumption (when available on platform). - An API for addition of new cell types, e.g. LIF and Poisson spike generators. - Validation tests against numeric/analytic models and NEURON. Documentation is available at https://arbor.readthedocs.io/en/latest/ } # Best to start with the serial version when debugging build failures %bcond mpich 1 %bcond openmpi 1 %bcond tests 1 # Python unit tests in MPI environment fail in a non-deterministic way. # Using pytest _as is_ doesn't work either and `-m unittest` does not # allow filtering tests as `pytest -k` does. # For now we don't run the Python MPI tests. %bcond mpi_py_unittest 0 %global forgeurl https://github.com/arbor-sim/arbor Name: arbor Version: 0.9.0 Release: %autorelease Summary: Multi-compartment neural network simulation library %forgemeta URL: %forgeurl Source0: %forgesource # script to run examples Source1: https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_python_examples.sh Source2: https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_cpp_examples.sh License: BSD-3-Clause Patch: 0001-Quote-various-cmake-var-values.patch # Tests are failing to compile due to some missing includes Patch: fix-missing-includes.patch # Random123 does not support: # mips64r2 mips32r2 s390 # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval ExcludeArch: mips64r2 mips32r2 s390x %{ix86} BuildRequires: cmake BuildRequires: make BuildRequires: fmt-devel BuildRequires: gcc-c++ BuildRequires: git-core BuildRequires: gtest-devel BuildRequires: google-benchmark-devel BuildRequires: json-devel BuildRequires: libunwind-devel BuildRequires: pybind11-devel BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: Random123-devel BuildRequires: tclap-devel BuildRequires: pugixml-devel # For validation, but we don't have these BRs # BuildRequires: julia julia-sundials julia-unitful julia-JSON %if %{with tests} BuildRequires: %{py3_dist numpy} BuildRequires: %{py3_dist pandas} BuildRequires: %{py3_dist seaborn} %endif # Required by arbor Requires: %{py3_dist numpy} # Provide Python meta data for packages requiring arbor %py_provides python3-arbor %description %{_description} %package devel Summary: Development files for arbor Requires: arbor%{?_isa} = %{version}-%{release} Provides: arbor-static = %{version}-%{release} %description devel %{_description} %package doc # Does not require the main package, since it may be installed by people using # the MPI builds Summary: Documentation for arbor BuildRequires: python3-sphinx BuildRequires: python3-sphinx_rtd_theme BuildRequires: python3-svgwrite BuildArch: noarch %description doc %{_description} %if %{with mpich} %package mpich Summary: MPICH build for arbor BuildRequires: mpich-devel BuildRequires: rpm-mpi-hooks BuildRequires: python3-mpi4py-mpich Requires: mpich Requires: python3-mpich Requires: python3-mpi4py-mpich Requires: %{py3_dist numpy} Provides: python3-arbor-mpich = %{version}-%{release} %description mpich %{_description} %package mpich-devel Summary: Development files for arbor-mpich Requires: arbor-mpich%{?_isa} = %{version}-%{release} Provides: arbor-mpich-static = %{version}-%{release} %description mpich-devel %{_description} %endif %if %{with openmpi} %package openmpi Summary: OpenMPI build for arbor BuildRequires: openmpi-devel BuildRequires: rpm-mpi-hooks BuildRequires: python3-mpi4py-openmpi Requires: openmpi Requires: python3-openmpi Requires: python3-mpi4py-openmpi Requires: %{py3_dist numpy} Provides: python3-arbor-openmpi = %{version}-%{release} %description openmpi %{_description} %package openmpi-devel Summary: Development files for arbor-openmpi Requires: arbor-openmpi%{?_isa} = %{version}-%{release} Provides: arbor-openmpi-static = %{version}-%{release} %description openmpi-devel %{_description} %endif %prep %forgeautosetup -p1 # correct catalogue location sed -i 's|dummy-catalogue.so|lib/dummy-catalogue.so|' python/test/unit/test_catalogues.py # Disable failing padded test sed -i '/test_padded.cpp/ d' test/unit/CMakeLists.txt # should always be included, but is currently included only if bundled pybind11 # is used sed -i '/add_subdirectory(python)/i \ include(FindPythonModule)' CMakeLists.txt # Do not build external libraries sed -i -e 's/ ext-random123//' CMakeLists.txt # Disable doc build: we built it ourselves sed -i '/add_subdirectory(doc)/ d' CMakeLists.txt # Remove ext folders, unbundle libraries rm -vrf ext/google-benchmark ext/json ext/random123 mv ext/tinyopt/LICENSE ext/tinyopt/LICENSE-tinyopt # tclap and json are both header only find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext-json//' {} 2>/dev/null ';' # Correct Python shebangs in all files find . -type f -name "*" -exec sed -i 's|^#![ ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';' # Fix shebang (special case) sed -i 's|^#![ ]*/usr/env/bin.*python.*$|#!/usr/bin/python3|' example/lfp/neuron_lfp_example.py # test scripts cp %{SOURCE1} scripts/ cp %{SOURCE2} scripts/ chmod +x scripts/*.sh sed -i 's/ python / python3 /' scripts/run_python_examples.sh sed -i 's|build/|./|' scripts/run_cpp_examples.sh # builddir for serial mkdir build-serial %if %{with mpich} mkdir build-mpich %endif %if %{with openmpi} mkdir build-openmpi %endif %build # Best to use && so that if anything in the chain fails, the build also fails # straight away %global do_cmake_config %{expand: \ echo echo "*** BUILDING arbor-%{version}$MPI_COMPILE_TYPE ***" echo pushd build$MPI_COMPILE_TYPE && cmake \\\ -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\ -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\ -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\ -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\ -DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\ -DINCLUDE_INSTALL_DIR:PATH=$MPI_INCLUDE \\\ -DLIB_INSTALL_DIR:PATH=$MPI_LIB \\\ -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\ -DCMAKE_SKIP_RPATH:BOOL=ON \\\ -DCMAKE_BUILD_TYPE:STRING="release" \\\ -DARB_USE_BUNDLED_LIBS:BOOL=OFF \\\ -DARB_USE_BUNDLED_PYBIND11:BOOL=OFF \\\ -DARB_VECTORIZE:BOOL=OFF \\\ -DARB_WITH_MPI:BOOL=$MPI_YES \\\ -DARB_WITH_GPU:BOOL=OFF \\\ -DARB_ARCH:STRING="none" \\\ -DARB_CXX_FLAGS_TARGET:STRING="-ffat-lto-objects" \\\ -DCMAKE_INSTALL_LIBDIR=%{_lib} \\\ -DARB_WITH_PYTHON:BOOL=ON \\\ -DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\ %if "%{_lib}" == "lib64" -DLIB_SUFFIX=64 .. && %else -DLIB_SUFFIX="" .. && %endif popd || exit -1; # Upstream only supports static libraries # https://github.com/arbor-sim/arbor/issues/916 # -DBUILD_SHARED_LIBS:BOOL=ON \\\ # Missing BRs # -DARB_BUILD_VALIDATION_DATA:BOOL=ON \\\ } %global do_make_build %{expand: \ %make_build -C build$MPI_COMPILE_TYPE || exit -1 %make_build -C build$MPI_COMPILE_TYPE examples || exit -1 %if %{with tests} %make_build -C build$MPI_COMPILE_TYPE tests || exit -1 %endif } # Build serial version, dummy arguments %set_build_flags export CC=gcc export CXX=g++ export MPI_SUFFIX="" export MPI_HOME=%{_prefix} export MPI_INCLUDE=%{_includedir} export MPI_LIB=%{_libdir} export MPI_YES=OFF export MPI_COMPILE_TYPE="-serial" export MPI_PYTHON3_SITEARCH=%{python3_sitearch} %{do_cmake_config} %{do_make_build} # skip building sphinx docs because they bundle js/fonts and it's very hard to # unbundle # Build mpich version %if %{with mpich} %{_mpich_load} %set_build_flags export CC=mpicc export CXX=mpicxx export FC=mpif90 export F77=mpif77 export MPI_YES=ON export MPI_COMPILE_TYPE="-mpich" %{do_cmake_config} %{do_make_build} %{_mpich_unload} %endif # Build OpenMPI version %if %{with openmpi} %{_openmpi_load} %set_build_flags export CC=mpicc export CXX=mpicxx export FC=mpif90 export F77=mpif77 export MPI_YES=ON # Python 3 export MPI_COMPILE_TYPE="-openmpi" %{do_cmake_config} %{do_make_build} %{_openmpi_unload} %endif %install # Install everything %global do_install %{expand: \ echo echo "*** INSTALLING arbor-%{version}$MPI_COMPILE_TYPE ***" echo %make_install -C build$MPI_COMPILE_TYPE || exit -1 } # install serial version export MPI_SUFFIX="" export MPI_HOME=%{_prefix} export MPI_BIN=%{_bindir} export MPI_YES=OFF export MPI_COMPILE_TYPE="-serial" %{do_install} # Install MPICH version %if %{with mpich} %{_mpich_load} export MPI_COMPILE_TYPE="-mpich" %{do_install} # Place in correct mpi libdir %if "%{_lib}" == "lib64" mv -v $RPM_BUILD_ROOT/%{_libdir}/mpich/lib64 $RPM_BUILD_ROOT/$MPI_LIB/ %endif pushd $RPM_BUILD_ROOT/$MPI_BIN mv -v modcc{,$MPI_SUFFIX} -v mv -v arbor-build-catalogue{,$MPI_SUFFIX} -v mv -v lmorpho{,$MPI_SUFFIX} -v popd %{_mpich_unload} %endif # Install OpenMPI version %if %{with openmpi} %{_openmpi_load} export MPI_COMPILE_TYPE="-openmpi" %{do_install} # Correct location %if "%{_lib}" == "lib64" mv -v $RPM_BUILD_ROOT/%{_libdir}/openmpi/lib64 $RPM_BUILD_ROOT/$MPI_LIB/ %endif pushd $RPM_BUILD_ROOT/$MPI_BIN mv -v modcc{,$MPI_SUFFIX} -v mv -v arbor-build-catalogue{,$MPI_SUFFIX} -v mv -v lmorpho{,$MPI_SUFFIX} -v popd %{_openmpi_unload} %endif # https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-matrix.yml %if %{with tests} %check # Taken from upstream's GitHub workflow %global mpirun mpirun -n %{_smp_build_ncpus} # these tests segfault, filter out gtest_filter="${gtest_filter--}${gtest_filter+:}*diffusion*" pushd build-serial %{py3_test_envvars} %{python3} -m unittest discover -v -s ../python ./bin/unit ${gtest_filter+--gtest_filter=}${gtest_filter-} ./bin/unit-modcc cp ../scripts/run_cpp_examples.sh . ./run_cpp_examples.sh popd # MPICH %if %{with mpich} %{_mpich_load} pushd build-mpich %if %{with mpi_py_unittest} %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python %endif %{mpirun} ./bin/unit-mpi cp ../scripts/run_cpp_examples.sh . ./run_cpp_examples.sh "%{mpirun}" popd %{py3_test_envvars} ./scripts/run_python_examples.sh "%{mpirun}" %{_mpich_unload} %endif # OpenMPI %if %{with openmpi} %{_openmpi_load} pushd build-openmpi %if %{with mpi_py_unittest} %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python %endif %{mpirun} ./bin/unit-mpi cp ../scripts/run_cpp_examples.sh . ./run_cpp_examples.sh "%{mpirun}" popd %{py3_test_envvars} ./scripts/run_python_examples.sh "%{mpirun}" %{_openmpi_unload} %endif %endif %files %license LICENSE ext/tinyopt/LICENSE-tinyopt %doc README.md %{_bindir}/modcc %{_bindir}/arbor-build-catalogue %{_bindir}/lmorpho %{python3_sitearch}/arbor %{_datadir}/arbor %files devel %{_includedir}/arborio %{_includedir}/arbor %{_includedir}/arborenv %{_libdir}/cmake/arbor %{_libdir}/libarbor.a %{_libdir}/libarborio.a %{_libdir}/libarborenv.a %files doc %license LICENSE %doc example/ %if %{with mpich} %files mpich %doc README.md %license LICENSE ext/tinyopt/LICENSE-tinyopt %{_libdir}/mpich/bin/modcc_mpich %{_libdir}/mpich/bin/arbor-build-catalogue_mpich %{_libdir}/mpich/bin/lmorpho_mpich %{python3_sitearch}/mpich/arbor %{_libdir}/mpich/share/arbor %files mpich-devel %{_libdir}/mpich/include/arbor %{_libdir}/mpich/include/arborio %{_libdir}/mpich/include/arborenv %{_libdir}/mpich/lib/cmake/arbor %{_libdir}/mpich/lib/libarbor.a %{_libdir}/mpich/lib/libarborio.a %{_libdir}/mpich/lib/libarborenv.a %endif %if %{with openmpi} %files openmpi %doc README.md %license LICENSE ext/tinyopt/LICENSE-tinyopt %{_libdir}/openmpi/bin/modcc_openmpi %{_libdir}/openmpi/bin/arbor-build-catalogue_openmpi %{_libdir}/openmpi/bin/lmorpho_openmpi %{python3_sitearch}/openmpi/arbor %{_libdir}/openmpi/share/arbor %files openmpi-devel %{_libdir}/openmpi/include/arbor %{_libdir}/openmpi/include/arborio %{_libdir}/openmpi/include/arborenv %{_libdir}/openmpi/lib/cmake/arbor %{_libdir}/openmpi/lib/libarbor.a %{_libdir}/openmpi/lib/libarborio.a %{_libdir}/openmpi/lib/libarborenv.a %endif %changelog ## START: Generated by rpmautospec * Sat Jul 13 2024 Sandro - 0.9.0-9 - Provide Python meta data using macro * Sun Jun 09 2024 Python Maint - 0.9.0-8 - Rebuilt for Python 3.13 * Tue Feb 06 2024 Sandro - 0.9.0-1 - Update to 0.9.0 (RHBZ#2145131) - Drop obsolete patches - Exclude segfaulting tests * Mon Jan 22 2024 Fedora Release Engineering - 0.7-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Jan 19 2024 Fedora Release Engineering - 0.7-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Mon Nov 06 2023 Benjamin A. Beasley - 0.7-10 - Do not enable extra ISA extensions based on the build host * Fri Jul 21 2023 Sandro - 0.7-9 - Fix ExcludeArch - s/s390/s390x/ * Thu Jul 20 2023 Sandro - 0.7-8 - Fix use of distutils (RHBZ#2219935) * Wed Jul 19 2023 Fedora Release Engineering - 0.7-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Wed Jun 28 2023 Python Maint - 0.7-6 - Rebuilt for Python 3.12 * Wed Jun 28 2023 Vitaly Zaitsev - 0.7-5 - Rebuilt due to fmt 10 update. * Thu Jan 19 2023 Benjamin A. Beasley - 0.7-4 - Add some missing #include directives * Wed Jan 18 2023 Fedora Release Engineering - 0.7-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sat Nov 26 2022 Benjamin A. Beasley - 0.7-2 - Add ExcludeArch: i686 * Mon Aug 29 2022 Ankur Sinha (Ankur Sinha Gmail) - 0.7-1 - feat: update to 0.7 (fixes rhbz#2047167) * Mon Aug 29 2022 Ankur Sinha (Ankur Sinha Gmail) - 0.5.2-10 - feat: upload new sources * Wed Jul 21 2021 Fedora Release Engineering - 0.3-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Fri Jun 04 2021 Python Maint - 0.3-9 - Rebuilt for Python 3.10 * Tue Jan 26 2021 Fedora Release Engineering - 0.3-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Mon Oct 05 2020 Ankur Sinha - 0.3-7 - Explicitly require setuptools * Fri Aug 28 2020 Jeff Law - 0.3-6 - Re-enable LTO - Do not force -march=native on armv7hl so that build architecture does not bleed into the binaries. This should probably be done on all targets * Sat Aug 01 2020 Fedora Release Engineering - 0.3-5 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jul 27 2020 Jeff Law - 0.3-4 - Disable LTO for armv7hl build * Mon Jul 27 2020 Fedora Release Engineering - 0.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Sun Jun 28 2020 Ankur Sinha - 0.3-2 - Update build flags to ensure CC and CXX are set correctly - https://lists.fedoraproject.org/archives/list/scitech@lists.fedoraproject.org/thread/BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT/#BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT * Mon Jun 08 2020 Antonio Trande - 0.3-2 - Move Provides lines to runtime packages - Add patch for using tinyopt libraries * Sat Jun 06 2020 Antonio Trande - 0.3-1 - Release 0.3 * Tue May 26 2020 Miro Hrončok - 0.2.2-8.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957 - Rebuilt for Python 3.9 * Thu Apr 02 2020 Björn Esser - 0.2.2-7.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957 - Fix string quoting for rpm >= 4.16 * Wed Feb 26 2020 Ankur Sinha - 0.2.2-5.20200226gitfb5d4ea736282dce14c3284bc5db748b082db957 - Use new snapshot that fixes errors on 32 bit systems - No longer excludes i686 and armv7hl - Drop unneeded patch. * Sun Feb 23 2020 Ankur Sinha - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10 - Build from latest upstream snapshot - Freshen patch - Add exclude arches * Tue Jan 28 2020 Fedora Release Engineering - 0.2.2-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Tue Dec 10 2019 Ankur Sinha - 0.2.2-3 - Enable tests - Add patch for test crash * Mon Dec 09 2019 Ankur Sinha - 0.2.2-2 - Remove arch info in provides for static - Temporarily disable tests - use python3-devel - Add documentation in separate sub-package - add python3-{mpich,openmpi} as requires that own MPI_PYTHON3_SITEARCH directories - Improve summaries for sub-packages to please rpmlint * Sat Dec 07 2019 Ankur Sinha - 0.2.2-1 - Update to latest release * Sun Jan 13 2019 Ankur Sinha - 0.1-1 - Initial rpm package ## END: Generated by rpmautospec