4. Charliecloud command reference

This section is a comprehensive description of the usage and arguments of the Charliecloud commands. Its content is identical to the commands’ man pages.

4.1. ch-build

Build an image and place it in the builder’s back-end storage.

4.1.1. Synopsis

$ ch-build [-b BUILDER] [--builder-info] -t TAG [ARGS ...] CONTEXT

4.1.2. Description

Build an image named TAG described by a Dockerfile. Place the result into the builder’s back-end storage.

Using this script is not required for a working Charliecloud image. You can also use any builder that can produce a Linux filesystem tree directly, whether or not it is in the list below. However, this script hides the vagaries of making the supported builders work smoothly with Charliecloud and adds some conveniences (e.g., pass HTTP proxy environment variables to the build environment if the builder doesn’t do this by default).

Supported builders, unprivileged:

  • buildah: Buildah in “rootless” mode with no setuid helpers, using ch-run (via ch-run-oci) for RUN instructions. This currently requires a patched Buildah; see the install instructions.
  • ch-grow: Our internal builder.

Supported builders, privileged:

  • buildah-runc: Buildah in “rootless” mode with setuid helpers, using the default runc for RUN instructions.
  • buildah-setuid: Buildah in “rootless” mode with setuid helpers, using ch-run (via ch-run-oci) for RUN instructions.
  • docker: Docker.

Specifying the builder, in descending order of priority:

-b, --builder BUILDER
Command line option.
$CH_BUILDER
Environment variable
Default
docker if Docker is installed; otherwise, ch-grow.

Other arguments:

--builder-info
Print the builder to be used and its version, then exit.
-f, --file DOCKERFILE
Dockerfile to use (default: $CONTEXT/Dockerfile)
-t TAG
Name (tag) of Docker image to build.
--help
Print help and exit.
--version
Print version and exit.

Additional arguments are accepted and passed unchanged to the underlying builder.

4.1.3. Bugs

The tag suffix :latest is somewhat misleading, as by default neither ch-build nor bare builders will notice if the base FROM image has been updated. Use --pull to make sure you have the latest base image.

4.1.4. Examples

Create an image tagged foo and specified by the file Dockerfile located in the context directory. Use /bar as the Docker context directory. Use the default builder.

$ ch-build -t foo /bar

Equivalent to above:

$ ch-build -t foo --file=/bar/Dockerfile /bar

Instead, use /bar/Dockerfile.baz:

$ ch-build -t foo --file=/bar/Dockerfile.baz /bar

Equivalent to the first example, but use ch-grow even if Docker is installed:

$ ch-build -b ch-grow -t foo /bar

Equivalent to above:

$ export CH_BUILDER=ch-grow
$ ch-build -t foo /bar

4.2. ch-build2dir

Build a Charliecloud image from Dockerfile and unpack it into a directory.

4.2.1. Synopsis

$ ch-build2dir -t TAG [ARGS ...] CONTEXT OUTDIR

4.2.2. Description

Build a Docker image named TAG described by a Dockerfile (default $CONTEXT/Dockerfile) and unpack it into OUTDIR/TAG. This is a wrapper for ch-build, ch-builder2tar, and ch-tar2dir; see also those man pages.

Arguments:

ARGS
additional arguments passed to ch-build
CONTEXT
Docker context directory
OUTDIR
directory in which to place image directory (named TAG) and temporary tarball
-t TAG
name (tag) of Docker image to build
--help
print help and exit
--version
print version and exit

4.2.3. Examples

To build using ./Dockerfile and create image directory /var/tmp/foo:

$ ch-build2dir -t foo . /var/tmp

Same as above, but build with a different Dockerfile:

$ ch-build2dir -t foo -f ./Dockerfile.foo . /var/tmp

4.3. ch-builder2tar

Flatten a builder image into a Charliecloud image tarball.

4.3.1. Synopsis

$ ch-builder2tar [-b BUILDER] [--nocompress] IMAGE OUTDIR

4.3.2. Description

Flatten the builder image tagged IMAGE into a Charliecloud tarball in directory OUTDIR.

The builder-specified environment (e.g., ENV statements) is placed in a file in the tarball at $IMAGE/ch/environment, in a form suitable for ch-run --set-env.

See ch-build(1) for details on specifying the builder.

Additional arguments:

-b, --builder BUILDER
Use specified builder; if not given, use $CH_BUILDER or default.
--nocompress
Do not compress tarball.
--help
Print help and exit.
--version
Print version and exit.

4.3.3. Example

$ ch-builder2tar hello /var/tmp
57M /var/tmp/hello.tar.gz
$ ls -lh /var/tmp
-rw-r-----  1 reidpr reidpr  57M Feb 13 16:14 hello.tar.gz

4.4. ch-checkns

Check ch-run prerequisites, e.g., namespaces and pivot_root(2).

4.4.1. Synopsis

$ ch-checkns

4.4.2. Description

Check ch-run prerequisites, e.g., namespaces and pivot_root(2).

4.4.3. Example

$ ch-checkns
ok

4.5. ch-dir2squash

Create a SquashFS file from an image directory.

4.5.1. Synopsis

$ ch-dir2squash IMGDIR OUTDIR [ARGS ...]

4.5.2. Description

Create Charliecloud SquashFS file from image directory IMGDIR under directory OUTDIR, named as last component of IMGDIR plus suffix .sqfs.

Optional ARGS will passed to mksquashfs unchanged.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.5.3. Example

$ ch-dir2squash /var/tmp/debian /var/tmp
Parallel mksquashfs: Using 6 processors
Creating 4.0 filesystem on /var/tmp/debian.sqfs, block size 131072.
[...]
-rw-r--r--  1 charlie charlie 41M Apr 23 14:41 /var/tmp/debian.sqfs

4.6. ch-docker2squash

Flatten a Docker image into a Charliecloud SquashFS file.

4.6.1. Synopsis

$ ch-docker2squash IMAGE OUTDIR [ARGS ...]

4.6.2. Description

Flattens the Docker image tagged IMAGE into a SquashFS file in OUTDIR.

Wrapper for ch-docker2tar --nocompress and ch-tar2sqfs. Intermediate files and directories are removed.

Sudo privileges are required to run docker export.

Optional ARGS passed to mksquashfs unchanged.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.6.3. Example

$ docker image list | fgrep debian
REPOSITORY   TAG       IMAGE ID       CREATED      SIZE
debian       stretch   2d337f242f07   3 weeks ago  101MB
$ ch-docker2squash debian /var/tmp
Parallel mksquashfs: Using 6 processors
Creating 4.0 filesystem on /var/tmp/debian.sqfs, block size 131072.
[...]
squashed /var/tmp/debian.sqfs OK
$ ls -lh /var/tmp/debian*
-rw-r--r-- 1 charlie charlie 41M Apr 23 14:37 debian.sqfs

4.7. ch-fromhost

Inject files from the host into an image directory.

4.7.1. Synopsis

$ ch-fromhost [OPTION ...] [FILE_OPTION ...] IMGDIR

4.7.2. Description

Note

This command is experimental. Features may be incomplete and/or buggy. Please report any issues you find, so we can fix them!

Inject files from the host into the Charliecloud image directory IMGDIR.

The purpose of this command is to provide host-specific files, such as GPU libraries, to a container. It should be run after ch-tar2dir and before ch-run. After invocation, the image is no longer portable to other hosts.

Injection is not atomic; if an error occurs partway through injection, the image is left in an undefined state. Injection is currently implemented using a simple file copy, but that may change in the future.

By default, file paths that contain the strings /bin or /sbin are assumed to be executables and placed in /usr/bin within the container. File paths that contain the strings /lib or .so are assumed to be shared libraries and are placed in the first-priority directory reported by ldconfig (see --lib-path below). Other files are placed in the directory specified by --dest.

If any shared libraries are injected, run ldconfig inside the container (using ch-run -w) after injection.

4.7.3. Options

4.7.3.1. To specify which files to inject

-c, --cmd CMD
Inject files listed in the standard output of command CMD.
-f, --file FILE
Inject files listed in the file FILE.
-p, --path PATH
Inject the file at PATH.
--cray-mpi
Cray-enable an MPICH installed inside the image. See important details below.
--nvidia
Use nvidia-container-cli list (from libnvidia-container) to find executables and libraries to inject.

These can be repeated, and at least one must be specified.

4.7.3.2. To specify the destination within the image

-d, --dest DST
Place files specified later in directory IMGDIR/DST, overriding the inferred destination, if any. If a file’s destination cannot be inferred and --dest has not been specified, exit with an error. This can be repeated to place files in varying destinations.

4.7.3.3. Additional arguments

--lib-path
Print the guest destination path for shared libraries inferred as described above.
--no-ldconfig
Don’t run ldconfig even if we appear to have injected shared libraries.
-h, --help
Print help and exit.
-v, --verbose
List the injected files.
--version
Print version and exit.

4.7.4. --cray-mpi dependencies and quirks

The implementation of --cray-mpi for MPICH is messy, foul smelling, and brittle. It replaces or overrides the open source MPICH libraries installed in the container. Users should be aware of the following.

  1. Containers must have the following software installed:
    1. Open source MPICH.
    2. PatchELF with our patches. Use the shrink-soname branch.
    3. libgfortran.so.3, because Cray’s libmpi.so.12 links to it.
  2. Applications must be linked to libmpi.so.12 (not e.g. libmpich.so.12). How to configure MPICH to accomplish this is not yet clear to us; test/Dockerfile.mpich does it, while the Debian packages do not.
  3. One of the cray-mpich-abi modules must be loaded when ch-fromhost is invoked.
  4. Tested only for C programs compiled with GCC, and it probably won’t work otherwise. If you’d like to use another compiler or another programming language, please get in touch so we can implement the necessary support.

Please file a bug if we missed anything above or if you know how to make the code better.

4.7.5. Notes

Symbolic links are dereferenced, i.e., the files pointed to are injected, not the links themselves.

As a corollary, do not include symlinks to shared libraries. These will be re-created by ldconfig.

There are two alternate approaches for nVidia GPU libraries:

  1. Link libnvidia-containers into ch-run and call the library functions directly. However, this would mean that Charliecloud would either (a) need to be compiled differently on machines with and without nVidia GPUs or (b) have libnvidia-containers available even on machines without nVidia GPUs. Neither of these is consistent with Charliecloud’s philosophies of simplicity and minimal dependencies.
  2. Use nvidia-container-cli configure to do the injecting. This would require that containers have a half-started state, where the namespaces are active and everything is mounted but pivot_root(2) has not been performed. This is not feasible because Charliecloud has no notion of a half-started container.

Further, while these alternate approaches would simplify or eliminate this script for nVidia GPUs, they would not solve the problem for other situations.

4.7.6. Bugs

File paths may not contain colons or newlines.

4.7.7. Examples

Place shared library /usr/lib64/libfoo.so at path /usr/lib/libfoo.so (assuming /usr/lib is the first directory searched by the dynamic loader in the image), within the image /var/tmp/baz and executable /bin/bar at path /usr/bin/bar. Then, create appropriate symlinks to libfoo and update the ld.so cache.

$ cat qux.txt
/bin/bar
/usr/lib64/libfoo.so
$ ch-fromhost --file qux.txt /var/tmp/baz

Same as above:

$ ch-fromhost --cmd 'cat qux.txt' /var/tmp/baz

Same as above:

$ ch-fromhost --path /bin/bar --path /usr/lib64/libfoo.so /var/tmp/baz

Same as above, but place the files into /corge instead (and the shared library will not be found by ldconfig):

$ ch-fromhost --dest /corge --file qux.txt /var/tmp/baz

Same as above, and also place file /etc/quux at /etc/quux within the container:

$ ch-fromhost --file qux.txt --dest /etc --path /etc/quux /var/tmp/baz

Inject the executables and libraries recommended by nVidia into the image, and then run ldconfig:

$ ch-fromhost --nvidia /var/tmp/baz

4.7.8. Acknowledgements

This command was inspired by the similar Shifter feature that allows Shifter containers to use the Cray Aires network. We particularly appreciate the help provided by Shane Canon and Doug Jacobsen during our implementation of --cray-mpi.

We appreciate the advice of Ryan Olson at nVidia on implementing --nvidia.

4.8. ch-grow

Build an image from a Dockerfile; completely unprivileged.

4.8.1. Synopsis

$ ch-grow [OPTIONS] [-t TAG] [-f DOCKERFILE] CONTEXT

4.8.2. Description

Warning

This script is experimental. Please report the bugs you find so we can fix them!

Build an image named TAG as specified in DOCKERFILE; use ch-run(1) to execute RUN instructions. This builder is completely unprivileged, with no setuid/setgid/setcap helpers.

ch-grow maintains state and temporary images using normal files and directories. This storage directory can reside on any filesystem, and its location is configurable. In descending order of priority:

-s, --storage DIR
Command line option.
$CH_GROW_STORAGE
Environment variable.
/var/tmp/ch-grow
Default.

Note

Images are stored unpacked, so place your storage directory on a filesystem that can handle the metadata traffic for large numbers of small files. For example, the Charliecloud test suite uses approximately 400,000 files and directories.

Other arguments:

CONTEXT
Context directory; this is the root of COPY and ADD instructions in the Dockerfile.
-f, --file DOCKERFILE
Use DOCKERFILE instead of CONTEXT/Dockerfile.
-h, --help
Print help and exit.
-n, --dry-run
Do not actually excute any Dockerfile instructions.
--parse-only
Stop after parsing the Dockerfile.
--print-storage
Print the storage directory path and exit.
-t, -tag TAG
Name of image to create. Append :latest if no colon present.
--verbose
Print lots of debugging chatter.
--version
Print version number and exit.

4.8.3. Bugs

This script executes RUN instructions with host EUID and EGID both mapped to zero in the container, i.e., with ch-run --uid=0 gid=0. This confuses many programs that appear in RUN, which see EUID 0 and/or EGID 0 and assume they can actually do privileged things, which then fail with “permission denied” and related errors. For example, chgrp(1) often appears in Debian package post-install scripts. We have worked around some of these problems, but many remain; please report any you find as bugs.

COPY and ADD source paths are not restricted to the context directory. However, because ch-grow is completely unprivileged, this cannot be used to add files not normally readable by the user to the image.

4.9. ch-mount

Mount a SquashFS image file using FUSE.

4.9.1. Synopsis

$ ch-mount SQFS PARENTDIR

4.9.2. Description

Create new empty directory named SQFS with suffix (e.g., .sqfs) removed, then mount SQFS on this new directory. This new directory must not already exist.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.9.3. Example

$ ch-mount /var/tmp/debian.sqfs /var/tmp
$ ls /var/tmp/debian
bin   dev  home  lib64  mnt  proc  run   srv  tmp  var
boot  etc  lib   media  opt  root  sbin  sys  usr  WEIRD_AL_YANKOVIC

4.10. ch-pull2dir

Pull image from a Docker Hub and unpack into directory.

4.10.1. Synopsis

$ ch-pull2dir IMAGE[:TAG] DIR

4.10.2. Description

Pull Docker image named IMAGE[:TAG] from Docker Hub and extract it into a subdirectory of DIR. A temporary tarball is stored in DIR.

Sudo privileges are required to run the docker pull command.

This runs the following command sequence: ch-pull2tar, ch-tar2dir. See warning in the documentation for ch-tar2dir.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.10.3. Examples

$ ch-pull2dir alpine /var/tmp
Using default tag: latest
latest: Pulling from library/alpine
Digest: sha256:621c2f39f8133acb8e64023a94dbdf0d5ca81896102b9e57c0dc184cadaf5528
Status: Image is up to date for alpine:latest
-rw-r--r--. 1 charlie charlie 2.1M Oct  5 19:52 /var/tmp/alpine.tar.gz
creating new image /var/tmp/alpine
/var/tmp/alpine unpacked ok
removed '/var/tmp/alpine.tar.gz'

Same as above, except optional TAG is specified:

$ ch-pull2dir alpine:3.6 /var/tmp
3.6: Pulling from library/alpine
Digest: sha256:cc24af836d1377e092ecb4e8f0a4324c3b1aa2b5295c2239edcc7bbc86a9cbc6
Status: Image is up to date for alpine:3.6
-rw-r--r--. 1 charlie charlie 2.1M Oct  5 19:54 /var/tmp/alpine:3.6.tar.gz
creating new image /var/tmp/alpine:3.6
/var/tmp/alpine:3.6 unpacked ok
removed '/var/tmp/alpine:3.6.tar.gz'

4.11. ch-pull2tar

Pull image from a Docker Hub and flatten into tarball.

4.11.1. Synopsis

$ ch-pull2tar IMAGE[:TAG] OUTDIR

4.11.2. Description

Pull a Docker image named IMAGE[:TAG] from Docker Hub and flatten it into a Charliecloud tarball in directory OUTDIR.

This runs the following command sequence: docker pull, ch-builder2tar but provides less flexibility than the individual commands.

Sudo privileges are required for docker pull.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.11.3. Examples

$ ch-pull2tar alpine /var/tmp
Using default tag: latest
latest: Pulling from library/alpine
Digest: sha256:621c2f39f8133acb8e64023a94dbdf0d5ca81896102b9e57c0dc184cadaf5528
Status: Image is up to date for alpine:latest
-rw-r--r--. 1 charlie charlie 2.1M Oct  5 19:52 /var/tmp/alpine.tar.gz

Same as above, except optional TAG is specified:

$ ch-pull2tar alpine:3.6
3.6: Pulling from library/alpine
Digest: sha256:cc24af836d1377e092ecb4e8f0a4324c3b1aa2b5295c2239edcc7bbc86a9cbc6
Status: Image is up to date for alpine:3.6
-rw-r--r--. 1 charlie charlie 2.1M Oct  5 19:54 /var/tmp/alpine:3.6.tar.gz

4.12. ch-run

Run a command in a Charliecloud container.

4.12.1. Synopsis

$ ch-run [OPTION...] NEWROOT CMD [ARG...]

4.12.2. Description

Run command CMD in a Charliecloud container using the flattened and unpacked image directory located at NEWROOT.

-b, --bind=SRC[:DST]
mount SRC at guest DST (default /mnt/0, /mnt/1, etc.)
-c, --cd=DIR
initial working directory in container
--ch-ssh
bind ch-ssh(1) into container at /usr/bin/ch-ssh
-g, --gid=GID
run as group GID within container
-j, --join
use the same container (namespaces) as peer ch-run invocations
--join-pid=PID
join the namespaces of an existing process
--join-ct=N
number of ch-run peers (implies --join; default: see below)
--join-tag=TAG
label for ch-run peer group (implies --join; default: see below)
--no-home
do not bind-mount your home directory (by default, your home directory is mounted at /home/$USER in the container)
-t, --private-tmp
use container-private /tmp (by default, /tmp is shared with the host)
--set-env=FILE
set environment variables as specified in host path FILE
-u, --uid=UID
run as user UID within container
--unset-env=GLOB
unset environment variables whose names match GLOB
-v, --verbose
be more verbose (debug if repeated)
-w, --write
mount image read-write (by default, the image is mounted read-only)
-?, --help
print help and exit
--usage
print a short usage message and exit
-V, --version
print version and exit

4.12.3. Host files and directories available in container via bind mounts

In addition to any directories specified by the user with --bind, ch-run has standard host files and directories that are bind-mounted in as well.

The following host files and directories are bind-mounted at the same location in the container. These cannot be disabled.

  • /dev
  • /etc/passwd
  • /etc/group
  • /etc/hosts
  • /etc/resolv.conf
  • /proc
  • /sys

Three additional bind mounts can be disabled by the user:

  • Your home directory (i.e., $HOME) is mounted at guest /home/$USER by default. This is accomplished by mounting a new tmpfs at /home, which hides any image content under that path. If --no-home is specified, neither of these things happens and the image’s /home is exposed unaltered.
  • /tmp is shared with the host by default. If --private-tmp is specified, a new tmpfs is mounted on the guest’s /tmp instead.
  • If file /usr/bin/ch-ssh is present in the image, it is over-mounted with the ch-ssh binary in the same directory as ch-run.

4.12.4. Multiple processes in the same container with --join

By default, different ch-run invocations use different user and mount namespaces (i.e., different containers). While this has no impact on sharing most resources between invocations, there are a few important exceptions. These include:

  1. ptrace(2), used by debuggers and related tools. One can attach a debugger to processes in descendant namespaces, but not sibling namespaces. The practical effect of this is that (without --join), you can’t run a command with ch-run and then attach to it with a debugger also run with ch-run.
  2. Cross-memory attach (CMA) is used by cooperating processes to communicate by simply reading and writing one another’s memory. This is also not permitted between sibling namespaces. This affects various MPI implementations that use CMA to pass messages between ranks on the same node, because it’s faster than traditional shared memory.

--join is designed to address this by placing related ch-run commands (the “peer group”) in the same container. This is done by one of the peers creating the namespaces with unshare(2) and the others joining with setns(2).

To do so, we need to know the number of peers and a name for the group. These are specified by additional arguments that can (hopefully) be left at default values in most cases:

  • --join-ct sets the number of peers. The default is the value of the first of the following environment variables that is defined: OMPI_COMM_WORLD_LOCAL_SIZE, SLURM_STEP_TASKS_PER_NODE, SLURM_CPUS_ON_NODE.
  • --join-tag sets the tag that names the peer group. The default is environment variable SLURM_STEP_ID, if defined; otherwise, the PID of ch-run‘s parent. Tags can be re-used for peer groups that start at different times, i.e., once all peer ch-run have replaced themselves with the user command, the tag can be re-used.

Caveats:

  • One cannot currently add peers after the fact, for example, if one decides to start a debugger after the fact. (This is only required for code with bugs and is thus an unusual use case.)
  • ch-run instances race. The winner of this race sets up the namespaces, and the other peers use the winner to find the namespaces to join. Therefore, if the user command of the winner exits, any remaining peers will not be able to join the namespaces, even if they are still active. There is currently no general way to specify which ch-run should be the winner.
  • If --join-ct is too high, the winning ch-run‘s user command exits before all peers join, or ch-run itself crashes, IPC resources such as semaphores and shared memory segments will be leaked. These appear as files in /dev/shm/ and can be removed with rm(1).
  • Many of the arguments given to the race losers, such as the image path and --bind, will be ignored in favor of what was given to the winner.

4.12.5. Environment variables

ch-run leaves environment variables unchanged, i.e. the host environment is passed through unaltered, except:

  • limited tweaks to avoid significant guest breakage;
  • user-set variables via --set-env; and
  • user-unset variables via --unset-env.

This section describes these features.

The default tweaks happen first, and then --set-env and --unset-env in the order specified on the command line. The latter two can be repeated arbitrarily many times, e.g. to add/remove multiple variable sets or add only some variables in a file.

4.12.5.1. Default behavior

By default, ch-run makes the following environment variable changes:

  • $HOME: If the path to your home directory is not /home/$USER on the host, then an inherited $HOME will be incorrect inside the guest. This confuses some software, such as Spack.

    Thus, we change $HOME to /home/$USER, unless --no-home is specified, in which case it is left unchanged.

  • $PATH: Newer Linux distributions replace some root-level directories, such as /bin, with symlinks to their counterparts in /usr.

    Some of these distributions (e.g., Fedora 24) have also dropped /bin from the default $PATH. This is a problem when the guest OS does not have a merged /usr (e.g., Debian 8 “Jessie”). Thus, we add /bin to $PATH if it’s not already present.

    Further reading:

4.12.5.2. Setting variables with --set-env

The purpose of --set-env=FILE is to set environment variables that cannot be inherited from the host shell, e.g. Dockerfile ENV directives or other build-time configuration. FILE is a host path to provide the greatest flexibility; guest paths can be specified by prepending the image path.

ch-builder2tar(1) lists variables specified at build time in Dockerfiles in the image in file /ch/environment. To set these variables: --set-env=$IMG/ch/environment.

Variable values in FILE replace any already set. If a variable is repeated, the last value wins.

The syntax of FILE is key-value pairs separated by the first equals character (=, ASCII 61), one per line, with optional single straight quotes (', ASCII 39) around the value. Empty lines are ignored. Newlines (ASCII 10) are not permitted in either key or value. No variable expansion, comments, etc. are provided. The value may be empty, but not the key. (This syntax is designed to accept the output of printenv and be easily produced by other simple mechanisms.) Examples of valid lines:

Line Key Value
FOO=bar FOO bar
FOO=bar=baz FOO bar=baz
FLAGS=-march=foo -mtune=bar FLAGS -march=foo -mtune=bar
FLAGS='-march=foo -mtune=bar' FLAGS -march=foo -mtune=bar
FOO= FOO (empty string)
FOO='' FOO (empty string)
FOO='''' FOO '' (two single quotes)

Example invalid lines:

Line Problem
FOO bar no separator
=bar key cannot be empty

Example valid lines that are probably not what you want:

Line Key Value Problem
FOO="bar" FOO "bar" double quotes aren’t stripped
FOO=bar # baz FOO bar # baz comments not supported
PATH=$PATH:/opt/bin PATH $PATH:/opt/bin variables not expanded
FOO=bar FOO bar leading space in key
FOO= bar FOO bar leading space in value

4.12.5.3. Removing variables with --unset-env

The purpose of --unset-env=GLOB is to remove unwanted environment variables. The argument GLOB is a glob pattern (dialect fnmatch(3) with no flags); all variables with matching names are removed from the environment.

Warning

Because the shell also interprets glob patterns, if any wildcard characters are in GLOB, it is important to put it in single quotes to avoid surprises.

GLOB must be a non-empty string.

Example 1: Remove the single environment variable FOO:

$ export FOO=bar
$ env | fgrep FOO
FOO=bar
$ ch-run --unset-env=FOO $CH_TEST_IMGDIR/chtest -- env | fgrep FOO
$

Example 2: Hide from a container the fact that it’s running in a Slurm allocation, by removing all variables beginning with SLURM. You might want to do this to test an MPI program with one rank and no launcher:

$ salloc -N1
$ env | egrep '^SLURM' | wc
   44      44    1092
$ ch-run $CH_TEST_IMGDIR/mpihello-openmpi -- /hello/hello
[... long error message ...]
$ ch-run --unset-env='SLURM*' $CH_TEST_IMGDIR/mpihello-openmpi -- /hello/hello
0: MPI version:
Open MPI v3.1.3, package: Open MPI root@c897a83f6f92 Distribution, ident: 3.1.3, repo rev: v3.1.3, Oct 29, 2018
0: init ok cn001.localdomain, 1 ranks, userns 4026532530
0: send/receive ok
0: finalize ok

Example 3: Clear the environment completely (remove all variables):

$ ch-run --unset-env='*' $CH_TEST_IMGDIR/chtest -- env
$

Note that some programs, such as shells, set some environment variables even if started with no init files:

$ ch-run --unset-env='*' $CH_TEST_IMGDIR/debian9 -- bash --noprofile --norc -c env
SHLVL=1
PWD=/
_=/usr/bin/env
$

4.12.6. Examples

Run the command echo hello inside a Charliecloud container using the unpacked image at /data/foo:

$ ch-run /data/foo -- echo hello
hello

Run an MPI job that can use CMA to communicate:

$ srun ch-run --join /data/foo -- bar

4.13. ch-run-oci

OCI wrapper for ch-run.

4.13.1. Synopsis

$ ch-run-oci OPERATION [ARG ...]

4.13.2. Description

Note

This command is experimental. Features may be incomplete and/or buggy. The quality of code is not yet up to the usual Charliecloud standards, and error handling is poor. Please report any issues you find, so we can fix them!

Open Containers Initiative (OCI) wrapper for ch-run(1). You probably don’t want to run this command directly; it is intended to interface with other software that expects an OCI runtime. The current goal is to support completely unprivileged image building (e.g. buildah --runtime=ch-run-oci) rather than general OCI container running.

Support of the OCI runtime specification is only partial. This is for two reasons. First, it’s an experimental and incomplete feature. More importantly, the philosophy and goals of OCI differ significantly from those of Charliecloud. Key differences include:

  • OCI is designed to run services, while Charliecloud is designed to run scientific applications.
  • OCI containers are persistent things with a complex lifecycle, while Charliecloud containers are simply UNIX processes.
  • OCI expects support for a variety of namespaces, while Charliecloud supports user and mount, no more and no less.
  • OCI expects runtimes to maintain a supervisor process in addition to user processes; Charliecloud has no need for this.
  • OCI expects runtimes to maintain state throughout the container lifecycle in a location independent from the caller.

For these reasons, ch-run-oci is a bit of a kludge, and much of what it does is provide scaffolding to satisfy OCI requirements.

Which OCI features are and are not supported is provided in the rest of this man page, and technical analysis and discussion are in the Contributor’s Guide.

This command supports OCI version 1.0.0 only and fails with an error if other versions are offered.

4.13.3. Operations

All OCI operations are accepted, but some are no-ops or merely scaffolding to satisfy the caller. For comparison, see also:

4.13.3.1. create

$ ch-run-oci create --bundle DIR --pid-file FILE [--no-new-keyring] CONTAINER_ID

Create a container. Charliecloud does not have separate create and start phases, so this operation only sets up OCI-related scaffolding.

Arguments:

--bundle DIR
Directory containing the OCI bundle. This must be /tmp/buildahYYY, where YYY matches CONTAINER_ID below.
--pid-file FILE
Filename to write the “container” process PID to. Note that for Charliecloud, the process given is fake; see above. This must be DIR/pid, where DIR is given by --bundle.
--no-new-keyring
Ignored. (Charliecloud does not implement session keyrings.)
CONTAINER_ID
String to use as the container ID. This must be buildah-buildahYYY, where YYY matches DIR above.

Unsupported arguments:

--console-socket PATH
UNIX socket to pass pseudoterminal file descriptor. Charliecloud does not support pseudoterminals; fail with an error if this argument is given. For Buildah, redirect its input from /dev/null to prevent it from requesting a pseudoterminal.

4.13.3.2. delete

$ ch-run-oci delete CONTAINER_ID

Clean up the OCI-related scaffolding for specified container.

4.13.3.3. kill

$ ch-run-oci kill CONTAINER_ID

No-op.

4.13.3.4. start

$ ch-run-oci start CONTAINER_ID

Eexecute the user command specified at create time in a Charliecloud container.

4.13.3.5. state

$ ch-run-oci state CONTAINER_ID

Print the state of the given container on standard output as an OCI compliant JSON document.

4.13.4. Unsupported OCI features

As noted above, various OCI features are not supported by Charliecloud. We have tried to guess which features would be essential to callers; ch-run-oci fails with an error if these are requested. Otherwise, the request is simply ignored.

We are interested in hearing about scientific-computing use cases for unsupported features, so we can add support for things that are needed.

Our goal is for this man page to be comprehensive: every OCI runtime feature should either work or be listed as unsupported.

Unsupported features that are an error:

  • Pseudoterminals
  • Hooks (prestart, poststart, and prestop)
  • Annotations
  • Joining existing namespaces
  • Intel Resource Director Technology (RDT)

Unsupported features that are ignored:

  • Mounts other than the root filesystem (we do use --no-home)
  • User/group mappings beyond one user mapped to EUID and one group mapped to EGID
  • Disabling prctl(PR_SET_NO_NEW_PRIVS)
  • Root filesystem propagation mode
  • sysctl directives
  • masked and read-only paths (remaining unprivileged protects you)
  • Capabilities
  • rlimits
  • Devices (all devices are inherited from the host)
  • cgroups
  • seccomp
  • SELinux
  • AppArmor
  • Container hostname setting

4.13.5. Environment variables

CH_RUN_OCI_LOGFILE

If set, send log chatter to this file. We use a side channel because standard error and standard output may be arbitrarily messed up by the caller.

CH_RUN_OCI_HANG

If set to the name of a command (e.g., create), sleep indefinitely when that command is invoked. The purpose here is to halt a build so it can be examined and debugged.

4.14. ch-ssh

Run a remote command in a Charliecloud container.

4.14.1. Synopsis

$ CH_RUN_ARGS="NEWROOT [ARG...]"
$ ch-ssh [OPTION...] HOST CMD [ARG...]

4.14.2. Description

Runs command CMD in a Charliecloud container on remote host HOST. Use the content of environment variable CH_RUN_ARGS as the arguments to ch-run on the remote host.

Note

Words in CH_RUN_ARGS are delimited by spaces only; it is not shell syntax.

4.14.3. Example

On host bar.example.com, run the command echo hello inside a Charliecloud container using the unpacked image at /data/foo with starting directory /baz:

$ hostname
foo
$ export CH_RUN_ARGS='--cd /baz /data/foo'
$ ch-ssh bar.example.com -- hostname
bar

4.15. ch-tar2dir

Unpack an image tarball into a directory.

4.15.1. Synopsis

$ ch-tar2dir TARBALL DIR

4.15.2. Description

Extract the tarball TARBALL into a subdirectory of DIR. TARBALL must contain a Linux filesystem image, e.g. as created by ch-builder2tar, and be compressed with gzip or xz. If TARBALL has no extension, try appending .tar.gz and .tar.xz.

Inside DIR, a subdirectory will be created whose name corresponds to the name of the tarball with .tar.gz or other suffix removed. If such a directory exists already and appears to be a Charliecloud container image, it is removed and replaced. If the existing directory doesn’t appear to be a container image, the script aborts with an error.

Additional arguments:

--help
print help and exit
--version
print version and exit

Warning

Placing DIR on a shared file system can cause significant metadata load on the file system servers. This can result in poor performance for you and all your colleagues who use the same file system. Please consult your site admin for a suitable location.

4.15.3. Example

$ ls -lh /var/tmp
total 57M
-rw-r-----  1 reidpr reidpr  57M Feb 13 16:14 hello.tar.gz
$ ch-tar2dir /var/tmp/hello.tar.gz /var/tmp
creating new image /var/tmp/hello
/var/tmp/hello unpacked ok
$ ls -lh /var/tmp
total 57M
drwxr-x--- 22 reidpr reidpr 4.0K Feb 13 16:29 hello
-rw-r-----  1 reidpr reidpr  57M Feb 13 16:14 hello.tar.gz

4.16. ch-tar2squash

Create a SquashFS file from a tarball image.

4.16.1. Synopsis

$ ch-tar2squash TARBALL OUTDIR [ARGS ...]

4.16.2. Description

Create Charliecloud SquashFS file from TARBALL in directory OUTDIR, named as TARBALL with extension .sqfs.

Wrapper for ch-tar2dir and ch-dir2sqfs.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.16.3. Example

$ ch-tar2squash /var/tmp/debian.tar.gz /var/tmp
Parallel mksquashfs: Using 6 processors
Creating 4.0 filesystem on /var/tmp/debian.sqfs, block size 131072.
[...]
-rw-r--r-- 1 charlie charlie 41M Apr 23 14:50 debian.sqfs
$ ls -lh /var/tmp/debian*
total 83M
-rw-r--r-- 1 charlie charlie 41M Apr 23 14:50 debian.sqfs
-rw-rw-r-- 1 charlie charlie 43M Apr 23 14:49 debian.tar.gz

4.17. ch-umount

Unmount a FUSE mounted squash filesystem and remove the mount point.

4.17.1. Synopsis

$ ch-umount MOUNTDIR

4.17.2. Description

Unmount Charliecloud SquashFS file at target directory MOUNTDIR. Remove empty MOUNTDIR after successful unmounting.

Additional arguments:

--help
print help and exit
--version
print version and exit

4.17.3. Example

$ ls /var/tmp/debian
bin   dev  home  lib64  mnt  proc  run   srv  tmp  var
boot  etc  lib   media  opt  root  sbin  sys  usr  WEIRD_AL_YANKOVIC
$ ch-umount /var/tmp/debian
unmounted and removed /var/tmp/debian
$ ls /var/tmp/debian
ls: cannot access /var/tmp/debian: No such file or directory