3. 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.

ch-build
ch-build2dir
ch-builder2tar
ch-checkns
ch-dir2squash
ch-builder2squash
ch-fromhost
ch-grow
ch-mount
ch-pull2dir
ch-pull2tar
ch-run
ch-run-oci
ch-ssh
ch-tar2dir
ch-test
ch-umount

3.1. ch-build ¶

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

3.1.1. Synopsis¶

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

3.1.2. 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 requires Buildah v1.10.1+; 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.

3.1.3. 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.

3.1.4. 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

3.2. ch-build2dir ¶

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

3.2.1. Synopsis¶

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

3.2.2. 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

3.2.3. 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

3.3. ch-builder2tar ¶

Flatten a builder image into a Charliecloud image tarball.

3.3.1. Synopsis¶

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

3.3.2. 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.

3.3.3. 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

3.4. ch-checkns ¶

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

3.4.1. Synopsis¶

$ ch-checkns

3.4.2. Description¶

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

3.4.3. Example¶

$ ch-checkns
ok

3.5. ch-dir2squash ¶

Create a SquashFS file from an image directory.

3.5.1. Synopsis¶

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

3.5.2. 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

3.5.3. 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

3.6. ch-builder2squash ¶

Flatten a builder image into a Charliecloud SquashFS file.

3.6.1. Synopsis¶

$ ch-builder2squash [-b BUILDER] IMAGE OUTDIR [ARGS ...]

3.6.2. Description¶

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

Wrapper for ch-builder2tar --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

3.6.3. Example¶

$ docker image list | fgrep debian
REPOSITORY   TAG       IMAGE ID       CREATED      SIZE
debian       stretch   2d337f242f07   3 weeks ago  101MB
$ ch-builder2squash 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

3.7. ch-fromhost ¶

Inject files from the host into an image directory.

3.7.1. Synopsis¶

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

3.7.2. 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.

3.7.3. Options¶

3.7.3.1. 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 MPICH/OpenMPI 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.

3.7.3.2. 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.

3.7.3.3. 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.

3.7.4. `--cray-mpi` dependencies and quirks¶

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

Containers must have the following software installed:
1. Corresponding open source MPI implementation. (MPICH and OpenMPI.)
2. PatchELF with our patches. Use the shrink-soname branch. (MPICH only.)
3. libgfortran.so.3, because Cray’s libmpi.so.12 links to it. (MPICH only.)
Applications must be dynamically linked to libmpi.so.12 (not e.g. libmpich.so.12).
1. How to configure MPICH to accomplish this is not yet clear to us; test/Dockerfile.mpich does it, while the Debian packages do not. (MPICH only.)
An ABI compatible module for the given MPI implementation must be loaded when ch-fromhost is invoked.
1. Load the cray-mpich-abi module. (MPICH only.)
2. We recommend loading the module of a version as close to what is installed in the image as possible. This OpenMPI install needs to be built such that libmpi contains all needed plugins (as opposed to them being standalone shared libraries). See OpenMPI’s documentation for how to do this. (OpenMPI only.)
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.

3.7.5. 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:

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.

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.

3.7.6. Bugs¶

File paths may not contain colons or newlines.

3.7.7. 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

Inject the Cray-enabled MPI libraries into the image, and then run ldconfig:

$ ch-fromhost --cray-mpi /var/tmp/baz

3.7.8. Acknowledgements¶

This command was inspired by the similar Shifter feature that allows Shifter containers to use the Cray Aries 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.

3.8. ch-grow ¶

Build and manage images; completely unprivileged.

3.8.1. Synopsis¶

$ ch-grow [...] build [-t TAG] [-f DOCKERFILE] [...] CONTEXT
$ ch-grow [...] list
$ ch-grow [...] pull [...] IMAGE_REF [IMAGE_DIR]
$ ch-grow [...] storage-path
$ ch-grow { --help | --version | --dependencies }

3.8.2. Description¶

ch-grow is a tool for building and manipulating container images, but not running them (for that you want ch-run). It is completely unprivileged, with no setuid/setgid/setcap helpers.

Options that print brief information and then exit:

-h, --help
Print help and exit successfully.

--dependencies
Report dependency problems on standard output, if any, and exit. If all is well, there is no output and the exit is successful; in case of problems, the exit is unsuccessful.

--version
Print version number and exit successfully.

Common options placed before the sub-command:

--no-cache
Download everything needed, ignoring the cache.

-s, --storage DIR
Set the storage directory (see below for important details).

-v, --verbose
Print extra chatter; can be repeated.

3.8.3. Storage directory¶

ch-grow maintains state using normal files and directories, including unpacked container images, located in its storage directory. There is no notion of storage drivers, graph drivers, etc., to select and/or configure. In descending order of priority, this directory is located at:

-s, --storage DIR
Command line option.

$CH_GROW_STORAGE
Environment variable.

/var/tmp/$USER/ch-grow
Default.

The storage directory can reside on any filesystem. However, it contains lots of small files and metadata traffic can be intense. For example, the Charliecloud test suite uses approximately 400,000 files and directories in the storage directory as of this writing. Place it on a filesystem appropriate for this; tmpfs’es such as /var/tmp are a good choice if you have enough RAM (/tmp is not recommended because ch-run bind-mounts it into containers by default).

While you can currently poke around in the storage directory and find unpacked images runnable with ch-run, this is not a supported use case. The supported workflow uses ch-builder2tar or ch-builder2squash to obtain a packed image; see the tutorial for details.

Warning

Network filesystems, especially Lustre, are typically bad choices for the storage directory. This is a site-specific question and your local support will likely have strong opinions.

3.8.4. Subcommands¶

3.8.4.1. `build`¶

Build an image from a Dockerfile and put it in the storage directory. Use ch-run(1) to execute RUN instructions.

Required argument:

CONTEXT
Path to context directory; this is the root of COPY and ADD instructions in the Dockerfile.

Options:

--build-arg KEY[=VALUE]
Set build-time variable KEY defined by ARG instruction to VALUE. If VALUE not specified, use the value of environment variable KEY.

-f, --file DOCKERFILE
Use DOCKERFILE instead of CONTEXT/Dockerfile. Specify a single hyphen (-) to use standard input; note that in this case, the context directory is still provided, which matches docker build -f - behavior.

-n, --dry-run
Do not actually execute any Dockerfile instructions.

--parse-only
Stop after parsing the Dockerfile.

-t, -tag TAG
Name of image to create. If not specified, use the final component of path CONTEXT. Append :latest if no colon present.

3.8.4.2. `storage-path`¶

Print the storage directory path and exit.

3.8.4.3. `pull`¶

Pull the image described by the image reference IMAGE_REF from a repository by HTTPS. See the FAQ for the gory details on specifying image references.

This script does a fair amount of validation and fixing of the layer tarballs before flattening in order to support unprivileged use despite image problems we frequently see in the wild. For example, device files are ignored, and file and directory permissions are increased to a minimum of rwx------ and rw------- respectively. Note, however, that symlinks pointing outside the image are permitted, because they are not resolved until runtime within a container.

Destination argument:

IMAGE_DIR
If specified, place the unpacked image at this path; it is then ready for use by ch-run or other tools. The storage directory will not contain a copy of the image, i.e., it is only unpacked once.

Options:

--parse-only
Parse IMAGE_REF, print a parse report, and exit successfully without talking to the internet or touching the storage directory.

3.8.5. Compatibility with other Dockerfile interpreters¶

ch-grow is an independent implementation and shares no code with other Dockerfile interpreters. It uses a formal Dockerfile parsing grammar developed from the Dockerfile reference documentation and miscellaneous other sources, which you can examine in the source code.

We believe this independence is valuable for several reasons. First, it helps the community examine Dockerfile syntax and semantics critically, think rigorously about what is really needed, and build a more robust standard. Second, it yields disjoint sets of bugs (note that Podman, Buildah, and Docker all share the same Dockerfile parser). Third, because it is a much smaller code base, it illustrates how Dockerfiles work more clearly. Finally, it allows straightforward extensions if needed to support scientific computing.

ch-grow tries hard to be compatible with Docker and other interpreters, though as an independent implementation, it is not bug-compatible.

This section describes differences from the Dockerfile reference that we expect to be approximately permanent. For an overview of features we have not yet implemented and our plans, see our road map on GitHub. Plain old bugs are in our GitHub issues.

None of these are set in stone. We are very interested in feedback on our assessments and open questions. This helps us prioritize new features and revise our thinking about what is needed for HPC containers.

3.8.5.1. Quirks of a fully unprivileged build¶

ch-grow is fully unprivileged. It runs all instructions as the normal user who invokes it, does not use any setuid or setcap helper programs, and does not use /etc/subuid or /etc/subgid, in contrast to the “rootless” mode of some competing builders.

RUN instructions are executed with ch-run --uid=0 --gid=0, i.e., host EUID and EGID both mapped to zero inside the container, and only one UID (zero) and GID (zero) are available inside the container. Also, /etc/passwd and /etc/group are bind-mounted from temporary files outside the container and can’t be written. (Strictly speaking, the files themselves are read-write, but because they are bind-mounted, the common pattern of writing a new file and moving it on top of the existing one fails.)

This has two consequences: the shell and its children appear to be running as root but only some privileged system calls are available, and manipulating users and groups will fail. This confuses some programs, which 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. Another manual workaround is to install fakeroot in the Dockerfile and prepend fakeroot to problem commands.

Note

Most of these issues affect any fully unprivileged container build, not just ch-grow. We are working to better characterize the problems and add automatic workarounds.

3.8.5.2. Context directory¶

The context directory is bind-mounted into the build, rather than copied like Docker. Thus, the size of the context is immaterial, and the build reads directly from storage like any other local process would. However, you still can’t access anything outside the context directory.

3.8.5.3. Authentication¶

ch-grow can authenticate using one-time passwords, e.g. those provided by a security token. Unlike docker login, it does not assume passwords are persistent.

3.8.5.4. Environment variables¶

Variable substitution happens for all instructions, not just the ones listed in the Dockerfile reference.

ARG and ENV cause cache misses upon definition, in contrast with Docker where these variables miss upon use, except for certain cache-excluded variables that never cause misses, listed below.

Like Docker, ch-grow pre-defines the following proxy variables, which do not require an ARG instruction. However, they are available if the same-named environment variable is defined; --build-arg is not required. Changes to these variables do not cause a cache miss.

HTTP_PROXY
http_proxy
HTTPS_PROXY
https_proxy
FTP_PROXY
ftp_proxy
NO_PROXY
no_proxy

The following variables are also pre-defined:

PATH=/ch/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
TAR_OPTIONS=--no-same-owner

Note that ARG and ENV have different syntax despite very similar semantics.

3.8.5.5. `COPY`¶

Especially for people used to UNIX cp(1), the semantics of the Dockerfile COPY instruction can be confusing.

Most notably, when a source of the copy is a directory, the contents of that directory, not the directory itself, are copied. This is documented, but it’s a real gotcha because that’s not what cp(1) does, and it means that many things you can do in one cp(1) command require multiple COPY instructions.

Also, the reference documentation is incomplete. In our experience, Docker also behaves as follows; ch-grow does the same in an attempt to be bug-compatible for the COPY instructions.

You can use absolute paths in the source; the root is the context directory.
Destination directories are created if they don’t exist in the following situations:
1. If the destination path ends in slash. (Documented.)
2. If the number of sources is greater than 1, either by wildcard or explicitly, regardless of whether the destination ends in slash. (Not documented.)
3. If there is a single source and it is a directory. (Not documented.)
Symbolic links are particularly messy (this is not documented):
1. If named in sources either explicitly or by wildcard, symlinks are dereferenced, i.e., the result is a copy of the symlink target, not the symlink itself. Keep in mind that directory contents are copied, not directories.
2. If within a directory named in sources, symlinks are copied as symlinks.

We expect the following differences to be permanent:

Wildcards use Python glob semantics, not the Go semantics.
COPY --chown is ignored, because it doesn’t make sense in an unprivileged build.

3.8.5.6. Features we do not plan to support¶

Parser directives are not supported. We have not identified a need for any of them.
EXPOSE: Charliecloud does not use the network namespace, so containerized processes can simply listen on a host port like other unprivileged processes.
HEALTHCHECK: This instruction’s main use case is monitoring server processes rather than applications. Also, implementing it requires a container supervisor daemon, which we have no plans to add.
MAINTAINER is deprecated.
STOPSIGNAL requires a container supervisor daemon process, which we have no plans to add.
USER does not make sense for unprivileged builds.
VOLUME: This instruction is not currently supported. Charliecloud has good support for bind mounts; we anticipate that it will continue to focus on that and will not introduce the volume management features that Docker has.

3.8.6. Environment variables¶

CH_LOG_FILE

If set, append log chatter to this file, rather than standard error. This is useful for debugging situations where standard error is consumed or lost.

Also sets verbose mode if not already set (equivalent to --verbose).

CH_LOG_FESTOON

If set, prepend PID and timestamp to logged chatter.

3.8.7. Examples¶

3.8.7.1. `build`¶

Build image bar using ./foo/bar/Dockerfile and context directory ./foo/bar:

$ ch-grow build -t bar -f ./foo/bar/Dockerfile ./foo/bar
[...]
grown in 4 instructions: bar

Same, but infer the image name and Dockerfile from the context directory path:

$ ch-grow build ./foo/bar
[...]
grown in 4 instructions: bar

3.8.7.2. `pull`¶

Download the Debian Buster image and place it in the storage directory:

$ ch-grow pull debian:buster
pulling image:   debian:buster

manifest: downloading
layer 1/1: d6ff36c: downloading
layer 1/1: d6ff36c: listing
validating tarball members
resolving whiteouts
flattening image
layer 1/1: d6ff36c: extracting
done

Same, except place the image in /tmp/buster:

$ ch-grow pull debian:buster /tmp/buster
[...]
$ ls /tmp/buster
bin   dev  home  lib64  mnt  proc  run   srv  tmp  var
boot  etc  lib   media  opt  root  sbin  sys  usr

3.9. ch-mount ¶

Mount a SquashFS image file using FUSE.

3.9.1. Synopsis¶

$ ch-mount SQFS PARENTDIR

3.9.2. 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

3.9.3. 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

3.10. ch-pull2dir ¶

Pull image from a Docker Hub and unpack into directory.

3.10.1. Synopsis¶

$ ch-pull2dir IMAGE[:TAG] DIR

3.10.2. 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

3.10.3. 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'

3.11. ch-pull2tar ¶

Pull image from a Docker Hub and flatten into tarball.

3.11.1. Synopsis¶

$ ch-pull2tar IMAGE[:TAG] OUTDIR

3.11.2. 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

3.11.3. 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

3.12. ch-run ¶

Run a command in a Charliecloud container.

3.12.1. Synopsis¶

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

3.12.2. 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

3.12.3. 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.

3.12.4. 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:

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.
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.

3.12.5. 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;
user-unset variables via --unset-env; and
set CH_RUNNING.

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.

3.12.5.1. Default behavior¶

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

$CH_RUNNING: Set to Weird Al Yankovic. While a process can figure out that it’s in an unprivileged container and what namespaces are active without this hint, the checks can be messy, and there is no way to tell that it’s a Charliecloud container specifically. This variable makes such a test simple and well-defined. (Note: This variable is unaffected by --unset-env.)
$HOME: If the path to your home directory is not /home/$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:

3.12.5.2. 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

3.12.5.3. 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
$

3.12.6. 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

3.13. ch-run-oci ¶

OCI wrapper for ch-run.

3.13.1. Synopsis¶

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

3.13.2. 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.

3.13.3. Operations¶

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

3.13.3.1. `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.

3.13.3.2. `delete`¶

$ ch-run-oci delete CONTAINER_ID

Clean up the OCI-related scaffolding for specified container.

3.13.3.3. `kill`¶

$ ch-run-oci kill CONTAINER_ID

No-op.

3.13.3.4. `start`¶

$ ch-run-oci start CONTAINER_ID

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

3.13.3.5. `state`¶

$ ch-run-oci state CONTAINER_ID

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

3.13.4. 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

3.13.5. Environment variables¶

CH_LOG_FILE

If set, append log chatter to this file, rather than standard error. This is useful for debugging situations where standard error is consumed or lost.

Also sets verbose mode if not already set (equivalent to --verbose).

CH_LOG_FESTOON

If set, prepend PID and timestamp to logged chatter.

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.

3.14. ch-ssh ¶

Run a remote command in a Charliecloud container.

3.14.1. Synopsis¶

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

3.14.2. 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.

3.14.3. 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

3.15. ch-tar2dir ¶

Unpack an image tarball into a directory.

3.15.1. Synopsis¶

$ ch-tar2dir TARBALL DIR

3.15.2. 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.

3.15.3. 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

3.16. ch-test ¶

Run some or all of the Charliecloud test suite.

3.16.1. Synopsis¶

$ ch-test [PHASE] [--scope SCOPE] [ARGS]

3.16.2. Description¶

Charliecloud comes with a comprehensive test suite that exercises the container workflow itself as well as a few example applications. ch-test coordinates running the test suite.

While the CLI has lots of options, the defaults are reasonable, and bare ch-test will give useful results in a few minutes on single-node, internet-connected systems with a few GB available in /var/tmp.

The test suite requires a few GB (standard scope) or tens of GB (full scope) of storage for test fixtures:

Builder storage (e.g., layer cache). This goes wherever the builder puts it.
Packed images directory: image tarballs or SquashFS files.
Unpacked images directory. Images are unpacked into and then run from here.
Filesystem permissions directories. These are used to test that the kernel is enforcing permissions correctly. Note that this exercises the kernel, not Charliecloud, and can be omitted from routine Charliecloud testing.

The first three are created when needed if they don’t exist, while the filesystem permissions fixtures must be created manually, in order to accommodate configurations where sudo is not available via the same login path used for running tests.

The packed and unpacked image directories specified for testing are volatile. The contents of these directories are deleted before the build and run phases, respectively.

In all four cases, when creating directories, only the final path component is created. Parent directories must already exist, i.e., ch-test uses the behavior of mkdir rather than mkdir -p.

Some of the tests exercise parallel functionality. If ch-test is run on a single node, multiple cores will be used; if in a Slurm allocation, multiple nodes too.

The subset of tests to run mostly splits along two key dimensions. The phase is which parts of the workflow to run. Different parts of the workflow can be tested on different systems by copying the necessary artifacts between them, e.g. by building images on one system and running them on another. The scope allows trading off thoroughness versus time.

PHASE must be one of the following:

build
Image building and associated functionality, with the selected builder.

run
Running containers and associated functionality. This requires a packed images directory produced by a successful build phase, which can be copied from the build system if it’s not also the run system.

examples
Example applications. Requires an unpacked images directory produced by a successful run phase.

all
Execute phases build, run, and examples, in that order.

mk-perm-dirs
Create the filesystem permissions directories. Requires --perm-dirs.

clean
Delete automatically-generated test files, and packed and unpacked image directories.

rm-perm-dirs
Remove the filesystem permissions directories. Requires --perm-dirs.

-f, --file FILE
Run the tests in the given file only, which can be an arbitrary .bats file, except for test.bats under examples, where you must specify the corresponding Dockerfile or Build file instead. This is somewhat brittle and typically used for development or debugging. For example, it does not check whether the pre-requisites of whatever is in the file are satisfied. Often running build and run first is sufficient, but this varies.

Scope is specified with:

-s, --scope SCOPE
SCOPE must be one of the following; the default is standard.

quick: Most important subset of workflow. Handy for development. Completion time: 1–2 minutes.

standard: All tested workflow functionality and a selection of more important examples. Completion time: 5–10 minutes.

full: All available tests, including all examples. Completion time, hot cache: 7–15 minutes; cold cache: 1–2 hours.

Additional arguments:

-b, --builder BUILDER
Image builder to use. See ch-build(1) for how the default is selected.

--dry-run
Print summary of what would be tested and then exit.

-h, --help
Print usage and then exit.

--img-dir DIR
Set unpacked images directory to DIR. In a multi-node allocation, this directory may not be shared between nodes. Default: $CH_TEST_IMGDIR if set; otherwise /var/tmp/img.

--pack-dir DIR
Set packed images directory to DIR. Default: $CH_TEST_TARDIR if set; otherwise /var/tmp/pack.

--pedantic (yes|no)
Some tests require configurations that are very specific (e.g., being a member of at least two groups) or unusual (e.g., sudo to a non-root group). If yes, then fail if the requirement is not met; if no, then skip. The default is yes for CI environments or people listed in README.md, no otherwise.

If yes and sudo seems to be available, implies --sudo.

--perm-dir DIR
Add DIR to filesystem permission fixture directories; can be specified multiple times. We recommend one such directory per mounted filesystem type whose kernel module you do not trust; e.g., you probably don’t need to test your tmpfses, but out-of-tree filesystems very likely need this.

Implies --sudo. Default: CH_TEST_PERMDIRS if set; otherwise skip the filesystem permissions tests.

--pack-fmt FMT
Use packed image format FMT (squash or tar).

--sudo
Enable things that require sudo, such as certain privilege escalation tests and creating/removing the filesystem permissions fixtures. Requires generic sudo capabilities. Note that the Docker builder uses sudo docker even without this option.

--lustre DIR
Use DIR for run-phase Lustre tests. Default: CH_TEST_LUSTREDIR if set; otherwise skip them.

The tests will create, populate, and delete a new subdirectory under DIR, leaving everything else in DIR untouched.

3.16.3. Exit status¶

Zero if all tests passed; non-zero if any failed. For setup and teardown phases, zero if everything was created or deleted correctly, non-zero otherwise.

3.16.4. Bugs¶

Bats will wait until all descendant processes finish before exiting, so if you get into a failure mode where a test sequence doesn’t clean up all its processes, ch-test will hang.

3.16.5. Examples¶

Many systems can simply use the defaults. To run the build, run, and examples phases on a single system, without the filesystem permissions tests:

$ ch-test
ch-test version 0.12

ch-run: 0.12 /usr/local/bin/ch-run
bats:   0.4.0 /usr/bin/bats
tests:  /usr/local/libexec/charliecloud/test

phase:                build run examples
scope:                standard (default)
builder:              docker (default)
use generic sudo:     no (default)
unpacked images dir:  /var/tmp/img (default)
packed images dir:    /var/tmp/tar (default)
fs permissions dirs:  skip (default)

checking namespaces ...
ok

checking builder ...
found: /usr/bin/docker 19.03.2

bats build.bats build_auto.bats build_post.bats
 ✓ documentation seems sane
 ✓ version number seems sane
[...]
All tests passed.

The next example is for a more complex setup like you might find in HPC centers:

Non-default fixture directories.

Non-default scope.

Different build and run systems.

Run the filesystem permissions tests.

Output has been omitted.

(mybox)$ ssh hpc-admin
(hpc-admin)$ ch-test mk-perm-dirs --perm-dir /scratch/$USER/perms \
                                  --perm-dir /home/$USER/perms
(hpc-admin)$ exit
(mybox)$ ch-test build --scope full
(mybox)$ scp -r /var/tmp/pack hpc:/scratch/$USER/pack
(mybox)$ ssh hpc
(hpc)$ salloc -N2
(cn001)$ export CH_TEST_TARDIR=/scratch/$USER/pack
(cn001)$ export CH_TEST_IMGDIR=/local/tmp
(cn001)$ export CH_TEST_PERMDIRS="/scratch/$USER/perms /home/$USER/perms"
(cn001)$ export CH_TEST_SCOPE=full
(cn001)$ ch-test run
(cn001)$ ch-test examples

3.17. ch-umount ¶

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

3.17.1. Synopsis¶

$ ch-umount MOUNTDIR

3.17.2. 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

3.17.3. 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

3. Charliecloud command reference¶

3.1.1. Synopsis¶

3.1.2. Description¶

3.1.3. Bugs¶

3.1.4. Examples¶

3.2.1. Synopsis¶

3.2.2. Description¶

3.2.3. Examples¶

3.3.1. Synopsis¶

3.3.2. Description¶

3.3.3. Example¶

3.4.1. Synopsis¶

3.4.2. Description¶

3.4.3. Example¶

3.5.1. Synopsis¶

3.5.2. Description¶

3.5.3. Example¶

3.6.1. Synopsis¶

3.6.2. Description¶

3.6.3. Example¶

3.7.1. Synopsis¶

3.7.2. Description¶

3.7.3. Options¶

3.7.3.1. To specify which files to inject¶

3.7.3.2. To specify the destination within the image¶

3.7.3.3. Additional arguments¶

3.7.4. --cray-mpi dependencies and quirks¶

3.7.5. Notes¶

3.7.6. Bugs¶

3.7.7. Examples¶

3.7.8. Acknowledgements¶

3.8.1. Synopsis¶

3.8.2. Description¶

3.8.3. Storage directory¶

3.8.4. Subcommands¶

3.8.4.1. build¶

3.8.4.2. storage-path¶

3.8.4.3. pull¶

3.8.5. Compatibility with other Dockerfile interpreters¶

3.8.5.1. Quirks of a fully unprivileged build¶

3.8.5.2. Context directory¶

3.8.5.3. Authentication¶

3.8.5.4. Environment variables¶

3.8.5.5. COPY¶

3.8.5.6. Features we do not plan to support¶

3.8.6. Environment variables¶

3.8.7. Examples¶

3.8.7.1. build¶

3.8.7.2. pull¶

3.9.1. Synopsis¶

3.9.2. Description¶

3.9.3. Example¶

3.10.1. Synopsis¶

3.10.2. Description¶

3.10.3. Examples¶

3.11.1. Synopsis¶

3.11.2. Description¶

3.11.3. Examples¶

3.12.1. Synopsis¶

3.12.2. Description¶

3.12.3. Host files and directories available in container via bind mounts¶

3.12.4. Multiple processes in the same container with --join¶

3.12.5. Environment variables¶

3.12.5.1. Default behavior¶

3.12.5.2. Setting variables with --set-env¶

3.12.5.3. Removing variables with --unset-env¶

3.12.6. Examples¶

3.13.1. Synopsis¶

3.13.2. Description¶

3.13.3. Operations¶

3.13.3.1. create¶

3.13.3.2. delete¶

3.13.3.3. kill¶

3.13.3.4. start¶

3.13.3.5. state¶

3.13.4. Unsupported OCI features¶

3.13.5. Environment variables¶

3.14.1. Synopsis¶

3.14.2. Description¶

3.14.3. Example¶

3.7.4. `--cray-mpi` dependencies and quirks¶

3.8.4.1. `build`¶

3.8.4.2. `storage-path`¶

3.8.4.3. `pull`¶

3.8.5.5. `COPY`¶

3.8.7.1. `build`¶

3.8.7.2. `pull`¶

3.12.4. Multiple processes in the same container with `--join`¶

3.12.5.2. Setting variables with `--set-env`¶

3.12.5.3. Removing variables with `--unset-env`¶

3.13.3.1. `create`¶

3.13.3.2. `delete`¶

3.13.3.3. `kill`¶

3.13.3.4. `start`¶

3.13.3.5. `state`¶