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ch-run - Man Page

Run a command in a Charliecloud container


$ ch-run [OPTION...] IMAGE -- COMMAND [ARG...]


Run command COMMAND in a fully unprivileged Charliecloud container using the image specified by IMAGE, which can be: (1) a path to a directory, (2) the name of an image in ch-image storage (e.g. example.com:5050/foo) or, if the proper support is enabled, a SquashFS archive. ch-run does not use any setuid or setcap helpers, even for mounting SquashFS images with FUSE.

-b,  --bind=SRC[:DST]

Bind-mount SRC at guest DST. The default destination if not specified is to use the same path as the host; i.e., the default is --bind=SRC:SRC. Can be repeated.

With a read-only image (the default), DST must exist. However, if --write or --write-fake are given, DST will be created as an empty directory (possibly with the tmpfs overmount trick described in --bind creates mount points within un-writeable directories!). In this case, DST must be entirely within the image itself, i.e., DST cannot enter a previous bind mount. For example, --bind /foo:/tmp/foo will fail because /tmp is shared with the host via bind-mount (unless $TMPDIR is set to something else or --private-tmp is given).

Most images have ten directories /mnt/[0-9] already available as mount points.

Symlinks in DST are followed, and absolute links can have surprising behavior. Bind-mounting happens after namespace setup but before pivoting into the container image, so absolute links use the host root. For example, suppose the image has a symlink /foo -> /mnt. Then, --bind=/bar:/foo will bind-mount on the host’s /mnt, which is inaccessible on the host because namespaces are already set up and also inaccessible in the container because of the subsequent pivot into the image. Currently, this problem is only detected when DST needs to be created: ch-run will refuse to follow absolute symlinks in this case, to avoid directory creation surprises.

-c,  --cd=DIR

Initial working directory in container.


Don’t expand variables when using --set-env.


If feature FEAT is enabled, exit with success. Valid values of FEAT are extglob for extended globs, seccomp for seccomp(2), and squash for squashfs archives.

-g,  --gid=GID

Run as group GID within container.


Bind-mount your host home directory (i.e., $HOME) at guest /home/$USER, hiding any existing image content at that path. Implies --write-fake so the mount point can be created if needed.

-j,  --join

Use the same container (namespaces) as peer ch-run invocations.


Join the namespaces of an existing process.


Number of ch-run peers (implies --join; default: see below).


Label for ch-run peer group (implies --join; default: see below).

-m,  --mount=DIR

Use DIR for the SquashFS mount point, which must already exist. If not specified, the default is /var/tmp/$USER.ch/mnt, which will be created if needed.


By default, temporary /etc/passwd and /etc/group files are created according to the UID and GID maps for the container and bind-mounted into it. If this is specified, no such temporary files are created and the image’s files are exposed.

-q,  --quiet

Be quieter; can be repeated. Incompatible with -v. See the How can I control Charliecloud’s quietness or verbosity? for details.

-s,  --storage DIR

Set the storage directory. Equivalent to the same option for ch-image(1).


Using seccomp, intercept some system calls that would fail due to lack of privilege, do nothing, and return fake success to the calling program. This is intended for use by ch-image(1) when building images; see that man page for a detailed discussion.

-t,  --private-tmp

By default, the host’s /tmp (or $TMPDIR if set) is bind-mounted at container /tmp. If this is specified, a new tmpfs is mounted on the container’s /tmp instead.

--set-env,  --set-env=FILE, --set-env=VAR=VALUE

Set environment variables with newline-separated file (/ch/environment within the image if not specified) or on the command line. See below for details.

--set-env0,  --set-env0=FILE, --set-env0=VAR=VALUE

Like --set-env, but file is null-byte separated.

-u,  --uid=UID

Run as user UID within container.


Enable various unsafe behavior. For internal use only. Seriously, stay away from this option.


Unset environment variables whose names match GLOB.

-v,  --verbose

Print extra chatter; can be repeated. See the FAQ entry on verbosity for details.

-w,  --write

Mount image read-write. By default, the image is mounted read-only. This option should be avoided for most use cases, because (1) changing images live (as opposed to prescriptively with a Dockerfile) destroys their provenance and (2) SquashFS images, which is the best-practice format on parallel filesystems, must be read-only. It is better to use --write-fake (for disposable data) or bind-mount host directories (for retained data).

-W,  --write-fake[=SIZE]

Overlay a writeable tmpfs on top of the image. This makes the image appear read-write, but it actually remains read-only and unchanged. All data “written” to the image are discarded when the container exits.

The size of the writeable filesystem SIZE is any size specification acceptable to tmpfs, e.g. 4m for 4MiB or 50% for half of physical memory. If this option is specified without SIZE, the default is 12%. Note (1) this limit is a maximum — only actually stored files consume virtual memory — and (2) SIZE larger than memory can be requested without error (the failure happens later if the actual contents become too large).

This requires kernel support and there are some caveats. See section “Writeable overlay with --write-fake” below for details.

-?,  --help

Print help and exit.


Print a short usage message and exit.

-V,  --version

Print version and exit.

Note: Because ch-run is fully unprivileged, it is not possible to change UIDs and GIDs within the container (the relevant system calls fail). In particular, setuid, setgid, and setcap executables do not work. As a precaution, ch-run calls prctl(PR_SET_NO_NEW_PRIVS, 1) to disable these executables within the container. This does not reduce functionality but is a “belt and suspenders” precaution to reduce the attack surface should bugs in these system calls or elsewhere arise.

Image Format

ch-run supports two different image formats.

The first is a simple directory that contains a Linux filesystem tree. This can be accomplished by:

The second is a SquashFS image archive mounted internally by ch-run, available if it’s linked with the optional libsquashfuse_ll shared library. ch-run mounts the image filesystem, services all FUSE requests, and unmounts it, all within ch-run. See --mount above to set the mount point location.

Like other FUSE implementations, Charliecloud calls the fusermount3(1) utility to mount the SquashFS filesystem. However, this executable does not need to be installed setuid root, and in fact ch-run actively suppresses its setuid bit if set (using prctl(2)).

Prior versions of Charliecloud provided wrappers for the squashfuse and squashfuse_ll SquashFS mount commands and fusermount -u unmount command. We removed these because we concluded they had minimal value-add over the standard, unwrapped commands.


Currently, Charliecloud unmounts the SquashFS filesystem when user command COMMAND’s process exits. It does not monitor any of its child processes. Therefore, if the user command spawns child processes and then exits before them (e.g., some daemons), those children will have the image unmounted from underneath them. In this case, the workaround is to mount/unmount using external tools. We expect to remove this limitation in a future version.

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 give access to the host’s devices and various kernel facilities. (Recall that Charliecloud provides minimal isolation and containerized processes are mostly normal unprivileged processes.) They cannot be disabled and are required; i.e., they must exist both on host and within the image.

Optional; bind-mounted only if path exists on both host and within the image, without error or warning if not.

Additional bind mounts done by default but can be disabled; see the options above.

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:


Writeable Overlay with --write-fake

If you need the image to stay read-only but appear writeable, you may be able to use --write-fake to overlay a writeable tmpfs atop the image. This requires kernel support. Specifically:

  1. To use the feature at all, you need unprivileged overlayfs support. This is available in upstream 5.11 (February 2021), but distributions vary considerably. If you don’t have this, the container will fail to start with error “operation not permitted”.
  2. For a fully functional overlay, you need a tmpfs that supports xattrs in the user namespace. This is available in upstream 6.6 (October 2023). If you don’t have this, most things will work fine, but some operations will fail with “I/O error”, for example creating a directory with the same path as a previously deleted directory. There will also be syslog noise about xattr problems.

    (overlayfs can also use xattrs in the trusted namespace, but this requires CAP_SYS_ADMIN on the host and thus is not helpful for unprivileged containers.)

Environment Variables

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

This section describes these features.

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

Default behavior

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


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, that 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.)


If --home is specified, then your home directory is bind-mounted into the guest at /home/$USER. If you also have a different home directory path on the host, an inherited $HOME will be incorrect inside the guest, which confuses lots of software, notably Spack. Thus, with --home, $HOME is set to /home/$USER (by default, it is unchanged.)


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:

  • The case for the /usr Merge
  • Fedora
  • Debian

Unset, because this is almost certainly a host path, and that host path is made available in the guest at /tmp unless --private-tmp is given.

Setting variables with --set-env or --set-env0

The purpose of these two options is to set environment variables within the container. Values given replace any already in the environment (i.e., inherited from the host shell) or set by earlier uses of the options. These flags take an optional argument with two possible forms:

  1. If the argument contains an equals sign (=, ASCII 61), that sets an environment variable directly. For example, to set FOO to the string value bar:

    $ ch-run --set-env=FOO=bar ...

    Single straight quotes around the value (', ASCII 39) are stripped, though be aware that both single and double quotes are also interpreted by the shell. For example, this example is similar to the prior one; the double quotes are removed by the shell and the single quotes are removed by ch-run:

    $ ch-run --set-env="'BAZ=qux'" ...
  2. If the argument does not contain an equals sign, it is a host path to a file containing zero or more variables using the same syntax as above (except with no prior shell processing).

    With --set-env, this file contains a sequence of assignments separated by newline (n or ASCII 10); with --set-env0, the assignments are separated by the null byte (i.e., 0 or ASCII 0). Empty assignments are ignored, and no comments are interpreted. (This syntax is designed to accept the output of printenv and be easily produced by other simple mechanisms.) The file need not be seekable.

    For example:

    $ cat /tmp/env.txt
    $ ch-run --set-env=/tmp/env.txt ...

    For directory images only (because the file is read before containerizing), guest paths can be given by prepending the image path.

  3. If there is no argument, the file /ch/environment within the image is used. This file is commonly populated by ENV instructions in the Dockerfile. For example, equivalently to form 2:

    $ cat Dockerfile
    ENV FOO=bar
    ENV BAZ=qux
    $ ch-image build -t foo .
    $ ch-convert foo /var/tmp/foo.sqfs
    $ ch-run --set-env /var/tmp/foo.sqfs -- ...

    (Note the image path is interpreted correctly, not as the --set-env argument.)

    At present, there is no way to use files other than /ch/environment within SquashFS images.

Environment variables are expanded for values that look like search paths, unless --env-no-expand is given prior to --set-env. In this case, the value is a sequence of zero or more possibly-empty items separated by colon (:, ASCII 58). If an item begins with dollar sign ($, ASCII 36), then the rest of the item is the name of an environment variable. If this variable is set to a non-empty value, that value is substituted for the item; otherwise (i.e., the variable is unset or the empty string), the item is deleted, including a delimiter colon. The purpose of omitting empty expansions is to avoid surprising behavior such as an empty element in $PATH meaning the current directory.

For example, to set HOSTPATH to the search path in the current shell (this is expanded by ch-run, though letting the shell do it happens to be equivalent):

$ ch-run --set-env='HOSTPATH=$PATH' ...

To prepend /opt/bin to this current search path:

$ ch-run --set-env='PATH=/opt/bin:$PATH' ...

To prepend /opt/bin to the search path set by the Dockerfile, as retrieved from guest file /ch/environment (here we really cannot let the shell expand $PATH):

$ ch-run --set-env --set-env='PATH=/opt/bin:$PATH' ...

Examples of valid assignment, assuming that environment variable BAR is set to bar and UNSET is unset or set to the empty string:

FLAGS=-march=foo -mtune=barFLAGS-march=foo -mtune=bar
FLAGS='-march=foo -mtune=bar'FLAGS-march=foo -mtune=bar
FOO=FOOempty string
FOO=$UNSETFOOempty string
FOO=baz:$UNSET:quxFOObaz:qux (not baz::qux)
FOO=''FOOempty string
FOO=''''FOO'' (two single quotes)

Example invalid assignments:

FOO barno equals separator
=barname cannot be empty

Example valid assignments that are probably not what you want:

FOO="bar"FOO"bar"double quotes aren’t stripped
FOO=bar # bazFOObar # bazcomments not supported
FOO=bartbazFOObartbazbackslashes are not special
FOO=bar FOObarleading space in key
FOO= barFOO barleading space in value
$FOO=bar$FOObarvariables not expanded in key
FOO=$BAR baz:quxFOOquxvariable BAR baz not set

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 the FNM_EXTMATCH flag where supported); all variables with matching names are removed from the environment.


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
$ 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

Example 4: Remove all environment variables except for those prefixed with either WANTED_ or ALSO_WANTED_:

$ export WANTED_1=yes
$ export ALSO_WANTED_2=yes
$ export NOT_WANTED_1=no
$ ch-run --unset-env='!(WANTED_*|ALSO_WANTED_*)' $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/debian_9ch -- bash --noprofile --norc -c env


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

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

Run an MPI job that can use CMA to communicate:

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


By default, ch-run logs its command line to syslog. (This can be disabled by configuring with --disable-syslog.) This includes: (1) the invoking real UID, (2) the number of command line arguments, and (3) the arguments, separated by spaces. For example:

Dec 10 18:19:08 mybox ch-run: uid=1000 args=7: ch-run -v /var/tmp/00_tiny -- echo hello "wor l}\$d"

Logging is one of the first things done during program initialization, even before command line parsing. That is, almost all command lines are logged, even if erroneous, and there is no logging of program success or failure.

Arguments are serialized with the following procedure. The purpose is to provide a human-readable reconstruction of the command line while also allowing each argument to be recovered byte-for-byte.

The verbatim command line typed in the shell cannot be recovered, because not enough information is provided to UNIX programs. For example, echo  'foo' is given to programs as a sequence of two arguments, echo and foo; the two spaces and single quotes are removed by the shell. The zero byte, ASCII NUL, cannot appear in arguments because it would terminate the string.

Exit Status

If there is an error during containerization, ch-run exits with status non-zero. If the user command is started successfully, the exit status is that of the user command, with one exception: if the image is an internally mounted SquashFS filesystem and the user command is killed by a signal, the exit status is 1 regardless of the signal value.

Reporting Bugs

If Charliecloud was obtained from your Linux distribution, use your distribution’s bug reporting procedures.

Otherwise, report bugs to: https://github.com/hpc/charliecloud/issues

See Also


Full documentation at: <https://hpc.github.io/charliecloud>

Referenced By

charliecloud(7), ch-convert(1), ch-run-oci(1).

2024-03-22 00:00 UTC 0.36 Charliecloud