7. ch-run

Run a command in a Charliecloud container.

7.1. Synopsis

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

7.2. Description

Run command CMD 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.

If --write is given and DST does not exist, it will be created as an empty directory. However, DST must be entirely within the image itself; 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 do 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.


Bind ch-ssh(1) into container at /usr/bin/ch-ssh.


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

-g, --gid=GID

Run as group GID within container.


Bind-mount your host home directory (i.e., $HOME) at guest /home/$USER. This is accomplished by over-mounting a new tmpfs at /home, which hides any image content under that path. By default, neither of these things happens and the image’s /home is exposed unaltered.

-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.

-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 variable(s). With:

  • no argument: as listed in file /ch/environment within the image. It is an error if the file does not exist or cannot be read. (Note that with SquashFS images, it is not currently possible to use other files within the image.)

  • FILE (i.e., no equals in argument): as specified in file at host path FILE. Again, it is an error if the file cannot be read.

  • NAME=VALUE (i.e., equals sign in argument): set variable NAME to VALUE.

See below for details on how environment variables work in ch-run.

-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

Be more verbose (can be repeated).

-w, --write

Mount image read-write (by default, the image is mounted read-only).

-?, --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.

7.3. 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:

  • ch-convert directly from ch-image or another builder to a directory.

  • Charliecloud’s tarball workflow: build or pull the image, ch-convert it to a tarball, transfer the tarball to the target system, then ch-convert the tarball to a directory.

  • Manually mount a SquashFS image, e.g. with squashfuse(1) and then un-mount it after run with fusermount -u.

  • Any other workflow that produces an appropriate directory tree.

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 CMD’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.

7.4. 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.

  • /dev

  • /proc

  • /sys

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

  • /etc/hosts and /etc/resolv.conf. Because Charliecloud containers share the host network namespace, they need the same hostname resolution configuration.

  • /etc/machine-id. Provides a unique ID for the OS installation; matching the host works for most situations. Needed to support D-Bus, some software licensing situations, and likely other use cases. See also issue #1050.

  • /var/lib/hugetlbfs at guest /var/opt/cray/hugetlbfs, and /var/opt/cray/alps/spool. These support Cray MPI.

  • $PREFIX/bin/ch-ssh at guest /usr/bin/ch-ssh. SSH wrapper that automatically containerizes after connecting.

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

  • $HOME at /home/$USER (and image /home is hidden). Makes user data and init files available.

  • /tmp (or $TMPDIR if set) at guest /tmp. Provides a temporary directory that persists between container runs and is shared with non-containerized application components.

  • temporary files at /etc/passwd and /etc/group. Usernames and group names need to be customized for each container run.

7.5. 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.


  • 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.

7.6. 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, 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.

7.6.1. 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:


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.

7.6.2. Setting variables with --set-env

The purpose of --set-env 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 --set-env. This flag takes 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). This file contains a sequence of assignments separated by newlines. Empty lines 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.) 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=bar


-march=foo -mtune=bar

FLAGS='-march=foo -mtune=bar'


-march=foo -mtune=bar









empty string



empty string



baz:qux (not baz::qux)






empty string



'' (two single quotes)

Example invalid assignments:



FOO bar

no equals separator


name cannot be empty

Example valid assignments that are probably not what you want:








double quotes aren’t stripped

FOO=bar # baz


bar # baz

comments not supported




backslashes are not special




leading space in key

FOO= bar



leading space in value




variables not expanded in key

FOO=$BAR baz:qux



variable BAR baz not set

7.6.3. 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 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

7.7. Examples

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

7.8. Syslog

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.

  • If an argument contains only printable ASCII bytes that are not whitespace, shell metacharacters, double quote (", ASCII 34 decimal), or backslash (\​, ASCII 92), then log it unchanged.

  • Otherwise, (a) enclose the argument in double quotes and (b) backslash-escape double quotes, backslashes, and characters interpreted by Bash (including POSIX shells) within double quotes.

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.

7.9. 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.