Provided by: charliecloud-runtime_0.38-1_amd64 
NAME
ch-run - Run a command in a Charliecloud container
SYNOPSIS
$ ch-run [OPTION...] IMAGE -- COMMAND [ARG...]
DESCRIPTION
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.
--env-no-expand
Don’t expand variables when using --set-env.
--feature=FEAT
If feature FEAT is enabled, exit successfully (zero); otherwise, exit unsuccessfully
(non-zero). Note this just communicates the results of configure rather than testing the
feature. Valid values of FEAT are:
• extglob: extended globs in --unset-env
• seccomp: --seccomp available
• squash: internal SquashFUSE image mounts
• overlayfs: unprivileged overlayfs support
• tmpfs-xattrs: user xattrs on tmpfs
-g, --gid=GID
Run as group GID within container.
--home 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-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).
-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.
--no-passwd
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).
--seccomp
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.
--unsafe
Enable various unsafe behavior. For internal use only. Seriously, stay away from this option.
--unset-env=GLOB
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.
--usage
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:
• 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.
WARNING:
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.
• /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.
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.
MULTIPLE PROCESSES IN THE SAME CONTAINER WITH --JOIN
By default, different ch-run invocations use different user and mount namespaces (i.e., different
containers). While this has no impact on sharing most resources between invocations, there are a few
important exceptions. These include:
1. ptrace(2), used by debuggers and related tools. One can attach a debugger to processes in descendant
namespaces, but not sibling namespaces. The practical effect of this is that (without --join), you
can’t run a command with ch-run and then attach to it with a debugger also run with ch-run.
2. Cross-memory attach (CMA) is used by cooperating processes to communicate by simply reading and
writing one another’s memory. This is also not permitted between sibling namespaces. This affects
various MPI implementations that use CMA to pass messages between ranks on the same node, because it’s
faster than traditional shared memory.
--join is designed to address this by placing related ch-run commands (the “peer group”) in the same
container. This is done by one of the peers creating the namespaces with unshare(2) and the others
joining with setns(2).
To do so, we need to know the number of peers and a name for the group. These are specified by additional
arguments that can (hopefully) be left at default values in most cases:
• --join-ct sets the number of peers. The default is the value of the first of the following environment
variables that is defined: OMPI_COMM_WORLD_LOCAL_SIZE, SLURM_STEP_TASKS_PER_NODE, SLURM_CPUS_ON_NODE.
• --join-tag sets the tag that names the peer group. The default is environment variable SLURM_STEP_ID,
if defined; otherwise, the PID of ch-run’s parent. Tags can be re-used for peer groups that start at
different times, i.e., once all peer ch-run have replaced themselves with the user command, the tag can
be re-used.
Caveats:
• One cannot currently add peers after the fact, for example, if one decides to start a debugger after
the fact. (This is only required for code with bugs and is thus an unusual use case.)
• ch-run instances race. The winner of this race sets up the namespaces, and the other peers use the
winner to find the namespaces to join. Therefore, if the user command of the winner exits, any
remaining peers will not be able to join the namespaces, even if they are still active. There is
currently no general way to specify which ch-run should be the winner.
• If --join-ct is too high, the winning ch-run’s user command exits before all peers join, or ch-run
itself crashes, IPC resources such as semaphores and shared memory segments will be leaked. These
appear as files in /dev/shm/ and can be removed with rm(1).
• Many of the arguments given to the race losers, such as the image path and --bind, will be ignored in
favor of what was given to the winner.
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:
• by default (--home not specified), HOME is set to /root, if it exists, and / otherwise.
• 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.
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, 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.)
$HOME If --home is specified, then your home directory is bind-mounted into the guest at /home/$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.)
$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:
• The case for the /usr Merge
• Fedora
• Debian
$TMPDIR
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
FOO=bar
BAZ='qux'
$ 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:$PATH' ...
Examples of valid assignment, assuming that environment variable BAR is set to bar and UNSET is unset or
set to the empty string:
┌─────────────────────────────┬───────┬────────────────────────┐
│ Assignment │ Name │ Value │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=bar │ FOO │ bar │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=bar=baz │ FOO │ bar=baz │
├─────────────────────────────┼───────┼────────────────────────┤
│ FLAGS=-march=foo -mtune=bar │ FLAGS │ -march=foo -mtune=bar │
├─────────────────────────────┼───────┼────────────────────────┤
│ FLAGS='-march=foo │ FLAGS │ -march=foo -mtune=bar │
│ -mtune=bar' │ │ │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=$BAR │ FOO │ bar │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=$BAR:baz │ FOO │ bar:baz │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO= │ FOO │ empty string │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=$UNSET │ FOO │ empty string │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=baz:$UNSET:qux │ FOO │ baz:qux (not baz::qux) │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO=:bar:baz:: │ FOO │ :bar:baz:: │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO='' │ FOO │ empty string │
├─────────────────────────────┼───────┼────────────────────────┤
│ FOO='''' │ FOO │ '' (two single quotes) │
└─────────────────────────────┴───────┴────────────────────────┘
Example invalid assignments:
┌────────────┬──────────────────────┐
│ Assignment │ Problem │
├────────────┼──────────────────────┤
│ FOO bar │ no equals separator │
├────────────┼──────────────────────┤
│ =bar │ name cannot be empty │
└────────────┴──────────────────────┘
Example valid assignments that are probably not what you want:
┌──────────────────┬───────┬───────────┬────────────────────────┐
│ Assignment │ Name │ Value │ Problem │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO="bar" │ FOO │ "bar" │ double quotes aren’t │
│ │ │ │ stripped │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO=bar # baz │ FOO │ bar # baz │ comments not supported │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO=bartbaz │ FOO │ bartbaz │ backslashes are not │
│ │ │ │ special │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO=bar │ FOO │ bar │ leading space in key │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO= bar │ FOO │ bar │ leading space in value │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ $FOO=bar │ $FOO │ bar │ variables not expanded │
│ │ │ │ in key │
├──────────────────┼───────┼───────────┼────────────────────────┤
│ FOO=$BAR baz:qux │ FOO │ qux │ variable 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.
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
$
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
WANTED_1=yes
ALSO_WANTED_2=yes
$
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
SHLVL=1
PWD=/
_=/usr/bin/env
$
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
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.
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
charliecloud(7)
Full documentation at: <https://hpc.github.io/charliecloud>
COPYRIGHT
2014–2023, Triad National Security, LLC and others
0.38 2024-06-15 19:23 UTC CH-RUN(1)