ch-run man page

ch-run — Run a command in a Charliecloud container

Synopsis

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

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

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.

Three additional bind mounts can be disabled by the user:

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:

Caveats:

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, 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.

Default behavior

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

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

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

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

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

    Further reading:

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

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:

LineKeyValue
FOO=barFOObar
FOO=bar=bazFOObar=baz
FLAGS=-march=foo -mtune=barFLAGS-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:

LineProblem
FOO barno separator
=barkey cannot be empty

Example valid lines that are probably not what you want:

LineKeyValueProblem
FOO="bar"FOO"bar"double quotes aren’t stripped
FOO=bar # bazFOObar # bazcomments not supported
PATH=$PATH:/opt/binPATH$PATH:/opt/binvariables not expanded
FOO=bar FOObarleading space in key
FOO= barFOO barleading space in value

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
$

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

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(1)

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

Referenced By

charliecloud(1), ch-grow(1), ch-run-oci(1).

2019-09-04 00:00 Coordinated Universal Time Charliecloud