apptainer exec

Run a command within a container

Synopsis

apptainer exec supports the following formats:

*.sif Singularity Image Format (SIF). Native to Singularity

(3.0+) and Apptainer (v1.0.0+)

*.sqsh SquashFS format. Native to Singularity 2.4+

*.img ext3 format. Native to Singularity versions < 2.4.

directory/ sandbox format. Directory containing a valid root file

system and optionally Apptainer meta-data.

instance://* A local running instance of a container. (See the instance

command group.)

library://* A SIF container hosted on a Library (no default)

docker://* A Docker/OCI container hosted on Docker Hub or another

OCI registry.

shub://* A container hosted on Singularity Hub.

oras://* A SIF container hosted on an OCI registry that supports

the OCI Registry As Storage (ORAS) specification.

apptainer exec [exec options...] <container> <command>

Examples

$ apptainer exec /tmp/debian.sif cat /etc/debian_version
$ apptainer exec /tmp/debian.sif python ./hello_world.py
$ cat hello_world.py | apptainer exec /tmp/debian.sif python
$ sudo apptainer exec --writable /tmp/debian.sif apt-get update
$ apptainer exec instance://my_instance ps -ef
$ apptainer exec library://centos cat /etc/os-release

Options

    --add-caps string               a comma separated capability list to add
    --allow-setuid                  allow setuid binaries in container (root only)
    --app string                    set an application to run inside a container
    --apply-cgroups string          apply cgroups from file for container processes (root only)
-B, --bind stringArray              a user-bind path specification.  spec has the format src[:dest[:opts]], where src and dest are outside and inside paths.  If dest is not given, it is set equal to src.  Mount options ('opts') may be specified as 'ro' (read-only) or 'rw' (read/write, which is the default). Multiple bind paths can be given by a comma separated list.
    --blkio-weight int              Block IO relative weight in range 10-1000, 0 to disable
    --blkio-weight-device strings   Device specific block IO relative weight
-e, --cleanenv                      clean environment before running container
    --compat                        apply settings for increased OCI/Docker compatibility. Infers --containall, --no-init, --no-umask, --no-eval, --writable-tmpfs.
-c, --contain                       use minimal /dev and empty other directories (e.g. /tmp and $HOME) instead of sharing filesystems from your host
-C, --containall                    contain not only file systems, but also PID, IPC, and environment
    --cpu-shares int                CPU shares for container (default -1)
    --cpus string                   Number of CPUs available to container
    --cpuset-cpus string            List of host CPUs available to container
    --cpuset-mems string            List of host memory nodes available to container
    --disable-cache                 do not use or create cache
    --dns string                    list of DNS server separated by commas to add in resolv.conf
    --docker-login                  login to a Docker Repository interactively
    --drop-caps string              a comma separated capability list to drop
    --env stringToString            pass environment variable to contained process (default [])
    --env-file string               pass environment variables from file to contained process
-f, --fakeroot                      run container with the appearance of running as root
    --fusemount strings             A FUSE filesystem mount specification of the form '<type>:<fuse command> <mountpoint>' - where <type> is 'container' or 'host', specifying where the mount will be performed ('container-daemon' or 'host-daemon' will run the FUSE process detached). <fuse command> is the path to the FUSE executable, plus options for the mount. <mountpoint> is the location in the container to which the FUSE mount will be attached. E.g. 'container:sshfs 10.0.0.1:/ /sshfs'. Implies --pid.
-h, --help                          help for exec
-H, --home string                   a home directory specification.  spec can either be a src path or src:dest pair.  src is the source path of the home directory outside the container and dest overrides the home directory within the container. (default "/home/runner")
    --hostname string               set container hostname
-i, --ipc                           run container in a new IPC namespace
    --keep-privs                    let root user keep privileges in container (root only)
    --memory string                 Memory limit in bytes
    --memory-reservation string     Memory soft limit in bytes
    --memory-swap string            Swap limit, use -1 for unlimited swap
    --mount stringArray             a mount specification e.g. 'type=bind,source=/opt,destination=/hostopt'.
-n, --net                           run container in a new network namespace (sets up a bridge network interface by default)
    --network string                specify desired network type separated by commas, each network will bring up a dedicated interface inside container (default "bridge")
    --network-args strings          specify network arguments to pass to CNI plugins
    --no-eval                       do not shell evaluate env vars or OCI container CMD/ENTRYPOINT/ARGS
    --no-home                       do NOT mount users home directory if /home is not the current working directory
    --no-https                      use http instead of https for docker:// oras:// and library://<hostname>/... URIs
    --no-init                       do NOT start shim process with --pid
    --no-mount strings              disable one or more 'mount xxx' options set in apptainer.conf and/or specify absolute destination path to disable a 'bind path' entry
    --no-privs                      drop all privileges from root user in container)
    --no-umask                      do not propagate umask to the container, set default 0022 umask
    --nv                            enable Nvidia support
    --nvccli                        use nvidia-container-cli for GPU setup (experimental)
    --oom-kill-disable              Disable OOM killer
-o, --overlay strings               use an overlayFS image for persistent data storage or as read-only layer of container
    --passphrase                    prompt for an encryption passphrase
    --pem-path string               enter an path to a PEM formatted RSA key for an encrypted container
-p, --pid                           run container in a new PID namespace
    --pids-limit int                Limit number of container PIDs, use -1 for unlimited
    --pwd string                    initial working directory for payload process inside the container
    --rocm                          enable experimental Rocm support
-S, --scratch strings               include a scratch directory within the container that is linked to a temporary dir (use -W to force location)
    --security strings              enable security features (SELinux, Apparmor, Seccomp)
-u, --userns                        run container in a new user namespace
    --uts                           run container in a new UTS namespace
    --vm                            enable VM support
    --vm-cpu string                 number of CPU cores to allocate to Virtual Machine (implies --vm) (default "1")
    --vm-err                        enable attaching stderr from VM
    --vm-ip string                  IP Address to assign for container usage. Defaults to DHCP within bridge network. (default "dhcp")
    --vm-ram string                 amount of RAM in MiB to allocate to Virtual Machine (implies --vm) (default "1024")
-W, --workdir string                working directory to be used for /tmp, /var/tmp and $HOME (if -c/--contain was also used)
-w, --writable                      by default all Apptainer containers are available as read only. This option makes the file system accessible as read/write.
    --writable-tmpfs                makes the file system accessible as read-write with non persistent data (with overlay support only)

SEE ALSO

Linux container platform optimized for High Performance Computing (HPC) and Enterprise Performance Computing (EPC)

Auto generated by spf13/cobra on 18-Aug-2022