apptainer run

Run the user-defined default command within a container

Synopsis

This command will launch an Apptainer container and execute a runscript if one is defined for that container. The runscript is a metadata file within the container that contains shell commands. If the file is present (and executable) then this command will execute that file within the container automatically. All arguments following the container name will be passed directly to the runscript.

apptainer run accepts the following container 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 run [run options...] <container>

Examples

# Here we see that the runscript prints "Hello world: "
$ apptainer exec /tmp/debian.sif cat /apptainer
#!/bin/sh
echo "Hello world: "

# It runs with our inputs when we run the image
$ apptainer run /tmp/debian.sif one two three
Hello world: one two three

# Note that this does the same thing
$ ./tmp/debian.sif one two three

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 run
-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)
    --unsquash                      Convert SIF file to temporary sandbox before running
-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 25-Oct-2022