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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.
-e, --cleanenv               clean environment before running container
    --compat                 apply settings for increased OCI/Docker compatibility. Infers --containall, --no-init, --no-umask, --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
    --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 strings            pass environment variable to contained process
    --env-file string        pass environment variables from file to contained process
-f, --fakeroot               run container in new user namespace as uid 0
    --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)
    --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-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
    --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)
-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
    --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, allowing Apptainer to run completely unprivileged on recent kernels. This disables some features of Apptainer, for example it only works with sandbox images.
    --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

apptainer -

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

Auto generated by spf13/cobra on 16-Feb-2023