RUN-SINGULARITY(1)

📦
version 4.1.5 · 3 versions
, in ubuntu resolute

💖 run-singularity 💖

okay so you opened the manual page for run-singularity, which lives in the User Commands corner of the man pages, and honestly? you ate by coming here. This is the whole entire guide to launching a Singularity container with a runscript. Buckle up bestie, it's a long one but every single flag matters. 🫶

🌸 DESCRIPTION 🌸

💅 Usage:

singularity run [run options...] <container>

🧚 Description:

So here's the tea ☕ — this command launches a Singularity container and executes a runscript if one is defined for that container. The runscript is literally a metadata file inside the container that holds shell commands. If that file is present (and executable, that part is doing a lot of work 💅) then this command will just go ahead and execute that file inside the container, automatically, no extra steps. And every argument you put after the container name gets passed directly to the runscript. periodt.

singularity run accepts these container formats:

  • *.sif — Singularity Image Format (SIF). Native to Singularity 3.0+
  • *.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 Singularity meta-data.
  • instance://* — A local running instance of a container. (See the instance command group.)
  • library://* — A SIF container hosted on a Library (default https://cloud.sylabs.io/library)
  • 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.

✨ OPTIONS ✨

okay this is the part where I need you to lock in 🔥. Every flag, every default, exactly as it is:

  • --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)
  • --authfile string — Docker-style authentication file to use for writing/reading OCI registry credentials
  • -B, --bind strings — 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
  • --cdi-dirs strings — comma-separated list of directories in which CDI should look for device definition JSON files. If omitted, default will be: /etc/cdi,/var/run/cdi
  • -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
  • --cwd string — initial working directory for payload process inside the container (synonym for --pwd)
  • --device strings — fully-qualified CDI device name(s). A fully-qualified CDI device name consists of a VENDOR, CLASS, and NAME, which are combined as follows: <VENDOR>/<CLASS>=<NAME> (e.g. vendor.com/device=mydevice). Multiple fully-qualified CDI device names can be given as a comma separated list.
  • --disable-cache — dont use cache, and dont create cache
  • --dns string — list of DNS server separated by commas to add in resolv.conf
  • --docker-host string — specify a custom Docker daemon host
  • --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 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")
  • --hostname string — set container hostname. Infers --uts.
  • -i, --ipc — run container in a new IPC namespace
  • --keep-layers — Keep layers when creating an OCI-SIF. Do not squash to a single layer.
  • --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-compat — (--oci mode) do not apply settings for increased OCI/Docker compatibility. Emulate native runtime defaults without --contain etc.
  • --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 singularity.conf, specify absolute destination path to disable a bind path entry, or 'bind-paths' to disable all bind path entries.
  • --no-oci — Launch container with native runtime
  • --no-pid — do not run container in a new PID namespace
  • --no-privs — drop all privileges in container (root only in non-OCI mode)
  • --no-setgroups — disable setgroups when entering --fakeroot user namespace
  • --no-tmp-sandbox — Prohibits unpacking of images into temporary sandbox dirs
  • --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)
  • --oci — Launch container with OCI runtime (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
  • --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)
  • --tmp-sandbox — Forces unpacking of images into temporary sandbox dirs when a kernel or FUSE mount would otherwise be used.
  • -u, --userns — run container in a new user namespace, allowing Singularity to run completely unprivileged on recent kernels. This disables some features of Singularity, for example it only works with sandbox images.
  • --uts — run container in a new UTS namespace
  • -W, --workdir string — working directory to be used for /tmp and /var/tmp (if -c/--contain was also used)
  • -w, --writable — by default all Singularity 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)
💀 heads up bestie: a couple of these are marked (experimental) — --nvccli and --oci — and several are (root only). Also -u/--userns disables some features of Singularity. Don't say I didn't warn you. 🙈

🌈 EXAMPLES 🌈

okay these are the examples, exactly as they show up in the page (the line wrapping is doing its thing, but I'm not touching a single character of it 🎀):

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

# It runs with our inputs when we run the image $ singularity 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

For additional help or support, please visit https://www.sylabs.io/docs/

and that's the whole page bestie, you're officially a run-singularity girlie now 👑

this was run-singularity version 4.1.5+ds4-1, from February 2025, and yes the man page name up top is RUN-SINGULARITY(1) — slay ✨ 💜

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