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Containers

Apptainer (formerly Singularity) is a container platform specifically designed for HPC clusters. Containers package software in a way that is portable and reproducible. Apptainer images are a single file called a Singularity Image File (.sif file).

info

Apptainer images are read-only. To make changes to the container filesystem, consider building a new image. See Storage for instructions on using writable filesystems from Palmetto. :

Apptainer executes the container as your user, so you are limited to the same user privileges as on Palmetto.

Downloading pre-existing containers​

Apptainer can download pre-existing Docker containers from a registry. Use the pull or build command to download and build a .sif file. Use the docker:// prefix for the image name.

Pull command
apptainer pull docker://rockylinux:8
Build command
apptainer build rocky.sif docker://rockylinux:8

Running container images​

There are 3 ways to execute commands inside the container: run, exec, and shell.

apptainer run​

run executes the default command for the image.

apptainer run rocky.sif <args>

apptainer exec​

exec runs a custom command inside the container.

apptainer exec rocky.sif <command> <args>

apptainer shell​

note

apptainer shell is documented here for completeness. It's recommended to use apptainer run to launch a shell in the image.

shell starts a bash shell inside of the container image. The prompt will change from the standard Palmetto prompt to Apptainer>

[username@node0001 ~]$ apptainer shell rocky.sif
Apptainer>

Storage​

The container has it's own filesystem, but a few directories are mounted from Palmetto automatically:

  • $HOME
  • $PWD

This differs from Docker where no directories are mounted by default.

To make a directory visible inside the container, use the -B flag to bind a directory. The -B flag requires an argument in the form /path/on/Palmetto:/path/inside/container.

Bind $TMPDIR and /scratch inside the container
apptainer shell -B $TMPDIR:$TMPDIR -B /scratch/$USER:/scratch/$USER rocky.sif

Graphical Applications​

X windows based applications should work fine even when containerized and can be run on the Palmetto Desktop without problems. If an application makes use of OpenGL, then you may need to build VirtualGL into the container in order for the application to run without crashing.