Apptainer

Apptainer#

Apptainer is a container platform similar to Docker, previously known as Singularity. It is a widely used container system for HPC, which allows you to create and run containers that package up pieces of software in a way that is portable and reproducible.

Container platforms allow users to create and use container images, which are self-contained software stacks.

aarch64 partitions only

Apptainer is only available on aarch64 nodes/partitions within Bede.

For ppc64le partitions, please see Singularity CE.

Apptainer is provided by default on aarch64 nodes/partitions, and can be used without loading any modules.

Note

Container images are not portable across CPU architectures. Containers created on x86_64 machines may not be compatible with the ppc64le and aarch64 nodes in Bede.

For more information on how to use singularity, please see the Apptainer Documentation.

Differences from Singularity CE#

Although Apptainer and Singularity share a common history, there are a number of important differences, as documented by apptainer, including:

  • SINGULARITY_ prefixed environment variables may issues warnings, preferring to be prefixed with APPTAINER_

  • The singularity command/binary is still available, but is just a symlink to apptainer

  • The library:// protocol is not supported by apptainer’s default configuration. See Restoring pre-Apptainer library behaviour for more information.

Rootless Container Builds#

The apptainer installation on Bede’s aarch64 nodes supports the creation of container images from apptainer definition files or docker containers without the need for root.

I.e. it is possible to build your aarch64 containers on the ghlogin interactive sessions rather than having to create containers on aarch64 machines elsewhere and copying them into bede.

APPTAINER_CACHEDIR#

Container images for GPU acceleated code are often very large, and if creating containers based on a docker image multiple copies of th container will exist in your file stores. Consider setting the APPTAINER_CACHEDIR environment variable to a location in /nobackup or /projects to avoid filling your home directory.