Apptainer

Apptainer is a containerisation platform that allows users to package software and its dependencies into portable, reproducible containers. Apptainer containers can be transferred between systems and run without requiring the software to be installed directly on the HPC system.

This page provides guidance on the general use of Apptainer on Calder. For detailed information about Apptainer, including advanced container usage and configuration, please refer to the official Apptainer documentation.

Apptainer on Calder

Apptainer is installed on Calder and is automatically available when you log in. No module needs to be loaded before using Apptainer. You can check the installed version with:

apptainer --version

apptainer version 1.5.3-1.el9

Running Apptainer containers

To run an Apptainer container, use:

apptainer run my_container.sif

You can also execute a specific command inside a container with apptainer exec:

apptainer exec my_container.sif command

For example, to check the Python version provided by a container:

apptainer exec my_container.sif python --version

Apptainer containers can be used within Slurm jobs in the same way as other applications. The resources required by the application should be requested from Slurm, while the container provides the required software environment.

Using Apptainer with MPI

Apptainer can be used with MPI applications, including applications running across multiple compute nodes. MPI container usage requires additional configuration and depends on how both the container and the host system are built.

For guidance and examples, including the use of Apptainer with Slurm, see the MPI section of the official Apptainer documentation.

Building Apptainer containers

If you need to build an Apptainer container from a definition file, use:

apptainer build my_container.sif my_definition.def

Building containers may require additional privileges or access to a suitable build environment. If you cannot build a container directly on Calder, you can build it elsewhere and transfer the resulting .sif file to Calder.

For detailed information about definition files, building containers, and other container workflows, see the official Apptainer documentation.

Note

More information about containers and their use on HPC is available in the HPC2 training course.