Apptainer

Apptainer is a containerization tool specifically designed for HPC systems. The HPC administrators can build a container if it is the right fit for your software stack. This is typically the case if your software has complex dependencies, or requires very specific versions of tools or dependencies.

Currently, users cannot build containers.

Usage

Apptainer containers can be used in two main ways:

• interactively, using apptainer shell
• in batch mode using apptainer exec

The shell mode is used for testing and interacting with the container software interactively, for example to enter into a bash shell in a container that has bash:

apptainer shell mycontainer.sif

will drop you into a shell in the container environment:

Apptainer>

The batch mode, usually used to run scripts or jobs, is similar to the shell command, but the trailing arguments are the command that you'd like to run:

apptainer exec mycontainer.sif ./myscript.sh

Accessing Scratch

In order to read/write data to your scratch directory, you must bind the path to the container via the command line. This is done by providing the -B argument to Apptainer:

apptainer exec -B /bsuscratch mycontainer.sif ./myscript.sh

Further Reading

The Apptainer Documentation has more information for users, and please email us with any questions.