Containers

Containers address the issue of software and dependency complexity by storing the software and its dependencies (including a minimal operating system) in a single image file, which runs on top of the host machine kernel.

Containers provide:

Flexibility: Bring your own environment (BYOE) and bring your own software (BYOS)
Reproducibility: Complete control over software versions
Portability: Run on your laptop or on HPC systems
Performance: Nearly as fast as as native applications
Compatibility: Supported on most Linux distributions

For more information, see Introduction to Containers from the Pawsey Supercomputer Centre.

Apptainer is a container platform available on Roar. Containers can either be downloaded from a container repository or built from a definition file.

Building containers requires root privileges.

Containers are built on your personal device and can be deployed on Roar. Alternatively, the fakeroot option can be used to build containers on Roar without root privileges; see fakeroot.

Containers with Slurm

In a Slurm batch script, a container can be launched with:

$ apptainer run <container> <args>

To use a container with parallel execution, the system version of MPI must be newer than the container MPI library. See Apptainer and MPI Applications.

In a Slurm batch script, a container with MPI can be launched with:

$ srun apptainer exec <container> <command> <args>

Apptainer commands

Command	Description
`apptainer build <container> <definition>`	Builds a container from a definition file
`apptainer shell <container>`	Runs a shell within a container
`apptainer exec <container> <command>`	Runs a command within a container
`apptainer run <container>`	Runs a container where a runscript is defined
`apptainer pull <resource>://<container>`	Pulls a container from a container registry
`apptainer build --sandbox <sbox> <container>`	Builds a sandbox from a container
`apptainer build <container> <sbox>`	Builds a container from a sandbox