Apptainer (formerly Singularity)

Description

Apptainer (formerly Singularity) is a free, cross-platform and open-source computer program that performs operating-system-level virtualization also known as containerization. One of the main uses of Apptainer is to bring containers and reproducibility to scientific computing and the high-performance computing (HPC) world.

The need for reproducibility requires the ability to use containers to move applications from system to system.

Using Apptainer containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms.

To learn more about Apptainer itself please consult the Apptainer documentation.

Module

Load the modulefile

$ module load apptainer

This provides access to the apptainer executable wich can be used to run containers.

Building images and running containers

On NHR you can build apptainer images directly on the login nodes.

For SCC you should use a compute node. For example by starting an interactive job:

$ srun --partition int --pty bash
$ module load apptainer

If you have written a container recipe foo.def you can create a foo.sif apptainer image in the following way:

$ module load apptainer
$ apptainer build foo.sif foo.def

Example Jobscripts

Here is an example job of running the local Apptainer image (.sif)

#!/bin/bash
#SBATCH -p medium40
#SBATCH -N 1
#SBATCH -t 60:00
 
module load apptainer
 
apptainer run --bind /local,/user,/projects,$HOME,$WORK,$TMPDIR,$PROJECT  $HOME/foo.sif

#!/bin/bash
#SBATCH -p grete:shared
#SBATCH -N 1
#SBATCH -G 1
#SBATCH -t 60:00
 
module load cuda
module load apptainer
 
apptainer run --nv --bind /local,/user,/projects,$HOME,$WORK,$TMPDIR,$PROJECT  $HOME/foo.sif

#!/bin/bash
#SBATCH -p medium
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 1:00:00
 
module load apptainer
 
apptainer run --bind /local,/user,/projects,/home,/scratch  $HOME/foo.sif