Apptainer

Put your scientific workflows, software and libraries in a container and run it on UBELIX

Examples

Work interactively

Submit an interactive SLURM job and then use the shell command to spawn an interactive shell within the Singularity container:

srun --time=01:00:00 --mem-per-cpu=2G --pty bash
apptainer shell <image>

Execute the containers “runscript”

#!/bin/bash
#SBATCH --partition=all
#SBATCH --mem-per-cpu=2G

apptainer run <image>   #or ./<image>

Run a command within your container image

apptainer exec <image> <command>

e.g:
apptainer exec container.img cat /etc/os-release

Bind directories

Per default the started application (e.g. cat in the last example) runs withing the container. The container works like a seperate machine with own operation system etc. Thus, per default you have no access to files and directories outside the container. This can be changed using binding paths.

If files are needed outside the container, e.g. in your HOME you can add the path to APPTAINER_BINDPATH="src1[:dest1],src2[:dest2]. All subdirectories and files will be accessible. Thus you could bind your HOME directory as:

export APPTAINER_BINDPATH="$HOME/:$HOME/"   
# or simply 
export APPTAINER_BINDPATH="$HOME"

Further Information

Official Apptainer Documentation can be found at https://apptainer.org/documentation/.