Singularity
Description
Put your scientific workflows, software and libraries in a Singularity 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
singularity shell <image>
Execute the containers “runscript”
#!/bin/bash
#SBATCH --partition=all
#SBATCH --mem-per-cpu=2G
singularity run <image> #or ./<image>
Run a command within your container image
singularity exec <image> <command>
e.g:
singularity 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 a path to SINGULARITY_BINDPATH="src1[:dest1],src2[:dest2]
. All subdirectories and files will be accessible. Thus you could bind your HOME directory as:
export SINGULARITY_BINDPATH="$HOME/:$HOME/"
# or simply
export SINGULARITY_BINDPATH="$HOME"
Further Information
Official Singularity Documentation can be found at https://sylabs.io/docs/