Computing : Singularity/Apptainer support in BIRD

Apptainer/Singularity enables users to have full control of their environment. Apptainer/Singularity containers can be used to package entire scientific workflows, software and libraries. This means that you don’t have to ask your cluster admin to install anything for you - you can put it in a Apptainer/Singularity container and run.

To use Apptainer/Singularity in BIRD please use (in your config file):

+MySingularityImage = "/path//container/sl6" # example path to your singularity image
Requirements = ( OpSysAndVer == "CentOS7" )

Optional:

+MySingularityArgs = "--my-args"

Can be used to put additional arguments into the Apptainer/Singularity call on the workernode, only use this options if you know what you are doing, check your additional options against the given options in the Apptainer/Singularity call (see below) and test your individual options with a single job before submitting bigger clusters.

The image can be located in any of the shared filesystem (CVMFS/DUST/AFS)

Testing a Apptainer/Singularity image

to test your Apptainer/Singularity image login on a remote-submit host and use the following: 

singularity exec --contain --bind /afs:/afs --bind /nfs:/nfs --bind /pnfs:/pnfs --bind /cvmfs:/cvmfs --bind /var/lib/condor:/var/lib/condor --pwd </working/directory/of/job><--your-singularity-args> </path/singularity:image> <your executable and args>

An alternative method for maybe further debugging would be an interactive job (condor_submit -i) which will log you into the Apptainer/Singularity jobcontainer.