Example Singularity image with help for binding to typical HPC data directories on Comet

Singularity

Bootstrap: docker
From: python:2.7.13

%help

This container creates internal directories to bind HPC system locations to as
follows...

/pfs_data      - The location of your high performance parallel file system data
/pfs_scratch   - The location of your high performance parallel file system scratch
/local_scratch - The location of you node-local scratch

Assuming the following ENV vars exist as would typically be the case in a Slurm
batch job on Comet...

    SLURM_JOB_USER, SLURM_JOB_ACCOUNT, SLURM_JOB_ID

You would run this container inside your Slurm job on Comet with...

$ singularity shell \
    --bind /oasis/projects/nsf/$SLURM_JOB_ACCOUNT/$SLURM_JOB_USER:/pfs_data \
    --bind /oasis/scratch/comet/$SLURM_JOB_USER/temp_project:/pfs_scratch
    --bind /scratch/$SLURM_JOB_USER/$SLURM_JOB_ID:/local_scratch
    <container_img> $OPTS

%labels
Maintainer HPCDevOps
Version v1.0

%post
    # Creating Comet compatible mount points
    mkdir -p /pfs_data /pfs_scratch /local_scratch

%test
    python --version
    /bin/ls /pfs_data /pfs_scratch /local_scratch