cocomice / hpc-submission-scripts

Example job submission scripts for HPC systems (PBS and SLURM)

Example job submission scripts for HPC systems

Contains PBS and SLURM examples

#####PBS

• To submit a single job from a *.sh file: qsub example-pbs-script.sh
• To submit multiple jobs in a loop: ./submit-pbs-loop.sh or python submit-pbs-loop.py (These do the same thing, but the Python example is easier to work with).

Note that the latter option does not require a *.sh file to exist for each job. It creates job submission strings and submits them without saving to a file. This is useful for large submissions.

#####SLURM The SLURM examples are connected to each other, because the "multiple-submission" case requires a *.sh file to exist for the job (as far as I know).

• To submit multiple jobs in a loop: ./submit-slurm-loop.sh
• To submit a single job, this example would require you to pass an environment variable like so:

sbatch -J my_job_name --export=VARIABLE=1 example-slurm-script.sh

The job name is optional. If you modify example-slurm-script.sh to not depend on ${VARIABLE}, then you could just run sbatch example-slurm-script.sh.