6.2.3. SLURM Script Options

The “Slurm” section of pyOver.json controls settings for SLURM scripts when OVERFLOW runs are submitted as SLURM jobs to a high-performance computing environment. Regardless of whether or not the user intends to submit SLURM jobs, pyOver creates scripts called run_overflow.pbs or run_overflow.01.pbs, run_overflow.02.pbs, etc. At the top of these files is a collection of SLURM directives, which will be ignored if the script is launched locally.

To run such a script locally without submitting it, call it with the appropriate shell.

$ bash run_overflow.pbs

If the job is to be submitted, simply submit it. A special script called psbatch is recommended over the usual sbatch because it also creates a file jobID.dat that saves the SLURM job number

$ pqsub run_overflow.pbs

The full description of the SLURM section can be found in the corresponding Cape SLURM section.