Running Jobs

Table of Contents:

At SaM, we have 2 active queuing systems PBS (frank) and SLURM (mpi and htc). Please see below for more generic information. Some useful links for interested readers:

PBS

To submit a job to PBS, you will need to generate a submission script. Examples are provided elsewhere and you are encouraged to check these out. We will present some basic PBS commands here, interested readers can find detailed information on "the Google".

After preparing a submission script (example.pbs used below), one can submit the script with:

qsub example.pbs

To view running jobs (the environment variable $USER is you!):

qstat -u $USER

To cancel a job (let's say the Job ID was 1111):

qdel 1111

To view some additional information about your running job (Job ID 1111 again):

qstat -f 1111

SLURM

Similarly to PBS, you will need to generate a SLURM submission script to run calculations. We have provided examples here. Google searches can provide a wealth of information well beyond the scope of this article.

After preparing a submission script (example.slurm used below), one can submit the script with:

sbatch example.slurm

To view running jobs (the environment variable $USER is you!):

squeue -u $USER

To cancel a job (let's say the Job ID was 1111):

scancel 1111

To view some additional information about your running job (Job ID 1111 again):

scontrol show jobid -dd 1111