2

I'm trying to write a code to submit a job on the cluster, and am using someone else's previous code as a template; is there any way someone could explain each line step by step to me? I think I understand the nodes and wall time since I've looked at some tutorials but I'm having trouble understanding the last 3 lines.

#!/bin/bash
#PBS -l nodes=1:ppn=12
#PBS -l walltime=96:00:00
#PBS -q python
cd $PBS_O_WORKDIR
perl cal_gerp_crmcre.pl GERP++ CRM_NCR.data  >CRECRM_NCR.gp

1 Answer 1

1

The first one is a shell that is your script using.

The lines starting with #PBS are passed to the qsub command. The first two (-l) specify the resource limits and the -q specifies the destination of the job (the name of a queue, a server, or a queue at a server). This looks like a queue named python.

The last two lines are the script itself. One is changing working directory to the current working directory of the qsub command (from where you submit the job?). The last is running the perl script cal_gerp_crmcre.pl, storing its output to CRECRM_NCR.gp.

I hope it makes sense for an overview. All the information I used is available in the manual page for qsub, where you can find also more examples and options.

0

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .