Using the Batch System

You can use the standard PBS commands qsub and qstat to submit and query jobs; or instead some more convenient local commands bqsub, qjobs, and qpeek.

PBS Commands

qsub -q prod script.sh
qstat -u USER 
qstat -q

The prod queue runs jobs on the 64-bit SL5 nodes.

Note that the prod queue has quite low default walltime, cputime and memory limits of 8 hours cpu or wall time and 500MB memory but more can be requested when submitting the job with the -l option:

qsub -q prod -l cput=24:00:00 -l walltime=36:00:00 -l mem=2000mb

Local Commands

The PPD interactive machines have some local commands for making the PBS batch system a bit more convenient to use and more like the LSF system used on lxplus at CERN.

You can use bqsub to submit jobs (similar to LSF's bsub command). This has nicer defaults than qsub (eg. you don't need to specify -q prod) and any command can be specified on the command-line ( qsub only allows a script to be given, with no arguments). Specify a time limit with bqsub -c hh:mm. The default is 8:00, with a maximum of 72:00 (3 days). eg.

bqsub -c 24:00 Sherpa PTCUT:=20 EVENTS=1000

qjobs (like LSF's bjobs) lists your running jobs (ie. you don't have to specify the -u option) with more helpful information.

qpeek (like LSF's bpeek) shows a running job's logfile (this prompts for your password to ssh to the batch worker node).

Use bqsub -h, qjobs -h, or qpeek -h for help.

-- ChrisBrew - 2010-06-29