Using the PBS / Torque queueing environment
The main commands for interacting with the Torque environment are:
- qstat View queued jobs.
- qsub Submit a job to the scheduler.
- qdel Delete one of your jobs from queue.
Job script parameters
Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:
#PBS -l nodes=1:ppn=14
sets the size of the job in number of processors:
nodes=N sets the number of nodes needed.
ppn=N sets the number of cores per node.
#PBS -l walltime=8:00:00
sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.
Example job scripts
A program using 14 cores on a single node:
#!/bin/bash #PBS -l nodes=1:ppn=14 #PBS -l walltime=8:00:00 #PBS -q normal #PBS -m ae #PBS -M your.email@address module load bowtie2-18.104.22.168 bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam
Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Troque scheduler is:
> qsub example.job
Much of this content has been adapted from the Quick Start Guide at CHPC.