Difference between revisions of "Using the PBS / Torque queueing environment"
From Centre for Bioinformatics and Computational Biology
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Revision as of 11:37, 11 April 2018
The main commands for interacting with the Torque environment are:
> qstatView queued jobs.
> qsubSubmit a job to the scheduler.
> qdelDelete one of your jobs from queue.
Contents
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=14sets 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=8:00:00sets 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 bowtie2-2.3.4.1 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 Torque scheduler is:
> qsub run_bowtie.sh
The different queues available
Single node jobs
| Queue Name | Max cores | Max nodes | Max time | Description |
|---|---|---|---|---|
| veryshort | 28 | 4 | 00:15:00 | Very short queue with 15 minute time limit |
| short | 28 | 4 | 01:00:00 | Short queue with 1 hour time limit |
| medium | 28 | 2 | 08:00:00 | Medium queue with 8 hour time limit |
| long | 28 | 1 | 48:00:00 | Long queue with 48 hour time limit |
| verylong | 14 | 1 | 96:00:00 | Long queue with 96 hour time limit |
- A useful Torque tutorial can be found at this link.
