Difference between revisions of "Using the PBS / Torque queueing environment"
From Centre for Bioinformatics and Computational Biology
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| − | Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the | + | Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is: |
<source lang="c"> | <source lang="c"> | ||
| − | > qsub | + | > qsub run_bowtie.sh |
</source> | </source> | ||
Much of this content has been adapted from the [http://wiki.chpc.ac.za/quick:start Quick Start Guide] at CHPC. | Much of this content has been adapted from the [http://wiki.chpc.ac.za/quick:start Quick Start Guide] at CHPC. | ||
Revision as of 11:08, 11 April 2018
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=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
Much of this content has been adapted from the Quick Start Guide at CHPC.
