Using the PBS / Torque queueing environment
The main commands for interacting with the Torque environment are:
View queued jobs.
Submit a job to the scheduler.
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 bowtie2-184.108.40.206 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 running||Max time||Description|
|veryshort||28||4||00:15:00||Very short queue with 15 minute time limit|
|short||28||2||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|
|bigmem||24||2||48:00:00||Long queue with 48 hour time limit|
|massivemem||24||1||48:00:00||Long queue with 48 hour time limit|
- A useful Torque tutorial can be found at this link.