Difference between revisions of "Using the PBS / Torque queueing environment"
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=== Additional information === | === Additional information === | ||
Revision as of 19:50, 31 May 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 -o /path/to/stdout.log #PBS -e /path/to/stderr.log #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
Interactive jobs
- If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:
> qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00
The different queues available
| Queue Name | Max user jobs running | Max user cores running per job |
Max memory | Max walltime | Description |
|---|---|---|---|---|---|
| short | 6 | 28 | 128 GB | 00:05:00 | Short queue with 5 minute time limit |
| normal | 4 | 28 | 128 GB | 08:00:00 | Medium queue with 8 hour time limit |
| long | 1 | 28 | 128 GB | 168:00:00 | Long queue with one week time limit |
| bigmem | 1 | 24 | 750 GB | 72:00:00 | High memory queue with 3 day time limit |
| #mpi | 1 | 112 | 128 GB | 72:00:00 | Queue for mpi parallel jobs with 3 day time limit |
- If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.
