Difference between revisions of "Using the PBS / Torque queueing environment"

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=== Additional information ===
  
 
* A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].
 
* A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].
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* Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].

Revision as of 13:00, 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=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 -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

Single node jobs

Queue Name Max cores Max nodes running Max memory Max time Description
veryshort 28 4 64 GB 00:15:00 Very short queue with 15 minute time limit
short 28 2 64 GB 01:00:00 Short queue with 1 hour time limit
medium 28 2 64 GB 08:00:00 Medium queue with 8 hour time limit
long 28 1 64 GB 48:00:00 Long queue with 48 hour time limit
verylong 14 1 64 GB 96:00:00 Very long queue with 96 hour time limit
bigmem 24 2 256 GB 48:00:00 Long queue with 48 hour time limit
massivemem 24 1 1024 GB 48:00:00 Long queue with 48 hour time limit

Multi-node jobs

Queue Name Max cores Max nodes running Max memory Max time Description
wide 28 2 128 GB 24:00:00 Queue to enable MPI-type jobs with up to 56 cores with 48 hour time limit
verywide 28 4 128 GB 08:00:00 Queue to enable MPI-type jobs with up to 112 cores with 24 hour time limit


Additional information

  • A useful Torque tutorial can be found at this link.
  • Detailed reference documentation for queue submission is available here.
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