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usingPBS.md

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Portable Batch System (PBS)

Used to run jobs on clusters.

TORQUE

TOURQUE is a fork of openPBS. Get the version on a cluster with

qstat --version

http://en.wikipedia.org/wiki/Portable_Batch_System

http://www.adaptivecomputing.com/products/open-source/torque/

Documentation:

http://docs.adaptivecomputing.com/ -> Archived Documentation

Commonly used commands

Command Result
qsub myPBSScript Submits a job to the cluster
qsub -W depend=afterok:pid myOtherPBSScript Submits a job to the cluster after pid is done
qstat Prints jobs currently running on the cluster
qstat -u username Prints the jobs submitted by username
qstat -f pid Displays full info of job with process id pid
`qstat -f pid grep -i Job_name`
qhold pid Prevent job pid to run until released
qrls pid Releases job pid from a hold
qdel pid Delete the job with process id pid
qdel `seq -f "%.0f" 512173 512175` Delete the jobs 512173, 512174 and 512175
qdel all Delete all jobs (your jobs if you are not admin)
qstat -q Shows available queues and their walltime-limit
showq Show the queue (works at least with Maui scheduler)

Example script

#!/bin/sh 
### Three #'s denotes a comment, one # denotes a PBS command
### ====================================================================
### Job name 
#PBS -N name
### ====================================================================
### ====================================================================
### Number of nodes and processors per node
### For optimal run, should run so that whole machines are
### occupied
#PBS -l nodes=2:ppn=12
### ====================================================================
### ====================================================================
### Maximum wallclock time, format HOURS:MINUTES:SECONDS
#PBS -l walltime=50:00:00
### ====================================================================
### ====================================================================
### Queue name (depends on cluster)
# PBS -q workq
### ====================================================================
### ====================================================================
### Output
### PBS -o is the terminal output
### PBS -e is the error produced by the code
#PBS -o nameOfLogfile.log
#PBS -e nameOfErrorfile.err 
### ====================================================================
### ====================================================================
### Mail notification when job is done
#PBS -m e
### ====================================================================
### ====================================================================
### $PBS_O_WORKDIR enables writing in the folder you do qsub from
cd $PBS_O_WORKDIR
### Command you want to run on the cluster, for example
mpirun -np 16 myCommand
exit
### ====================================================================

Maui cluster scheduler

http://en.wikipedia.org/wiki/Maui_Cluster_Scheduler

Documentation:

http://docs.adaptivecomputing.com/maui/pdf/mauiadmin.pdf

Links

https://www.osc.edu/supercomputing/batch-processing-at-osc/monitoring-and-managing-your-job