Personal tools
You are here: Home → User Support → User Documentation → DEISA Batch Systems → 3 PBS Pro
 

3 PBS Pro

private

3.1 PBS Pro Commands

qsub <jobscript>

Submit a jobscript for execution.

qstat

Display all queued jobs

qstat –Q

Status of queues

qdel <job_id>

Delete a job

private

3.2 PBS Pro Directives

#PBS –l mppwidth= <number of nodes>

Sets the number of nodes

#PBS –l mppnppn = <number of cores per node>

Sets the number of cores per node

#PBS –l walltime = <HH:MM:SS>

Sets the maximum wall clock time for the job

#PBS –j oe

Merges both standard output and standard error

#PBS –m e

Send email when job is done

#PBS –M user@home.com

Email address for notification email.

private

3.3 Example MPI script

#!/bin/bash

#PBS -N test
#PBS -j oe
#PBS -l walltime=1:00:00
#PBS -l mppwidth=256
#PBS -m abe
#PBS -M user@home.com
#PBS -r n

module load deisa
cp input.dat
$DEISA_SCRATCH
cp program $DEISA_SCRATCH

cd $DEISA_SCRATCH
aprun –n 256 ./program
cp output.dat ~/.
private

3.4 CSC: Louhi

For more information on the Cray XT4/XT5 at CSC, please visit: http://www.csc.fi/english/pages/louhi_guide/batch_jobs/parallel_jobs

 
3.5 EPCC: HECToR XE6

3.5 EPCC: HECToR XE6

This section describes some localised PBS Pro directives particular to the Cray XE6 at EPCC. For more information, please visit http://www.hector.ac.uk/support/documentation/userguide/batch.php
private

3.5.1 Local executable statements

export TASKS=`qstat -f $PBS_JOBID | awk '/mppwidth/ {print $3}'`
export TASKSPERNODE=`qstat -f $PBS_JOBID | awk '/mppnppn/  {print $3}'`
aprun -n $TASKS -N $TASKSPERNODE ./program

 

 
3.6 LRZ: HLRB II

3.6 LRZ: HLRB II

This section describes some localised PBS Pro Directives particular to the SGI Altix at LRZ. For more information, please visit: http://www.lrz-muenchen.de/services/compute/hlrb/batch/batch.html
private

3.6.1 Local PBS Pro Directives

The PBS directives mppwidth and mppnppn are not available on HLRB II. Their function is subsumed by the select directive, as illustrated in the following example.

#PBS -l select=280:ncpus=1
private

3.6.2 Local executable statements

. /etc/profile.d/modules.sh
module load deisa
cd $DEISA_DATA
mpiexec ./myprog
Document Actions