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3 PBS Pro

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

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.

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 ~/.

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

3.5.1 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

 

3.6.1 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

3.6.2 Local executable statements

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