Sample PBS Scripts for R


Here is a sample of PBS Scripts that can be used for R. This is just a suggested PBS script. Modify and comment at will. The script below is named as R.sh

#!/bin/bash
#PBS -N R-job
#PBS -j oe
#PBS -V
#PBS -m bea
#PBS -M myemail@hotmail.com
#PBS -l nodes=1:ppn=8

# comment these out if you wish
echo "qsub host = " $PBS_O_HOST
echo "original queue = " $PBS_O_QUEUE
echo "qsub working directory absolute = " $PBS_O_WORKDIR
echo "pbs environment = " $PBS_ENVIRONMENT
echo "pbs batch = " $PBS_JOBID
echo "pbs job name from me = " $PBS_JOBNAME
echo "Name of file containing nodes = " $PBS_NODEFILE
echo "contents of nodefile = " $PBS_NODEFILE
echo "Name of queue to which job went = " $PBS_QUEUE

# Pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo "Number of requested processors = " $NCPUS

# Load R Module
module load mpi/intel_1.4.3
module load intel/12.0.2
module load R/R-2.15.1

# ###############
# Execute Program
# ################
/usr/local/R-2.15.1/bin/R CMD BATCH $file

The corresponding qsub command and its parameter should be something like

$ qsub -q dqueue -l nodes=1:ppn=8 R.sh -v file=Rjob.r
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