Example submission script for bluecrystal3

submit.sh

#!/bin/bash

#PBS -N test
#PBS -o test-output
#PBS -e test-error
#PBS -t 1-500
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=1
#PBS -S /bin/bash

set -e

echo "Running on ${HOSTNAME}"

# If there is an argument passed at commandline then set PBS_ARRAYID as that
# Else, PBS_ARRAYID is either empty if run in commandline, 
# or set by the job scheduler if run by qsub
if [ -n "${1}" ]; then
  echo "${1}"
  PBS_ARRAYID=${1}
fi

i=${PBS_ARRAYID}

# Analysis
R --no-save --args ${i} < test.R

test.R

# Pass arguments from shell to R
arguments <- commandArgs(T)

i <- as.numeric(arguments[1])
print(i)

To run a test (e.g. for process 1 of 500) in the frontend of bluecrystal, type:

chmod 755 submit.sh
./submit.sh 1

Otherwise just submit and it will make 500 jobs

qsub submit.sh