example_PBSMPI

#!/bin/bash
#!
#PBS -S /bin/bash
#PBS -N Silly_JOB_NAME
#PBS -j oe
#PBS -l walltime=6:00:00
#PBS -l nodes=8:ppn=16,pmem=2gb
#PBS -r n
#PBS -q batch
#PBS -m e
#PBS -M $USER@soton.ac.uk
###############################################################
###                      Bash job script                   ####
###############################################################

#! Change the working directory (default is home directory)
#! PBS_O_WORKDIR = directory from which the batch job is launched

cd $PBS_O_WORKDIR
echo Directory is `pwd`
# load openmpi module so that we find the mpirun command
module load openmpi/1.6.4/intel_of2
#module load intel/2013.4
module list
echo "PATH"
echo $PATH
echo "LD_LIBRARY_PATH"
echo $LD_LIBRARY_PATH

echo Time is `date`
echo PBS job ID is $PBS_JOBID
echo This jobs runs on the following machines:
echo `cat $PBS_NODEFILE | uniq`

echo "MITgcm job starting"
date
echo "-----------------------------"
#limit coredumpsize 0
ulimit -s 819200
#numnodes= `wc $PBS_NODEFILE | awk '{ print $1 }'`

#! Create a machine file for MPI
#cat $PBS_NODEFILE | head -$numnodes > host.file.$PBS_JOBID

##echo export LD_LIBRARY_PATH=$/home/jrb1/packages/netcdf3/netcdf-3.6.3/x86_64/intel11.1/lib/:/home/local/software/intel/2013.4.183/lib/:${LD_LIBRARY_PATH}

##export LD_LIBRARY_PATH= $/home/jrb1/packages/netcdf3/netcdf-3.6.3/x86_64/intel11.1/lib/:/home/local/software/intel/2013.4.183/lib/:${LD_LIBRARY_PATH}

#export LD_LIBRARY_PATH=/home/jrb1/packages/netcdf3/netcdf-3.6.3/x86_64/intel11.1/lib/:${LD_LIBRARY_PATH}

##! Run the parallel MPI executable (nodes*ppn)

echo "Running mpirun ./mitgcmuv >& socn.output"

mpirun -mca btl_openib_ib_min_rnr_timer 25 -mca btl_openib_ib_timeout 20 ./mitgcmuv >& socn.output

date
echo "-----------------------------"
echo "MITgcm job finished"

exit