Script Example - GridChem DDSCAT

#!/bin/sh

#PBS -m bae

#PBS -N default_job 

#PBS -q normal 

#PBS -M ccg-admin@gridchem.uits.iu.edu

#PBS  -V

#PBS -j oe 

#PBS -l walltime=4:30:0,nodes=1:ppn=8

#PBS -A uic151

set -x

export X509_USER_PROXY=/home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/x509up_p11500.fileZMyQbl.1

###2007/05/03 export LD_LIBRARY_PATH=/opt/gnu/gmp/lib:/opt/gnu/mpc/lib:/opt/gnu/gcc/lib64:/opt/gnu/mpfr/lib:/opt/gnu

/lib:/opt/gnu/lib64:/opt/mvapich2/pgi/ib/lib:/opt/pgi/linux86-64/13.2/libso   # NOT NEEDED

jobid=`echo $PBS_JOBID |sed 's/\..*//' `

jobdir="default_job.trestles.sdsc.teragrid.org.$jobid.141125"

export OutDir=/home/gridchem/spamidig/spamidig_proj/$jobdir

export OutDir0=/home/gridchem/spamidig/spamidig_proj

if [ ! -d $OutDir0 ] ; then

  echo "Making dir: $OutDir0"; 

  mkdir -p $OutDir0 || exit 1;  # let us stop if we can not make this dir - it is too important

fi

# we need to export SCRATCH_BATCH 

export HOME_BATCH=/home/gridchem/spamidig/spamidig_proj/$jobdir

export SCRATCH_BATCH=/oasis/scratch/trestles/$USER/$PBS_JOBID

if [ ! -d $HOME_BATCH ] ; then 

  echo "Linking HOME_BATCH to SCRATCH_BATH: $HOME_BATCH -> $SCRATCH_BATCH"   ; 

  ln -s $SCRATCH_BATCH $HOME_BATCH  || exit 1;

fi

# change directory to SCRATCH_BATCH

cd $SCRATCH_BATCH

pwd

# 2006/03/31 make a link of the Outdir into OutDir for convenience

#/bin/ln -s  /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ $OutDir/

###which uberftp

###echo "DEBUG: TEMP01AAAAAA 20070301 skk ";  ls -l $X509_USER_PROXY

cp -p /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/*.par  ./ddscat.par

cp -p /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/*.tab  ./

cp -p /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/*.*  ./

Diskoutputfile_with_dir=$SCRATCH_BATCH/default_job.out

trap ". /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/qsubin11505_cleanup ; exit 99 " XCPU INT TERM CHLD  

cp -p /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/*.* /oasis/scratch/trestles/$USER/$PBS_JOBID

. /etc/profile.d/modules.sh; module load mkl/10.3.3;ldd /home/gridchem/apps/ddscat/ddscat7.2.2/src/ddscat 

mpirun_rsh -np 8 -hostfile $PBS_NODEFILE /home/gridchem/apps/ddscat/ddscat7.2.2/src/ddscat >& default_job.out

. /home/gridchem/spamidig/tempdirs/tempdirG1o_AxZ/qsubin11505_cleanup