Script Example - GridChem Gaussian

    Example script qsubin1417

Another example script below.

#!/bin/sh

#PBS -m bae

#PBS -N 1p-Au1 

#PBS -q shared 

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

#PBS  -V

#PBS -j oe 

#PBS -l walltime=40:30:0,nodes=1:ppn=1

#PBS -A uic151

set -x

. /etc/profile.d/modules.sh;

module load globus;

module load uberftp;

module load gaussian

export X509_USER_PROXY=/home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/x509up_p2359.fileeDwNRE.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="1p-Au1.trestles.sdsc.teragrid.org.$jobid.141125"

export OutDir=/home/gridchem/ramasami/ramasami_proj/$jobdir

export OutDir0=/home/gridchem/ramasami/ramasami_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/ramasami/ramasami_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/ramasami/tempdirs/tempdirG4ZH7K7 $OutDir/

###which uberftp

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

g03lscr=$SCRATCH_BATCH

/bin/cp /home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/1p-Au1.gjf input.com

" ]; then home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/job.chk

 job.chkp /home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/job.chk

else 

_x86_64_Linux  | awk ' { print $NF } ' | sed 's/\r//' `du   "cd mss/internal/ramasami; ls job.chk

  ChkTest=`ssh ccguser@gridchem-mw.ncsa.illinois.edu   "cd mss/internal/ramasami; ls job.fchk"     | /bin/grep -i jo

b.fchk  | awk ' { print $NF } ' | sed 's/\r//'  `

  echo "DEBUG: ChkTest_arch= $ChkTest_arch"  

  checkpoint_file_not_found_or_invalid=1 

_x86_64_Linux ]; then -null} = job.chk

_x86_64_Linux ./@gridchem-mw.ncsa.illinois.edu:mss/internal/ramasami/job.chk

_x86_64_Linux.old"   hem-mw.ncsa.illinois.edu   "cd mss/internal/ramasami; mv job.chk

 x86_64_Linux  job.chk

 2>/dev/null 1>/dev/null ; then checkpoint_file_not_found_or_invalid=0 ; else echo "WARNING: chkchk command failed -

 we will use the formatted checkpoint if it exists "  ;fi 

  fi 

  if  [ $checkpoint_file_not_found_or_invalid -eq 1 ] ; then 

    echo "DEBUG: ChkTest= $ChkTest"  

    if [ ${ChkTest:-null} = job.fchk ]; then 

      scp   ccguser@gridchem-mw.ncsa.illinois.edu:mss/internal/ramasami/job.fchk ./

      unfchk job.fchk job.chk

    else 

      echo "WARNING: no formated checkpoint file exists on MSS "  

    fi 

  fi 

fi

###echo "DEBUG: TEMP01BBBB 20070301 skk ";  ls -l $X509_USER_PROXY

# (for OSC) THIS HAS TO COME AFTER THE module command since module would overwrite with default GAUSS_SCRDIR

export GAUSS_SCRDIR="/scratch/$USER/$PBS_JOBID"

NODELIST=`cat $PBS_NODEFILE|perl -pe 's/\\n/ /' ` 

export GAUSS_LFLAGS="-vv -nodelist \\"$NODELIST\\""

echo "THIS IS THE INPUT FILE:"

cat /home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/1p-Au1.gjf

Diskoutputfile_with_dir=$SCRATCH_BATCH/1p-Au1.out

trap ". /home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/qsubin2364_cleanup ; exit 99 " XCPU INT TERM CHLD  

#

# RUN GAUSSIAN

#Jayeeta commented following line

#soft add +gaussian-09

echo "DEBUG: PATH is $PATH "; echo

g09 input.com $Diskoutputfile_with_dir

. /home/gridchem/ramasami/tempdirs/tempdirG4ZH7K7/qsubin2364_cleanup