gaussian.pbs

#!/bin/bash

if [ -z "$GAUSSVER" ]; then
    GAUSSVER=g03
fi

early() 
{
	echo ' '
	echo ' ############ WARNING:  EARLY TERMINATION, saving chk #############'
	echo ' '

echo IN is $IN, CHK is $CHK

	ls *.wfn| while read file; do
	    mv "$file" $PBS_O_WORKDIR/ ;
	done

	ls *.chk| while read file; do
	    mv "$file" $PBS_O_WORKDIR/ ;
	done
}

#set -x
#set -v

#Important!!  load Gaussian settings
source /etc/gaussian/$GAUSSVER.sh
jobid=$(echo $PBS_JOBID|cut -d[ -f1)

echo ~~~scratch is "$scratch", raid is "$raid"
#setting scratch directory
if [ ! -z "$scratch" ]; then
        GAUSS_SCRDIR="$scratch"
else
	if [ ! -z "$raid" ]; then
		GAUSS_SCRDIR=/mnt/scratch_raid
	fi
	GAUSS_SCRDIR="$GAUSS_SCRDIR/$jobid-$PBS_ARRAYID-$PBS_O_LOGNAME-$GAUSSVER"
fi
# This job's working directory
WORKDIR="$GAUSS_SCRDIR"

#VER=01
if [ -z "$INFILE" ]; then
    INFILE="joblist"
fi

echo Time is `date`
echo Running on host `hostname`
echo Scratch directory is $GAUSS_SCRDIR
echo PBS working directory is $PBS_O_WORKDIR

echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
# Determine number of processors
#old variant
#NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $PBS_NP threads

if ! mkdir -p "$WORKDIR"; then
	echo "Cannot create work directory. Please, free space on `hostname` node";
	exit 1;
fi 

pushd "$WORKDIR"
echo Working directory is `pwd`

if [ ! -f "$PBS_O_WORKDIR/$INFILE" ]; then
	echo Joblist file $PBS_O_WORKDIR/$INFILE is not found
	exit 1;
fi
#extracting input file from jobs list
IN=$(sed -n "$PBS_ARRAYID p" $PBS_O_WORKDIR/$INFILE)
dos2unix "$PBS_O_WORKDIR/$IN"
#generating output file name
OUT="$PBS_O_WORKDIR/$(echo "$IN" | sed 's/\.\S*//')-t$jobid-$PBS_ARRAYID.out"
if [ -f "$OUT" ]; then
    mv "$OUT" "$OUT.bak"
fi

#generating standart chk file name, and if it exists copy in to job working directory
CHK=$PBS_O_WORKDIR/chk/$(grep %chk "$PBS_O_WORKDIR/$IN" | cut -d= -f2)
if [ -f "$CHK" ]; then
    echo "Copying checkpoint file $CHK"
    cp "$CHK" "$WORKDIR"
    mv "$CHK" "$CHK.bak"
fi

echo IN is $IN, OUT is $OUT, CHK is $CHK

cp "$PBS_O_WORKDIR/$IN" ./

#adding new line to Gaussian job - just in case
echo -e "\n" >> ./"$IN"

#export
#TBD: memory specification in GJF
#mem=111mb; 
#if ! grep -i "%mem" $IN; then 
#	sed -i "s/^#/%mem=$mem\n#/" $IN; 
#fi
#adding nproc specification
if ! grep -i "%nproc" "$IN"; then 
	sed -i "s/^#/%nproc=$PBS_NP\n#/" "$IN"; 
fi
#head $IN; 

trap 'early' 2 9 15
#run Gaussian
$gexec "$IN" "$OUT"

#copy CHK files to user directory
#CHKFILE=`echo "$IN" | sed 's/\.\S*/.chk/'`
#CHKFILE=`ls *.chk`
ls *.chk| while read file; do
    if [ ! -d "$PBS_O_WORKDIR/chk" ]; then
      mkdir "$PBS_O_WORKDIR/chk"; 
    fi
    mv "$file" "$PBS_O_WORKDIR/chk" ;
done

#if we have WFN file then analyze it with AIMAll
#then moving result files to user directory
#WFNFILE=`echo "$IN" | sed 's/\.\S*/.wfn/'`
#WFNFILE=`ls *.wfn`
#echo WFNFILE is $WFNFILE
#if [ -e "$WFNFILE" ]; then
#    aimext_single.sh "$WORKDIR/$WFNFILE"
#    AIMFILE=`echo "$IN" | sed 's/\.\S*/.extout/'`
#
#    if [ ! -e $PBS_O_WORKDIR/wfn ]; then
#      mkdir $PBS_O_WORKDIR/wfn; 
#    fi
#    mv "$WFNFILE" $PBS_O_WORKDIR/wfn/ ;
#    mv "$AIMFILE" $PBS_O_WORKDIR/wfn/ ;
#fi
ls *.wfn| while read file; do
    aimext_single.sh "$file"
    AIMFILE=`echo "$IN" | sed 's/\.\S*/.extout/'`

    if [ ! -d "$PBS_O_WORKDIR/wfn" ]; then
      mkdir "$PBS_O_WORKDIR/wfn"; 
    fi
    mv "$file" "$PBS_O_WORKDIR/wfn" ;
    mv "$AIMFILE" "$PBS_O_WORKDIR/wfn/" ;
done
ls *.wfx| while read file; do
    if [ ! -d "$PBS_O_WORKDIR/wfn" ]; then
      mkdir "$PBS_O_WORKDIR/wfn"; 
    fi
    mv "$file" "$PBS_O_WORKDIR/wfn" ;
done

popd
#cleaning
rm -f "$WORKDIR"/*.gjf
#for now removing only empty directories
rmdir -v "$WORKDIR"

    if [ -d "$WORKDIR" ]; then
      ls -l "$WORKDIR";
    fi

#!!!check that all useful is saved to user directory
rm -rf $WORKDIR