User:Fkannema

Here is a bash script to submit Gaussian jobs on placentia2 (Download). Put it in your home directory, do

chmod u+x g03sub

Then you can submit jobs with

./g03sub filename [jobname] [test | runtimehours]

The requested memory and number of CPUs for parallel jobs is read from the Gaussian input file. The default runtime is 48 hours which can be overwritten by specifying the runtime in hours on the commandline, eg:

./g03sub ch4.gjf ch4 20

to request a runtime of 20 hours.

#!/bin/bash
#
# bash script for submitting gaussian jobs on placentia2 (Acenet)
# Felix Kannemann <felix.kannemann [ AT ] dal.ca>, 2009-02-11
#
# usage:   g03sub filename [jobname] [test | runtimehours]
# example: g03sub ch4.gjf ch4 20
#
# reads memory (MB, GB, MW or GW) and number of CPUs for parallel jobs
# from input file and adjusts job submission parameters accordingly
# also works for multi-step jobs
#
# to submit all *.gjf in current directory at once (bash):
#	for i in *.gjf; do g03sub $i `expr substr ${i%.*} 1 10`; done
# the job name is given by the name of the input file (without extension)
# truncated to 10 characters, names of input files therefore have to
# start with character


# get name of input file
if [ "$1" == "" ]; then
	echo "Name of input file with or without extension (*.gjf or *.com):"
	read FILE
else
	if [ -e "$1" ]; then
		FILE="$1"
	else
		echo "File $1 does not exist!"
		echo "Name of input file with or without extension (*.gjf or *.com):"
		read FILE
	fi
fi

# remove filename extensions for internal use
FILENAME=`basename $FILE .gjf`
FILENAME=`basename $FILENAME .com`

# rename input file from .gjf to .com
if [ -e ${FILENAME}.gjf ]; then
	echo "Renaming ${FILENAME}.gjf to ${FILENAME}.com"
	mv ${FILENAME}.gjf ${FILENAME}.com
fi

# convert input file to unix line endings
dos2unix ${FILENAME}.com

# get jobname
if [ "$2" == "" ]; then
	echo "Job name (start with character):"
	read JOBNAME
else
	JOBNAME=$2
fi

# get number of processors from gaussian input file
# works with "%nproc=" and "%nprocs="
nprocline=`grep -m 1 nproc ${FILENAME}.com`
nproc=${nprocline#%nproc*=}

# set default number of processors to 1
if [ "$nproc" == "" ]; then
	nproc=1
fi

# get memory from gaussian input file
memline=`grep -m 1  mem ${FILENAME}.com`
memIn=${memline#%mem=}
case "$memIn" in
	*MB )
		mem=${memIn%MB}
		memMB=$mem ;;
	*GB )
		mem=${memIn%GB}
		memMB=$[$mem * 1024] ;;
	*MW )
		mem=${memIn%MW}
		memMB=$[$mem * 8] ;;
	*GW )
		mem=${memIn%GW}
		memMB=$[$mem * 8192] ;;
esac

# calculate memory requirements
if [ "$nproc" -eq 1 ]; then
	# for serial jobs add 1024MB to memory from gaussian input file
	memJob=$[$memMB + 1024]
else
	# for parallel jobs use formula from acenet wiki
	memJob=$[($memMB + 1024) * ($nproc + 1) / $nproc]
fi

# write job parameters to output
echo "filename:" ${FILENAME}.com
echo "jobname:" ${JOBNAME}
echo "requested number of CPUs:" $nproc
echo "requested memory in input file:" $memIn "=" $memMB"MB"
echo "requested memory in job script:" $memJob"MB"

# write jobfile
# default options: serial job, 1024MB memory, runtime 48 hours
cat > ${JOBNAME}.csh <<JOBFILE
#$ -S /bin/csh
#$ -N $JOBNAME
#$ -cwd
#$ -j y
#$ -o ${JOBNAME}.out
#$ -l h_vmem=${memJob}M
#$ -l h_rt=48:00:00
source /usr/local/lib/gaussian.sh
hostname
date
g03 < $FILENAME.com > $FILENAME.log

JOBFILE

# submit job to Gaussian
# if 3rd command line argument equals "test", submit as test job
if [ "$3" == "test" ]; then
	echo "qsub command line: qsub -l h_rt=0:30:0,test=true ${JOBNAME}.csh"
	qsub -l h_rt=0:30:0,test=true ${JOBNAME}.csh

# if 3rd command line argument is not empty, use as runtime in hours
elif [ -n "$3" ]; then
	if [ $nproc -gt 1 ]; then
		echo "qsub command line: qsub -l h_rt=${3}:0:0 -pe gaussian $nproc ${JOBNAME}.csh"
		qsub -l h_rt=${3}:0:0 -pe gaussian $nproc ${JOBNAME}.csh
	else
		echo "qsub command line: qsub -l h_rt=${3}:0:0 ${JOBNAME}.csh"
		qsub -l h_rt=${3}:0:0 ${JOBNAME}.csh
	fi

# otherwise submit job with default runtime from job script
else
	if [ $nproc -gt 1 ]; then
		echo "qsub command line: qsub -pe gaussian $nproc ${JOBNAME}.csh"
		qsub -pe gaussian $nproc ${JOBNAME}.csh
	else
		echo "qsub command line: qsub ${JOBNAME}.csh"
		qsub ${JOBNAME}.csh
	fi
fi

# cat ${JOBNAME}.csh

# delete job script
#~ rm ${JOBNAME}.csh

# eof