Talk:Useful PBS scripts - Revision history

import>Mm695 at 17:34, 12 March 2008

2008-03-12T17:34:38Z

← Older revision		Revision as of 17:34, 12 March 2008
Line 1:		Line 1:
	'#'PBS -q s32

	'#'PBS -l walltime=18:00:00

	'#'PBS -l nodes=8:ppn=4

	HERE=/home/mm695/whatever

	file=dho2498_singlePoint

	inpfile=${file}.inp

	outfile=${file}.out

	SCRATCH=/scratch/mm695/$file

	nodes=`cat $PBS_NODEFILE \| uniq`

	for node in $nodes
	do
	rsh $node "rm -f $SCRATCH/*"
	rsh $node "rmdir $SCRATCH"
	rsh $node "mkdir $SCRATCH"
	rsh $node "cp ${HERE}/gromos* $SCRATCH"
	rsh $node "cp ${HERE}/geom_end_of_sim.crd $SCRATCH"
	rsh $node "cp ${HERE}/RESTART $SCRATCH"
	rsh $node "cp ${HERE}/${inpfile} $SCRATCH"
	done

	exe=/home/mm695/SOURCE/cpmd.x

	pp=/home/mm695/pseudopot

	cd $SCRATCH

	'#'Write out some helpful info to the output file

	echo "Starting job $PBS_JOBID"
	echo
	echo "PBS assigned me this node:"
	cat $PBS_NODEFILE
	echo

	mvapichwrapper $exe $inpfile $pp > ${HERE}/${outfile}

	for node in $nodes
	do
	rsh $node 'mv ${SCRATCH}/* ${HERE}'
	rsh $node 'rm -f ${SCRATCH}/*'
	rsh $node 'rmdir /scratch/mm695/$file'
	done

	qstat -f $PBS_JOBID

import>Mm695: CPMD runscript for when several nodes are used

2008-03-12T17:30:24Z

CPMD runscript for when several nodes are used

← Older revision		Revision as of 17:30, 12 March 2008
Line 1:		Line 1:
	##PBS -q s32		'#'PBS -q s32

	##PBS -l walltime=18:00:00		'#'PBS -l walltime=18:00:00

	##PBS -l nodes=8:ppn=4		'#'PBS -l nodes=8:ppn=4

	HERE=/home/mm695/whatever		HERE=/home/mm695/whatever
Line 34:		Line 34:
	cd $SCRATCH		cd $SCRATCH

		⚫	'#'Write out some helpful info to the output file
	#

⚫	## Write out some helpful info to the output file
	#
	echo "Starting job $PBS_JOBID"		echo "Starting job $PBS_JOBID"
	echo		echo

import>Mm695: CPMD runscript for when several nodes are used

2008-03-12T17:29:21Z

CPMD runscript for when several nodes are used

← Older revision		Revision as of 17:29, 12 March 2008
Line 1:		Line 1:
	#PBS -q s32		##PBS -q s32

	#PBS -l walltime=18:00:00
	#PBS -l ~~nodes~~=8:~~ppn=4~~		##PBS -l walltime=18:00:00

			##PBS -l nodes=8:ppn=4

	HERE=/home/mm695/whatever		HERE=/home/mm695/whatever

	file=dho2498_singlePoint		file=dho2498_singlePoint

	inpfile=${file}.inp		inpfile=${file}.inp

	outfile=${file}.out		outfile=${file}.out

	SCRATCH=/scratch/mm695/$file		SCRATCH=/scratch/mm695/$file

	nodes=`cat $PBS_NODEFILE \| uniq`		nodes=`cat $PBS_NODEFILE \| uniq`

	for node in $nodes		for node in $nodes
	do		do
Line 21:		Line 29:

	exe=/home/mm695/SOURCE/cpmd.x		exe=/home/mm695/SOURCE/cpmd.x

	pp=/home/mm695/pseudopot		pp=/home/mm695/pseudopot

	cd $SCRATCH		cd $SCRATCH
	~~ls -la~~
	#		#
	# Write out some helpful info to the output file		## Write out some helpful info to the output file
	#		#
	echo "Starting job $PBS_JOBID"		echo "Starting job $PBS_JOBID"
Line 43:		Line 52:
	done		done

	echo
	echo
	qstat -f $PBS_JOBID		qstat -f $PBS_JOBID

import>Mm695: /CPMD runscript to generate a directory on all nodes and copying there input files needed for the calculation/

2008-03-12T17:26:37Z

CPMD runscript to generate a directory on all nodes and copying there input files needed for the calculation

New page

#PBS -q s32
#PBS -l walltime=18:00:00
#PBS -l nodes=8:ppn=4
HERE=/home/mm695/whatever
file=dho2498_singlePoint
inpfile=${file}.inp
outfile=${file}.out
SCRATCH=/scratch/mm695/$file

nodes=`cat $PBS_NODEFILE | uniq`
for node in $nodes
do
rsh $node "rm -f $SCRATCH/*"
rsh $node "rmdir $SCRATCH"
rsh $node "mkdir $SCRATCH"
rsh $node "cp ${HERE}/gromos* $SCRATCH"
rsh $node "cp ${HERE}/geom_end_of_sim.crd $SCRATCH"
rsh $node "cp ${HERE}/RESTART $SCRATCH"
rsh $node "cp ${HERE}/${inpfile} $SCRATCH"
done

exe=/home/mm695/SOURCE/cpmd.x
pp=/home/mm695/pseudopot

cd $SCRATCH
ls -la
#
# Write out some helpful info to the output file
#
echo "Starting job $PBS_JOBID"
echo
echo "PBS assigned me this node:"
cat $PBS_NODEFILE
echo

mvapichwrapper $exe $inpfile $pp > ${HERE}/${outfile}

for node in $nodes
do
rsh $node 'mv ${SCRATCH}/* ${HERE}'
rsh $node 'rm -f ${SCRATCH}/*'
rsh $node 'rmdir /scratch/mm695/$file'
done

echo
echo
qstat -f $PBS_JOBID

Talk:Useful PBS scripts - Revision history

import>Mm695 at 17:34, 12 March 2008

import>Mm695: CPMD runscript for when several nodes are used

import>Mm695: CPMD runscript for when several nodes are used

import>Mm695: /*CPMD runscript to generate a directory on all nodes and copying there input files needed for the calculation*/

import>Mm695: /CPMD runscript to generate a directory on all nodes and copying there input files needed for the calculation/