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Nazarudin Wijee Mohd Sidek SallehGrid Computing LabMIMOS Berhad

7 Stages Heating System Amber Job Submission in P-GRADE Portal

Background

• User: Universiti Sains Malaysia• Amber Version: 9• Job Type: MPI• No of processor: 32

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Amber 7 Stages Heating System Workflow

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#PBS -N Amber #PBS -l select=4:ncpus=8

STAGE=1PROJECT_DIR=job_execution_directoryEXE=/share/apps/amber9/exe/sanderGBIN=$PROJECT_DIR/gbin$STAGEPRMTOP=$PROJECT_DIR/prmtop$STAGEINPCRD=$PROJECT_DIR/inpcrd$STAGERESTRT=$PROJECT_DIR/restrt$STAGETRAJECTORY=$PROJECT_DIR/trajectory$STAGEMDINF=$PROJECT_DIR/mdinfo$STAGEMDOUT=$PROJECT_DIR/mdout$STAGEMDEN=$PROJECT_DIR/mden$STAGEMDVEL=$PROJECT_DIR/mdvel$STAGE

cd $PBS_O_WORKDIR

mpirun -np 32 -machinefile $PBS_NODEFILE $EXE -O -i $GBIN -p $PRMTOP -c $INPCRD -r $RESTRT -x $TRAJECTORY -inf $MDINF -o $MDOUT -e $MDEN -v $MDVEL

• RESTRT file from Stage1 Heating will be used as INPCRD for Stage2 Heating

Amber 7 Stages Heating System Workflow

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STAGE=1

. /etc/pbs.conf

. executor.infoecho "PBS_SERVER = $PBS_SERVER"echo "PBS_JOBID = $PBS_JOBID"echo "EXEC_NODE = `hostname`"echo "MONITOR_JOB_DIR = `pwd`"echo

# begin monitoringFINISH_STATUS="0"until [[ $FINISH_STATUS -eq "1" ]]do WC=`ssh $PBS_SERVER "tracejob -n 30 $PBS_JOBID | grep 'dequeuing from' | wc -l"` if [[ $WC -eq 1 ]]; then FINISH_STATUS="1" else FINISH_STATUS="0" fidone

echo $WC > tracejob.out

echo "Job $PBS_JOBID has finished..."

RESTRT=$PROJECT_DIR/restrt$STAGETRAJECTORY=$PROJECT_DIR/trajectory$STAGEMDINF=$PROJECT_DIR/mdinfo$STAGEMDOUT=$PROJECT_DIR/mdout$STAGEMDEN=$PROJECT_DIR/mden$STAGEMDVEL=$PROJECT_DIR/mdvel$STAGE

# in case some files were not produced...touch restrt$STAGEtouch trajectory$STAGEtouch mdinfo$STAGEtouch mdout$STAGEtouch mden$STAGEtouch mdvel$STAGE

cp $RESTRT .cp $TRAJECTORY .cp $MDINF .cp $MDOUT .cp $MDEN .cp $MDVEL .

exit 0

What will Monitor job do?1. It will receive PBS Job ID from Submit job2. During runtime, it will goes to cluster head

node and do PBS Pro tracejob to check it the given PBS Job ID already finished.

THANK YOU

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