1. www.mimos.my© 2010 MIMOS Berhad. All Rights Reserved. Nazarudin Wijee Mohd Sidek Salleh Grid Computing Lab MIMOS Berhad 7 Stages Heating System Amber Job Submission in P-GRADE Portal

2. Background User: Universiti Sains Malaysia Amber Version: 9 Job Type: MPI No of processor: 32 www.mimos.my© 2010 MIMOS Berhad. All Rights Reserved.

3. Amber 7 Stages Heating System Workflow www.mimos.my© 2010 MIMOS Berhad. All Rights Reserved. #PBS -N Amber #PBS -l select=4:ncpus=8 STAGE=1 PROJECT_DIR=job_execution_directory EXE=/share/apps/amber9/exe/sander GBIN=$PROJECT_DIR/gbin$STAGE PRMTOP=$PROJECT_DIR/prmtop$STAGE INPCRD=$PROJECT_DIR/inpcrd$STAGE RESTRT=$PROJECT_DIR/restrt$STAGE TRAJECTORY=$PROJECT_DIR/trajectory$STAGE MDINF=$PROJECT_DIR/mdinfo$STAGE MDOUT=$PROJECT_DIR/mdout$STAGE MDEN=$PROJECT_DIR/mden$STAGE MDVEL=$PROJECT_DIR/mdvel$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

4. Amber 7 Stages Heating System Workflow www.mimos.my© 2010 MIMOS Berhad. All Rights Reserved. STAGE=1. /etc/pbs.conf. executor.info echo "PBS_SERVER = $PBS_SERVER" echo "PBS_JOBID = $PBS_JOBID" echo "EXEC_NODE = `hostname`" echo "MONITOR_JOB_DIR = `pwd`" echo # begin monitoring FINISH_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" fi done echo $WC > tracejob.out echo "Job $PBS_JOBID has finished..." RESTRT=$PROJECT_DIR/restrt$STAGE TRAJECTORY=$PROJECT_DIR/trajectory$STAGE MDINF=$PROJECT_DIR/mdinfo$STAGE MDOUT=$PROJECT_DIR/mdout$STAGE MDEN=$PROJECT_DIR/mden$STAGE MDVEL=$PROJECT_DIR/mdvel$STAGE # in case some files were not produced... touch restrt$STAGE touch trajectory$STAGE touch mdinfo$STAGE touch mdout$STAGE touch mden$STAGE touch 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 job 2.During runtime, it will goes to cluster head node and do PBS Pro tracejob to check it the given PBS Job ID already finished.

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