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Sample Script - NAMD

This document contains scripts for running molecular dynamics simulations using NAMD on both CPU-only and CPU+GPU nodes on a Cray supercomputer. The scripts specify the queue to submit to, load required modules, echo environment variables, create output directories, copy input files, and run NAMD linking to the correct executable using aprun to distribute across nodes.

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Arupjyoti Das
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42 views2 pages

Sample Script - NAMD

This document contains scripts for running molecular dynamics simulations using NAMD on both CPU-only and CPU+GPU nodes on a Cray supercomputer. The scripts specify the queue to submit to, load required modules, echo environment variables, create output directories, copy input files, and run NAMD linking to the correct executable using aprun to distribute across nodes.

Uploaded by

Arupjyoti Das
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Scripts for running on CPU nodes

## Queue it will run in


#PBS -N test
#PBS -q regular
#PBS -l select=2:ncpus=40:vntype=cray_compute
#PBS -l walltime=00:10:00
#PBS -l place=scatter
#PBS -j oe
##PBS -o namd_cpu.batch-log
##PBS -V

. /opt/modules/default/init/sh

cd $PBS_O_WORKDIR

module load namd/2.12/intel-18.0.1

echo ------------------------------------------------------
echo -n 'Job is running on node '; cat $PBS_NODEFILE
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------

EXEC=/home/apps/namd/2.12/intel/18.0.1/CRAY-XC-intel/namd2
RUN_DIR=$PBS_O_WORKDIR/cpu_out/run.${PBS_JOBID}

mkdir -p ${RUN_DIR}
cp cpu_input/* ${RUN_DIR}

cd ${RUN_DIR}
ln -s ${EXEC} .

time aprun -n 80 -N 40 ${RUN_DIR}/namd2 pm9-15wations-prod2.conf > $


{RUN_DIR}/prod2.log
Scripts for running on CPU+GPU nodes

## Queue it will run in

#PBS -N ngc_2_1_1
#PBS -q gpuq
##PBS -q gpu_nodes
#PBS -l select=2:ncpus=1:accelerator=True:vntype=cray_compute
#PBS -l place=scatter
#PBS -o ngc_2_1_1.batch-log
#PBS -V

. /opt/modules/default/init/sh

cd $PBS_O_WORKDIR

module load namd/2.12/gpu-8.0

echo ------------------------------------------------------
echo -n 'Job is running on node '; cat $PBS_NODEFILE
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------

EXEC=/home/apps/namd/2.12/gpu/8.0/CRAY-XC.cuda.arch/namd2

RUN_DIR=$PBS_O_WORKDIR/gpu_out/run.${PBS_JOBID}

mkdir -p ${RUN_DIR}
cp gpu_input/* ${RUN_DIR}

cd ${RUN_DIR}
ln -s ${EXEC} .

time aprun -n 80 -N 40 ${RUN_DIR}/namd2 pm9-15wations-prod2.conf > $


{RUN_DIR}/prod2.log

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