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