nwchem

About

NWChem is a computational quantum chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources.

Versions and Availability

Module Names for nwchem on smic
Machine Version Module Name
smic 6.3 nwchem/6.3/INTEL-140-MVAPICH2-2.0
▶ **FIX-ME** FAQ?

Usage

For clusters using softenv, you will need to add the keys to your software environment for both NWChem, and the MPI library used with it. For instance, if you use +nwchem-6.1-intel-11.1-mvapich-1.1, make sure you also include +mvapich-1.1-intel-11.1 in your .soft file.

▶ Open Example?
#!/bin/sh
#
#PBS -A <your allocation>
#PBS -q checkpt
#PBS -M <your email>
#PBS -l nodes=1:ppn=8
#PBS -l walltime=HH:MM:SS
#PBS -V
#PBS -o <standard output filename>
#PBS -e <standard error filename>
#PBS -N NAME

export EXEC=nwchem
export EXEC_DIR=/usr/local/packages/nwchem/6.1/intel-11.1-mvapich-1.1/bin/LINUX64
export WORK_DIR=$PBS_O_WORKDIR
export INPUT=$WORK_DIR/h2o.nw
export OUTPUT=$WORK_DIR/h2o.nwo
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` 

cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC $INPUT > $OUTPUT

For clusters using module, you will need to load the module key to your software environment. For instance, module load nwchem/6.3/INTEL-140-MVAPICH2-2.0, you will also need to create a ~/.nwchemrc file in your home directory for nwchem to load the necessary environmental variables, you can simply copy example nwchemrc file from nwchem installation directory(e.g. /usr/local/packages/nwchem/6.3/INTEL-140-MVAPICH2-2.0/).

▶ Open Example?
#!/bin/sh
#
#PBS -A <your allocation>
#PBS -q checkpt
#PBS -M <your email>
#PBS -l nodes=1:ppn=20
#PBS -l walltime=HH:MM:SS
#PBS -V
#PBS -o <standard output filename>
#PBS -e <standard error filename>
#PBS -N NAME

export EXEC=nwchem
export EXEC_DIR=/usr/local/packages/nwchem/6.3/INTEL-140-MVAPICH2-2.0/bin
export WORK_DIR=$PBS_O_WORKDIR
export INPUT=$WORK_DIR/h2o.nw
export OUTPUT=$WORK_DIR/h2o.nwo
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` 

cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC $INPUT > $OUTPUT

Resources

Last modified: August 14 2015 12:53:49.