NWChem

Description

NWChem is a computational chemistry package 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.

How to access NWChem

NERSC uses modules to manage access to software. To use the default version of NWChem, type:

% module load nwchem

To see where the nwchem executables reside (the bin directory) and what environment variables it defines:

% module show nwchem

e.g., on Hopper:

% module avail nwchem
--------------------------------------------------- /usr/common/usg/Modules/modulefiles ---------------------------------------------------
nwchem/6.0(default) nwchem/6.1 nwchem/6.1.1
% module show nwchem
-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/nwchem/6.0:
module-whatis NWChem is a parallel computational chemistry package 
setenv SHMEM_SWAP_BACKOFF 150 
setenv CRAY_PORTALS_USE_BLOCKING_POLL yes 
setenv NWCHEM_BASIS_LIBRARY /usr/common/usg/nwchem/6.0/data/libraries/ 
prepend-path PATH /usr/common/usg/nwchem/6.0/bin 
prepend-path PYTHONPATH /usr/common/usg/nwchem/6.0/contrib/python

When you first start to use NWChem, you should copy a default ".nwchemrc" file to your home directory. This file is used to set certain default options for the program:

% cp ${NWCHEM_DIR}/default.nwchemrc ~/.nwchemrc

How to Use NWChem on Hopper

There are two ways of running NWChem on Hopper, submitting a batch job, or running interactively in an interactive batch session. A sample batch script to run NWChem on Hopper is shown below:

#PBS -S /usr/bin/tcsh 
#PBS -N test_nwchem
#PBS -q debug
#PBS -l mppwidth=32
#PBS -l walltime=00:30:00
#PBS -j eo
#PBS -V

cd $PBS_O_WORKDIR
module load nwchem

aprun -n 32 nwchem test1.nw > &! test1.out

Then submit the job script using qsub command, e.g., assume the job script name is test_nwchem.pbs,

% qsub  test_nwchem.pbs

2) To request an interactive batch session, issue a command (e.g., requesting 32 PEs):

% qsub  -I -V -q interactive -l mppwidth=32

when a new batch session is returned to you, issue the following commands:

%  cd $PBS_O_WORKDIR 
%  module load nwchem 
%  aprun -n 32 nwchem

How to use NWChem on Carver

Here is a sample batch job script

#PBS -N test_nwchem
#PBS -q debug
#PBS -l nodes=2:ppn=8 
#PBS -l walltime=00:30:00
#PBS -j eo
#PBS -V

cd $PBS_O_WORKDIR
module load nwchem

mpirun -n 16 nwchem test1.nw > &! test1.out

Documentation

NWChem was developed by the High-Performance Computational Chemistry group in the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL).

NWChem User Manual

Availability