Package	Platform	Category	Version	Module	Install Date	Date Made Default
nwchem	carver	applications/chemistry	5.1.1	nwchem/5.1.1	2010-03-14	2010-03-14
nwchem	franklin	applications/chemistry	5.1	nwchem/5.1	2008-12-31	2008-02-12
nwchem	franklin	applications/chemistry	5.1.1	nwchem/5.1.1	2009-07-21	2009-09-09
nwchem	hopper	applications/chemistry	5.1.1	nwchem/5.1.1	2009-10-29	2009-10-29

NWChem at NERSC

NWChem is a computational 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.

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

Access to NWChem
Running on Franklin and Hopper
Running on Carver
Documentation and Help

Access

Usually, a number of different versions of NWChem are installed on the systems. Each version can be made available by loading a different module. To use the default and recommended version, use the command:

% module load nwchem

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

% module show nwchem

e.g., on franklin,

% module show nwchem
-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/nwchem/5.1.1:

module-whatis	 NWChem Computational Chemistry Package 
setenv		 NWCHEM_DIR /usr/common/usg/nwchem/5.1.1 
setenv		 NWCHEM_BASIS_LIBRARY /global/common/hopper/usg/nwchem/5.1.1/data/libraries/ 
setenv		 SHMEM_SWAP_BACKOFF 150 
setenv		 CRAY_PORTALS_USE_BLOCKING_POLL yes 
prepend-path	 PATH /usr/common/usg/nwchem/5.1.1/bin 
-------------------------------------------------------------------

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

Running on Franklin and Hopper

There are two ways of running nwchem on franklin/hopper, submitting a batch job, or running interactively in an interactive batch session.
1) Sample batch script to run nwchem on franklin/hopper:

#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

Note:

If you compile your own version of nwchem, please set the following two environment variables in your job script before running nwchem to avoid the possible job hangs.
```
setenv           SHMEM_SWAP_BACKOFF 150
setenv           CRAY_PORTALS_USE_BLOCKING_POLL yes
```
NWChem 5.1.1 was compiled with ARMCI_NETWORK=PORTALS instead of ARMCI_NETWORK=CRAY-SHMEM. The two environment variables, XT_SYMMETRIC_HEAP_SIZE and XT_LINUX_SHMEM_HEAP_SIZE, are not needed to run nwchem anymore.

Running 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 and Help

NWchem User Manual

HPC Users

Resources

Software