CUNY High Performance Computing Facility
 NWChem

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 Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL).

For additional information on NWChem please refer to NWChem web site.

Usage

To run a NWChem job, create the following submit script file in your home directory:

prompt$ vi submit_file

Sample submit script:

#!/bin/bash
#$ -S /bin/sh
#$ -N name_of_your_job
#$ -q default
#$ -pe mpich n  (where n is the number of_processors  requested)
#$ -cwd
$path_to_mpi -machinefile $TMPDIR/mpd.machines -n $NSLOTS $path_to_nwchem $path_to_datafile

On Athena

$path_to_mpi = /share/apps/mpich/bin/mpirun
$path_to_nwchem = /share/apps/NWChem/bin/nwchem

After you have saved your script, make it executable:

prompt$ chmod 0755 ./submit_file

Run it with:

prompt$ qsub submit_file

Example:

Suppose you want to run a test job on 12 processors. And you want your job to have name “h2o_example” Your script will look as follows:

#!/bin/bash
#$ -S /bin/sh
#$ -N h2o_example
#$ -q default
#$ -pe mpich 12
#$ -cwd
/share/apps/mpich/bin/mpirun -machinefile $TMPDIR/mpd.machines -n $NSLOTS /share/apps/NWChem/bin/nwchem /share/apps/NWChem/examples/h2o/h2o.nw

Save it and make executable.  Run it.

You can see output in the following files:
h2o_example.po# - output from parallel environment
h2o_example.pe# - error messages from parallel environment
h2o_example.o# - output of your job
h2o_example.e# - error messages
Save that script and make it executable:
prompt$ chmod 0755 ./submit_file

Acknowledgements

Please use the following acknowledgment where appropriate for results obtained with NWChem:  "NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1" (2007), Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA.

CITATION

Please use the following citation when publishing results obtained with NWChem:

E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma, M. Valiev, D. Wang, E. Apra, T. L. Windus, J. Hammond, P. Nichols, S. Hirata, M. T. Hackler, Y. Zhao, P.-D. Fan, R. J. Harrison, M. Dupuis, D. M. A. Smith, J. Nieplocha, V. Tipparaju, M. Krishnan, Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, E. Brown, G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan, K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe, B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng, T. Nakajima, S. Niu, L. Pollack, M. Rosing, G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. van Lenthe, A. Wong, and Z. Zhang, "NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1" (2007), Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA.