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GAMESS on Biowulf

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is maintained by the members of the Gordon research group at Iowa State University.

Our license for GAMESS requires that if results obtained with GAMESS are published in the scientific literature, you reference the program from the article M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J. Comput. Chem. 14, 1347-1363 (1993). Using specific methods included in GAMESS may require citing additional articles, as described in the manual.

Versions

27 JUN 2005 (R2), version 00
24 MAR 2007 (R6), version 00 (default)

Submitting GAMESS jobs to the batch system

GAMESS on the Biowulf cluster is configured to be run as a batch job. Interactive sessions are not supported. Here is a sample batch script for submitting a GAMESS job: 
---------------------------file gms.bat-----------------------------
#!/bin/bash
#PBS -N GMSscf_44
#PBS -k oe
#
cd $PBS_O_WORKDIR
/usr/local/gamess/rungms scf_44 $ver $np > scf_44.out
--------------------------------------------------------------------
The arguments to the rungms command are:

rungms inp [version][nprocs]

where,

  • inp - input file name (.inp extension assumed)
  • nprocs - total number of processes to run (optional, defaults to the maximum number of CPUs allocated by the batch system)
  • version - GAMESS version number (optional, defaults to system default which is always 00)

    • To submit a 4-node (8-processor job), you would use the following command: 

    qsub -l nodes=4 gms.bat

    For some jobs, running 2 processes per node will result in insufficient memory for the job. In these cases, run a single process per node (note that you must also specify a version number as a place holder):

    qsub -v ver=00,np=4 -l nodes=4 gms.bat

    The job should be submitted with the "-v" switch to the qsub command, so as to pass parameters from the command line to the batch script. This is used here to allow differing combinations of processors and versions to be specified without having to "hard code" them into the script.

    Running older versions

    In order to run older versions of GAMESS, use the full pathname to the GAMESS directory. For 27Jun2005-R2, you would call

    /usr/local/gamess-27Jun2005-R2/rungms

    This document is available as http://biowulf.nih.gov/apps/gamess.html
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