GAMESS-pcluster

Category

Chemistry

Program On

pcluster

Version

Mar. 24, 2007 R6, Apr.11, 2008 R1, Aug.11, 2011 R1

Author / Distributor

GAMESS is maintained by the members of the Gordon research group at Iowa State University.

If results obtained with GAMESS are published in the scientific literature, please 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.

The GAMESS user manual and other information can be obtained from http://www.msg.chem.iastate.edu/gamess/

Description

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

Running Program

1.To run GAMESS in the batch queue:

Use the command gmssub to submit a GAMESS (version Mar. 24, 2007 R6) job to the batch queue. Use the command gmssub2 to submit a GAMESS (version Apr. 11, 2008 R1) job to the batch queue. Use the command gmssub3 to submit a GAMESS (version Aug. 11, 2011 R1) job to the batch queue. Usage for gmssub, gmssub2, and gmssub3:

pcluster> gmssub3 nprocs nhours parameter_file [extrabasis]

where nprocs is the number of processors, nhours is the maximum run time in hours per processor, parameter_file is the name of your input parameter file, and extrabasis is an optional argument to give a directory where extra basis sets are located.

Note

• Maximum allowed number of processors per job is 32.
• Maximum cputime per processor for a 1 processor job is 240 hours.
• Maximum cputime per processor for a 2 to 8 processor job is 96 hours.
• Maximum cputime per processor for a 9 to 32 processor job is 24 hours.

For example, to submit a job using 4 processors, using a maximum of 24 hours of runtime per processor, and a parameter file called xxx.inp, type:

pcluster> gmssub3 4 24 xxx

The standard output and error from GAMESS will be written into a file called xxx.log in the example above. Note that if this file already exists, it will be overwritten. However, the file with the results (e.g. xxx.dat in the sample above) will not be overwritten. The job will fail if this latter file already exists.

In the example above, if you have extra basis sets in a directory called basisdir under your home directory, you can submit your job with

pcluster> gmssub3 4 24 xxx ~username/basisdir/

The command gmssub and gmssub2 have the same usage as gmssub3.

Type gmssub, gmssub2 or gmssub3 at your pcluster login prompt to get more information about the maximum number of processors and runtime that you can request per job.

2.To run GAMESS interactively:

First login into the interactive node, which is node19:

pcluster> ssh node19

Then use gmsinter to run the job (version Mar. 24, 2007 R6. To run a job with version Apr. 11, 2008 R1, use gmsinter2. To run a job with version Aug. 11, 2011 R1, use gmsinter3). Usage for gmsinter, gmsinter2, gmsinter3:

node19> gmsinter3 nprocs parameter_file [extrabasis]

where nprocs is the number of processors (up to 8), parameter_file is the name of your input parameter file, and extrabasis is an optional argument to give a directory where extra basis sets are located. A sample run using 4 processors:

node19> gmsinter3 4 xxx

where xxx.inp is your input parameter file. Note that unlike gmssub, gmsinter does not require a maximum time argument.

Note For both batch jobs and interactive ones, scratch files are written in your scratch area (for example, /rcc_scratch/username ) in a subdirectory called gamess.jobid for batch jobs (where jobid is the batch job ID) and gamess.pid for interactive jobs (where pid is the unix ID number for your interactive process). At the end of the job, the scratch files are automatically deleted.

Documentation

http://www.msg.chem.iastate.edu/gamess/

Installation

Compiled with the IBM compilers (xlf 9.1 and xlc 7.0), SYSV and TCP/IP (not MPI) for parallelization.

Version Mar. 24, 2007 R6 is installed in /usr/local/gamess

Version Apr. 11, 2008 R1 is installed in /usr/local/gamess-Apr11-2008R1

Version Aug. 11, 2011 R1 is installed in /usr/local/gamess-Aug11-2011R1

System

Unix (AIX)