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gamess

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Gamess

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. It is maintained by Mark Gordon's research group at Iowa State University. Source code, documentation and examples are available at the GAMESS website.

Environment Setup

You will need to add these lines to your $HOME/.bashrc file to load the dependencies for the Gamess module. This will load the dependencies when you login to the system, however if you can also add these lines to your scripts instead.

module load mkl/12.1.5
module load intel/12.1.5
module load mvapich2/1.8
module load gamess

Serial Example

Create a directory to specify where to run the examples named GAMESS-JOBS in your $HOME directory, and copy one of the example files from /share/apps/gamess/test/standard. In this example we use file exam47.inp.

razor-l3:jokinsey:~$ mkdir GAMESS-JOBS
razor-l3:jokinsey:~$ cp /share/app/gamess/test/standard/exam47.inp GAMESS-JOBS/

Create a script named gamess.pbs, with your favorite text editor, in your $HOME/GAMESS-JOBS directory to run our example job.

#!/bin/bash
#PBS -N gamess
#PBS -q tiny16core
#PBS -j oe
#PBS -o gamess.$PBS_JOBID
#PBS -l nodes=1:ppn=16
#PBS -l walltime=1:00:00

cd $PBS_O_WORKDIR

rungms exam47 01 1 16 >& exam47.log

Notice the 3 numbers following the input file name in the last line of the script. 01 stands for a version number of the GAMESS executable (this number will not change since we have a single comipled version of gamess labeled gamess.01.x). The next number 1 is the number of parallel processes to run (all of the example input files provided with gamess are small and have to be executed serially). 16 is the number of cores per node (in the queue tiny16core each node has 16 cores). Submit the job to the queue:

razor-l3:jokinsey:~/GAMESS-JOBS$ qsub gamess.pbs

This should yield two files as output a schedule file for the job and a file exam47.log, which holds the most important information.

Parallel Example

Since all of the standard examples are small and must be executed serially we have to use a custom example that has been added to demonstrate Gamess's parallel functionality. This is a larger example located in /share/apps/gamess/tests/custom, which we will add to our $HOME/GAMESS-JOBS directory to run.

razor-l3:jokinsey:~$ cp /share/apps/gamess/tests/custom/azobiscis-3CH2NO2-pentazole-g3mp2.inp ~/GAMESS-JOBS
razor-l3:jokinsey:~$ cd GAMESS-JOBS/

Create a gamess.pbs to run this job or edit the one from the serial example.

#!/bin/bash

#PBS -N gamess
#PBS -q tiny16core
#PBS -j oe
#PBS -o gamess.$PBS_JOBID
#PBS -l nodes=3:ppn=16
#PBS -l walltime=2:00:00

cd $PBS_O_WORKDIR

rungms azobiscis-3CH2NO2-pentazole-g3mp2  01 48 16 >& azobiscis-3CH2NO2-pentazole-g3mp2.log

You may notice we changed the number of nodes to 3 and the time to 2 hours. The input and log files were changed to reflect the example and the number of parallel processes was changed to 48.

Submit the job and when its done the relevant output will be in the azobiscis-3CH2NO2-pentazole-g3mp2.log file.

razor-l3:jokinsey:~/GAMESS-JOBS$ qsub gamess.pbs
gamess.1506019167.txt.gz · Last modified: 2017/09/21 18:39 by jokinsey