Arkansas High Performace Computing Center [hpcwiki]

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.

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

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 $PBS_O_WORKDIR
cp exam47.inp  /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

rungms exam47 01 1 16 >& exam47.log

mv exam47.log $PBS_O_WORKDIR/

When we run this job we copy over the input file to the /scratch/$PBS_JOBID directory where we will run the computation. Then when the job finishes we move the exam47.log file back to the directory we submitted the job from.

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.