gamess¶

Summary

Source: https://www.msg.chem.iastate.edu/gamess/index.html
License: Free but you must agree to the license terms: https://www.msg.chem.iastate.edu/gamess/License_Agreement.html
Path: /software/gamess
Documentation: https://www.msg.chem.iastate.edu/gamess/documentation.html
Citation: if results obtained with GAMESS are published in the scientific literature, you have to 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. You agree to honor the request to cite additional papers, as appropriate.

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.

Using gamess with an alternative launch script¶

The original rungms script is a long c-shell-beast, invoking a few other scripts on the way to executing the binary. The installed rungms is NOT configured. You would need to obtain a copy and adjust it according to your needs.

Alternatively and to make handling a bit easier we offer a simplified bash-script named rgms. For a description of the original script see below.

module load maxwell gamess
rgms
   rgms -i input [-c cores] [-t threads] [-l logn] [-h] [-v]

       -i|--input   name of input file with or without .inp extension

       -c|--cores   cores (MPI-threads) used per node (default: all physical cores) 
       -l|--logn    gamess logical nodes (default: 0)
       -t|--threads used per node. Identical to setting OMP_NUM_THREADS (default: 1)

       -h|--help    display this
       -v|--verbose display debug information 

    Defaults:
        number of nodes: 1 or number of SLURM nodes
        USERSCR:         /home/user/gamess/restart
        TMPDIR:          /scratch/user
        OMP_NUM_THREADS: 1

Some notes¶

There are two options to run gamess on Maxwell

you run it interactively. In this case, the script forces to run on a single node, without slurm-support. The script will per default use all physical cores.
you run it as a slurm batch-job. The script uses again all physical cores by default, and all nodes allocated to this job. It assume that all nodes have an identical number of cores!

The number of threads is controlled by '-t' OR OMP_NUM_THREADS. rgms will by default assume a single thread. Running some simple tests (see below for some benchmarks), it appears best to use a smaller number of cores and rather increase the number of threads.

Note however, that the use of GDDI NGROUP>0 does not seem to work for OMP_NUM_THREADS>1. rgms does not enforce it, but if you run into MPI errors while running GDDI-jobs with OMP_NUM_THREADS>1, try to run it with OMP_NUM_THREADS=1 instead.

Sample batch script¶

#!/bin/bash
#SBATCH --partition=maxcpu
#SBATCH --time=4-00:00:00  
#SBATCH --constraint='[75F3]'
#SBATCH --nodes=4
unset LD_PRELOAD
unset TMPDIR

source /etc/profile.d/modules.sh
module purge

target=l-e7402-n4

np=$(nproc)

export CORES=4
export THREADS=$(( $np / $CORES ))

/software/gamess/2023R1/rgms -i $target -c $CORES -t $THREADS  > $target.log