Uppsala Multidisciplinary Center for Advanced Computational Science

GAMESS-US user guide

GAMESS-US versions 20070324R1, 20101001R1, and 20110818R1 are installed on Milou. No GAMESS is installed on Rackham, but this can be done on request.

Citing GAMESS papers

It is essential that you read the GAMESS manual thoroughly to properly reference the papers specified in the instructions. All publications using gamess should cite at least the following paper:

@Article{GAMESS,
author={M.W.Schmidt and K.K.Baldridge and J.A.Boatz and S.T.Elbert and
M.S.Gordon and J.J.Jensen and S.Koseki and N.Matsunaga and
K.A.Nguyen and S.Su and T.L.Windus and M.Dupuis and J.A.Montgomery},
journal={J.~Comput.~Chem.},
volume=14,
pages={1347},
year=1993,
comment={The GAMESS program}}

The GAMESS documentation can be found in /sw/apps/gamess/x86_64/RELEASE, where RELEASE is 20070324R1 or 20101001R1, or 20110818R1-*, as six text files:

INPUT.DOC INTRO.DOC IRON.DOC PROG.DOC REFS.DOC TESTS.DOC

If you need to obtain GAMESS yourself, please visit the GAMESS website for further instructions.

Running GAMESS


Instructions for Milou

On milou, release 20070324R1, 20101001R1, and 20110811R1 are installed. They have been compiled with the intel compiler using the mkl math library. Load the preferred version using

module load gamess/20070324R1

or

module load gamess/20101001R1-kalkyl-intel-12.1-mvapich2

or

module load gamess/20110818R1-kalkyl-intel12.0-mvapich2

Below is an example submitscript for Milou, running on 32 cores (2 nodes with 16 cores each). It is essential to specify the project name:

#!/bin/bash -l
#SBATCH -J jobname
#SBATCH -p node -n 32
#SBATCH -A PROJECT
#SBATCH -t 03:00:00
 
module load gamess/20110818R1-kalkyl-intel12.0-mvapich2
 
rungms gms >gms.out

Memory specification

GAMESS uses two kinds of memory: replicated memory and distributed memory. Both kinds of memory should be given in the $SYSTEM specification. Replicated memory is specified using the MWORDS keyword and distributed memory with the MEMDDI keyword. It is very important that you understand the uses of these keywords. Check the GAMESS documentation for further information.

If your job requires 16MW (mega-words) of replicated memory and 800MW of distributed memory, as in the example below, the memory requirements per CPU core varies as 16+800/N where N is the number of cores. Each word is 8 bytes of memory, why the amount of memory per core is (16+800/N)*8. The amount of memory per node depends on the number of cores per node. Milou and Tintin both have 16 cores per node. Also take into account that some memory (per core) is required for the program code itself and for local variables at least 200MB should be added to the numbers of memory per core.

Use the information below as a guide to how many CPUs to request for your calculation:

On Milou:

174 nodes with two 8-core CPUs and 128GB memory
17 nodes with two 8-core CPUs and 256GB memory
17 nodes with two 8-core CPUs and 512GB memory


Communication

For intra-node communication shared memory is used. For inter-node communication MPI is used which uses the Infiniband interconnect.