GAMESS: Quick Run with MPI method

GAMESS, a quantum chemistry program package, is executed using rungms script, provided by program developer. It is okay to use rungms for running GAMESS calculation in single or parallel with SMP method. But, for running with MPI parallel method especially on Linux cluster, you may find that it is quite difficult setting up or modifying the rungms script. So we can write our own rungms-like script for GAMESS in combination with MPI method.

The following code is my rungms script, called rungms.MPI. Comparing an original rungms with my rungms.MPI, you can see that they are very different. A rungms.MPI is very compact and user friendly. With rungms.MPI script, you can understand how many parameter and environmental variables you have to define for GAMESS calculation. By the way, each code portions is documented with comment message after # symbol.

#!/bin/csh

# rungms.MPI is a rungms-like script for executing GAMESS calculation on

# distributed memory parallel system using MPI protocol.

# This script is tested on TAIWANIA cluster, NCHC, Taiwan, Intel Xeon

# cluster equiped with Intel Omni-Path high-speed interconnect.

# GAMESS on TAIWANIA was built with Intel Parallel Studio XE 2018 update 1

# and Intel Math Kernel Library (MKL) and Intel MPI library.

# Updated 20180708  Rangsiman Ketkaew  rangsiman1993@gmail.com

# https://github.com/rangsimanketkaew/QM-on-TAIWANIA/

###########################################################################

echo "/*****************************************************************************"

echo "This calculation was carried out by GAMESS program package executed by using"

echo "subgmsmpi program and rungms.MPI script, written by Rangsiman Ketkaew"

echo "Computational Chemistry Research Unit, Department of Chemistry,"

echo "Faculty of Science and Technology, Thammasat University, Thailand."

echo "rangsiman1993@gmail.com and https://github.com/rangsimanketkaew/QM-on-TAIWANIA"

echo "*****************************************************************************/"

echo ""

#      TARGET is normally set to mpi in order to enable MPI method.

#      SCR & USERSCR directories are set to directory where is

#      network shared-file system, which large enough to store the

#      temporary scratch files.

set TARGET=mpi

set SCR=TEMPLATE_1

set USERSCR=TEMPLATE_2

set GMSPATH=TEMPLATE_3

echo "Configuration and Settings created by rungms.MPI script."

echo "========================================================"

echo "TARGET  is set to $TARGET"

echo "SCR     is set to $SCR"

echo "USERSCR is set to $USERSCR"

echo "GMSPATH is set to $GMSPATH"

echo ""

#      USER-defined MPI executable. Default setting is 'mpiexec' of

#      Intel Studio Suite 2018

set CHECK_MPI = `which mpiexec.hydra`

if ( -e $CHECK_MPI ) then

  set MPIEXE = "$CHECK_MPI"

  echo "MPI executable is $MPIEXE"

  echo ""

else

  echo "Error: Intel MPI executable 'mpiexec.hydra' not found."

  echo "This GAMESS runtime was built with Intel compiler and Intel MPI library."

  echo "please purge all loaded module and load Intel module, e.g. 'intel/2018_u1'."

  echo "If you have problem about Intel MPI, please talk to admin/staff of HPC."

  exit 1

endif

#      The following command lines are carefuly extracted from the

#      original rungms. Please carefully modify the code in case

#      you want to change the default setting. However, the default

#      setting is the best solution.

set GET_JOB=$1

set VERNO=$2

set NCPUS=$3

echo "Assgined input file    is $GET_JOB"

echo "GAMESS program version is $VERNO"

echo "Number of processors   is $NCPUS"

echo ""

set JOB = `basename $GET_JOB .inp`

#      Copy input to scratch directory.

#      and define the path of all relavant files.

cp $JOB.inp $SCR/$JOB.F05

setenv INPUT $SCR/$JOB.F05

setenv TRAJECT $USERSCR/$JOB.trj

setenv RESTART $USERSCR/$JOB.rst

setenv DATA $USERSCR/$JOB.dat

echo "Following environment variables were set by SETENV command."

echo '$INPUT  ' "Input file      is $INPUT"

echo '$TRAJECT' "Trajectory file is $TRAJECT"

echo '$RESTART' "Restarting file is $RESTART"

echo '$DATA   ' "Data file       is $DATA"

#      Delete trajectory and scratch files of previous calculation.

if ( -e $TRAJECT ) then

  rm $TRAJECT

  echo "$TRAJECT of previous calculation has been deleted."

endif

if ( -e $RESTART ) then

  rm $RESTART

  echo "$RESTART of previous calculation has been deleted."

endif

if ( -e $DATA ) then

  rm $DATA

  echo "$DATA of previous calculation has been deleted."

endif

echo ""

if ( ! -e $GMSPATH/gms-files.csh ) then

  echo "Error: gms-files.csh not found in $GMSPATH directory."

  exit 1

endif

source $GMSPATH/gms-files.csh

echo "GAMESS execute command: $MPIEXE -n $NCPUS $GMSPATH/gamess.$VERNO.x $INPUT"

echo ""

#      GAMESS is clever to recognize input file from $JOB environment variable.

#      Print of output will be defined in submission script of server scheduler.

#      Normally, as default setting, base name of input will be used to name

#      output automatically.

$MPIEXE -n $NCPUS $GMSPATH/gamess.$VERNO.x

#      For run quick test on front-end node, the above command is validate.

It can run easily by using following command

export OMP_NUM_THREADS=1

rungms.MPI input.inp 00 N >& output.out

Rangsiman Ketkaew