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GAMESS on Mimosa
GAMESS on Mimosa has been recently upgraded, the latest source code was obtained from Gordon Research Group at Iowa State
and it has been built with the Portland Group compilers version 5.2 (pgi-5.2).
With this upgrade there have been several changes in the way GAMESS functions and the way we invoke GAMESS, some of which are:
- GAMESS brings about parallization by using the recomended DDI instead of MPI as it used to be before
- Hence GAMESS is invoked differently, we use a script called "rungms" instead of "gamess-mpi" to invoke it
- The number of processors supplied to GAMESS as a parameter is the same as that specified to PBS, unlike before when it used to be half!
- Memory is allocated within in GAMESS as multiples of "word", where a word size is defined as 8 bytes
- When we invoke GAMESS, it does not need to know the location of PGI (Portland group compilers), we have built
GAMESS using PGI-5.2 but we do not need to know where it lies when GAMESS is running
So please read the new documentation on using GAMESS on Mimosa, especially the document on inputs to GAMESS.
Invoking GAMESS on Mimosa
When we submit a GAMESS PBS job, within the PBS script, GAMESS is invoked on Mimosa using the script, "rungms" as follows:
rungms $JOB $NCPUS $PTMP >& exam01.log
- rungms: This script resides in /usr/local/apps/bin, If this location is not in your path please add it to your path
or invoke it using the complete file location: /usr/local/apps/bin/rungms
- $JOB:
This is the name of the input file you want to use without the ".inp" extension, for example if the name
of the input file is exam01.inp, $JOB is set to exam01. If this parameter is bad or if it is not specified, GAMESS will fail
and exit.
- $NCPUS:The number of CPUS that GAMESS will run parallely on. This parameter ha sto be exactly same as the "nodes"
paramter specified to PBS
- $PTMP:A location on users permanent disk space, where the text files will be written out by GAMESS, its the users
job to delete the text files after every run. Note: The $PTMP parameter does not specify the location for scratch files where GAMESS
writes out all its binary files during an execution. This paramter is set to "/tmp" on the local nodes to facilitate faster
access. The scratch files are deleted automatically by GAMESS
NOTE:
Memory: The specifications for memory has changed, please read the documents On inputs to GAMESS, before you create input files that specify memory requirements. Memory is allocated within GAMESS as
words, where the size of word is 8 bytes. Also remember that the maximum amount of memory available to use is 512MB on each node.
Sample PBS script for GAMESS on Mimosa
The GAMESS application is invoked using the script "rungms" that resides in /usr/local/apps/bin, if this location is not in your path,
do add it to path. In this example we have a parallel execution of GAMESS using 4 processors.
[jghale@mimosa gamess]$ cat sample.pbs
#PBS -S /bin/bash
#PBS -l cput=2:00:00
#PBS -l nodes=4
#PBS -l mem=32MW
# Change to your working directory, where your input file should also be
cd /ptmp/$USER/gamess
# PTMP is the users permanent disk space used to store the text files returned
export PTMP=/ptmp/$USER/gamess
# NCPUS is the number of processors required same as the "nodes" parameter of PBS
export NCPUS=4
# JOB is the input file of the job to run minus the ".inp" extension
export JOB=exam01
rm $PTMP/exam01.dat
rm $PTMP/exam01.irc
rm sample.pbs.o*
rm sample.pbs.e*
rm exam01.log
rungms $JOB $NCPUS $PTMP >& exam01.log
[jghale@mimosa gamess]$
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