Gaussian03

Systems & Access :: Learning to Use :: Linux Computing Resource

The user should be a part of the 'g03' UNIX group to run Gaussian03. Before running Gaussian03, the user should set up the environment with the following command. The same command needs to be in your .login as well.

if (-e /usr/usc/gaussian/g03-B05/setup.csh) then
  source /usr/usc/gaussian/g03-B05/setup.csh
endif

Use the command 'g03' to run the scalar version of Gaussian03. Use the 'g03l' (last character is a lowercase 'L') command to run the parallel (Linda) version of Gaussian03. While using the parallel version of Gaussian03, you need to specify the number of processors to be used in the '%nproc' as a link 0 command in your Gaussian program. The following should be the first few lines of your Gaussian program:

%chk=/scratch/test.chk
%mem=80MW
%NProcShared=2
%NProcLinda=4

Note: The %NProc options listed above make Linda utilize four nodes and two processes in each node.

Users are not required to manually source PGI compiler's setup file. However, if the user needs a particular version of a PGI compiler, then that PGI compiler's setup file should be sourced before sourcing gaussian's setup file. The user should not override the following variables' default values: PGI, PGIDIR, GAUSS_SCRDIR, and GUASS_LFLAGS.

The following is a sample PBS script file for running Gaussian programs. To learn more about PBS, please refer to the Portable Batch System section.

#!/bin/csh

#** The "#PBS" lines must come before any 
##** non-blank non-comment lines ***

##**PBS -l walltime=1:00:00,nodes=1:ppn=4
##**For almaak remove comments on the above line 
##**and comment out the line below

#PBS -l walltime=1:00:00,nodes=2:ppn=2

#The following should contain your program and any arguments
set inputfile  = "./test.com"		# G03 Input file

set outputfile = "test.out"		# G03 Output file

if ($?PBS_JOBID) then		# if this is a PBS job
  echo "Starting" $PBS_JOBID `date`
  echo "Initiated on `hostname`"
  echo ""
  cd "$PBS_O_WORKDIR" || exit 1		# connect to working directory of qsub
  cp -v $inputfile /scratch/ || exit 1	# Copy the input file to /scratch
					# if you run on the linux cluster
  cd /scratch || exit 1
else
  echo "This script must be run as a PBS job"
  exit 1
endif

if ($?PBS_NODEFILE) then
  #count the number of processors assigned by PBS
  set NP = `wc -l < $PBS_NODEFILE `
  echo "Running on $NP processors: "`cat $PBS_NODEFILE`
else
  echo "This job did not have the number of nodes specified with"
  echo "the node= resource"
  exit 1
endif

# run the program on the linux cluster using Linda
  g03l < `basename $inputfile` > `basename $outputfile`

set ret = $?

## For almaak use the following line and comment out the previous line
## g03 < $inputfile >& $outputfile

cp -v /scratch/* $PBS_O_WORKDIR		# Copy all the output and temp files 
					## from /scratch to home directory

echo "Done   " `date`

exit $ret