Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. We have Gaussian g03 D.01 with Linda 7.1 installed.

To load Gaussian type the following:

$ module load md/gaussian-g03.d01

Gaussian and Linda are both commercial software. They require licenses to use. If you have a license let us know (send an email to help@cse) and we will enable access for you to use this software.

Here is an example submit script that will run test #727 from the distribution using 8 cpus. To submit just type qsub submit.sh.

#!/bin/sh
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -N gausstest
#$ -e 727.err
#$ -o 727.out
#$ -pe linda 8

# Load the gaussian environment
module load md/gaussian-g03.d01

infile=~/gaussian/727/test727.com
tmpinfile=$TMPDIR/infile.com
outfile=~/gaussian/727/test727.log

# Populate the input file with the nodes SGE gives us
# nprocshared = number of cpus per node
# nproclinda = number of nodes
# lindaworkers = CSV hostnames (ie "ecompute-5-1,ecompute-5-2")
awk -v nprocshared="4" -v nproclinda="2" -v lindaworkers="`cat $TMPDIR/machines`" -f $g03root/sge_linda.awk $infile > $tmpinfile

time g03l < $tmpinfile > $outfile

The awk line in the above script just makes sure Gaussian knows how many CPUs you have been allocated, how many nodes, and which nodes. The only thing that you need to modify is the nproclinda option.

Gaussian allows you to specify where to put temporary files. This is specified in the input file. The following will use a file called scott.rwf in the directory /state/partition1 for scratch space.

    %RWF=/state/partition1/scott
    %NoSave

The No Save option removes the temporary file after the run completes.

For more information see this online documentation.

By default Gaussian 03 will put the checkpoint file into your current working directory. However you may want to save this file in order to restart your job or visualize your result. You can name your checkpoint file in the input file, for example by:

    %Chk=/home/foo/gaussian/727/727

the checkpoint file will be saved in /home/foo/gaussian/727 as 727.chk.

Note: Saving the checkpoint file over NFS will likely slow your job down.

There is a help program installed called ghelp. Once you load Gaussian into your environment it will be in your path. You can also browse the online documentation.

$ ghelp
         
         

  to get help on a particular topic type:
         
         ghelp <topic>   
  or     
         
         ghelp <topic> <sub-topic> ...   
         
  '<topic>' or <sub-topic> may be the name of some particular    
  information desired, one of the special words 'topics' or      
  'options', or the wild card symbol '*'.  abbreviations are allowed     
  for any name, but no checking for ambiguity is done.   
         
  example:       
  --------       
       ghelp route rhf   
         

 Other information available:
  buckets          common           fileio           geometry        
  ghelp            introduction     l101             l103            
  l202             l401             ov4              l502            
  l503             l506             l601             l602            
  l1002            l9999            loop             ov1             
  ov3              ov5              ov6              ov7             
  ov8              ov9              putil            recursion       
  recursion        restart          route            links           
  rwf              references       util             general_basis   
  Utilities        c8695            chkmove          cubman          
  cubegen          g03opt           ham506           mm              
  formchk          newzmat          rwfdump          testrt          
  unfchk           Browse           Archive          arctmp          
  crendx           reform