Gaussian Guide

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Revision as of 11:18, 8 April 2016 by Pan14001 (talk | contribs) (Match ntasks to nprocs)
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Gaussian electronic structure modeling
Author Gaussian Inc
Website gaussian.com
Source Proprietary Closed Source
Category Quantum Chemistry
Help User guide
Workshops


From Wikipedia:

Gaussian is a computer program for computational chemistry initially released in 1970 by John Pople and his research group at Carnegie-Mellon University. Originally available through the Quantum Chemistry Program Exchange, it was later licensed out of Carnegie Mellon University, and since 1987 has been developed and licensed by Gaussian, Inc.

Extra Step before Use

Due to the way Gaussian is built by the Gaussian Inc company, you must contact us to add you to the gaus09.D.01 Linux group to have permission to run the program. You can check whether you are in the group by running the groups command. You should see your Net ID and gaus09.D.01 listed.

Loading the Gaussian module

Best practise is to specify the module with the version number for programs to run consistently. To see the versions of modules on the cluster, use the module avail command:

module avail gaussian

Now we can load the latest available LAMMPS module, which at the time of writing is 28Jun14:

module load gaussian/09.D.01

One can avoid loading the module at each log in, by using module initadd:

module initadd gaussian/09.D.01

Running Gaussian

Our site license for Gaussian does not include TCP-Linda software to run on multiple nodes.

Below is a SLURM example script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --exclusive

# Make sure the value of --ntasks above matches %nproc in your
# Gaussian input ".com" file!

# Run gaussian, using output file of gaussian.out
g09 < your_file.com > gaussian.out

In your Gaussian input .com file, always specify the number of processors using %proc and the amount of memory using %mem (the default memory is just 256MB!). Conservatively one can use about 80% of the node memory, so for Haswell 128GB RAM nodes we can set 100GB, and use all 24 cores if we use the node exclusively.

%proc=24
%mem=100GB

There are a range of tests on can try with Gaussian as listed in /apps2/gaussian/09.D.01/g09/tests/tests.idx

For example one can try running test 296:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --exclusive

# Make sure the value of --ntasks above matches %nproc in your
# Gaussian input ".com" file!

# None of the test files that Gaussian provides make use of %proc.
# For the sake of testing we will add the line %proc to the beginning
# of a Gaussian test input file.
test_file=test0296.com
cp /apps2/gaussian/09.D.01/g09/tests/com/${test_file} .
sed -i -e "1 s#^#%nproc=8\n%mem=100GB\n#" ${test_file}

# Run gaussian, using output file of gaussian.out
g09 < ${test_file} > gaussian.out