Gaussian
From UF HPC Wiki
Contents |
Overview
Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.
Starting from the basic laws of quantum mechanics, 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. This article introduces several of its new and enhanced features.
WebGauss
There is now a web-based interface for Gaussian called WebGauss.
PBS Sample Submission Scripts
You can find an example of a PBS/Torque job submission script for Gaussian '03 here.
Please note that our version of Gaussian only supports shared-memory parallelism. This means that if you want to use more than one processor for a Gaussian job, you are limited to the number of processors in a single machine. You cannot run Gaussian '03 across multiple machines on the HPC Center cluster.
This forces you to a resource request of the form
#PBS -l nodes=1:ppn=<N> where N <=8 for phase III nodes and N <= 4 for phase II nodes.
GaussWeb
There is now a web-based Gaussian submission system in place for the UF HPC Center. It can be accessed via the following website:
This submission system is currently experimental, so if there are any issues or problems with it, please submit a bug report to Bugzilla detailing what happened.
Submission Scripts
To get the gaussian scripts to autoload when you run your jobs, you can add the following to your submission scripts:
bash
The following are for bash submission scripts. It should be added in your submission script prior to using accessing gaussian. We recommend this over running it as a part of your login script because the gaussian scripts overwrite some environment variables that you do not want to have happen normally.
As of version E.01, Gaussian releases executables optimised for Intel (EM64T) and AMD processors. Selecting the correct version will cause your calculation to run faster, perhaps by as much as 10%. If you use the code under "automatic CPU detection" in your PBS submission script, the script will choose the best version of Gaussian on the computer where it runs. This is the recommended option. Otherwise, you can request the AMD or EM64T version.
Version E.01 (automatic CPU detection)
cpuFamily=`grep -m 1 vendor /proc/cpuinfo | awk -F : '{print $2}'`
case "${cpuFamily}" in
*GenuineIntel*)
g03root="/apps/gaussian/e01/em64t"
;;
*AuthenticAMD*)
g03root="/apps/gaussian/e01/amd64"
;;
*)
echo "Gaussian has no dedicated version for CPU type ${cpuFamily}."
echo "Defaulting to Intel/EM64T version."
g03root="/apps/gaussian/e01/em64t"
;;
esac
source ${g03root}/g03/bsd/g03.profile
Version E.01 (AMD64)
g03root=/apps/gaussian/e01/amd64
source ${g03root}/g03/bsd/g03.profile
Version E.01 (EM64T)
g03root=/apps/gaussian/e01/em64t
source ${g03root}/g03/bsd/g03.profile
Version D.01 (AMD64)
g03root=/apps/gaussian/d01
source ${g03root}/g03/bsd/g03.profile
Version C.02 (AMD64)
g03root=/apps/gaussian/c02
source ${g03root}/g03/bsd/g03.profile
csh/tcsh
The following are for csh/tcsh submission scripts. It should be added in your submission script prior to using accessing gaussian. We recommend this over running it as a part of your login script because the gaussian scripts overwrite some environment variables that you do not want to have happen normally.
Version C.02 (AMD64)
set g03root = /apps/gaussian/c02
source ${g03root}/g03/bsd/g03.login
Version D.01 (AMD64)
set g03root = /apps/gaussian/d01
source ${g03root}/g03/bsd/g03.login
Version E.01 (AMD64)
set g03root = /apps/gaussian/e01/amd64
source ${g03root}/g03/bsd/g03.login
Version E.01 (EM64T)
set g03root = /apps/gaussian/e01/em64t
source ${g03root}/g03/bsd/g03.login
