GAUSSIAN-Teaching

Category

Chemistry

Program On

Teaching

Version

09

Author / Distributor

See http://www.gaussian.com

Description

Gaussian is a set of programs for performing semi-empirical, density functional theory and ab initio molecular orbital calculations.

NOTE: Users are required to sign a license agreement form before being allowed to run this software. Please fill out the GACRC General Support Form to check if you have permission to use this software.

After you sign the license agreement form and send the signed form to us (or after the course instructor sends your signed form to us) you will be added to the Gaussian group. Then you should be able to run gaussian on this cluster.

Running Program

Also refer to Running Jobs on the teaching cluster.

For more information on Environment Modules on the teaching cluster please see the Lmod page.

Gaussian09 (g09) is installed in /usr/local/apps/eb/gaussian and it was installed without TCP-Linda, so it can only use cores within a single node (and you cannot specify %LindaWorkers larger than one). The number of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete.

For AMD processors:

Gaussian binaries optimized by AMD processors are installed in /usr/local/apps/eb/gaussian/09-AMD-SSE4a. To use this version of Gaussian, please first load the gaussian/09-AMD-SSE4a module and source g09.profile with

module load gaussian/09-AMD-SSE4a

. $g09root/g09/bsd/g09.profile

For Intel processors:

Gaussian binaries optimized by Intel processors are installed in /usr/local/apps/eb/gaussian/09-Intel-SSE4_2. To use this version of Gaussian, please first load the gaussian/09-Intel-SSE4_2 module and source g09.profile with

module load gaussian/09-Intel-SSE4_2

. $g09root/g09/bsd/g09.profile

Example of a shell script sub.sh to run g09 on the batch queue (Intel processors):

#!/bin/bash
#SBATCH --partition=batch
#SBATCH --job-name=testgauss
#SBATCH --ntasks=4
#SBATCH --time=20:00:00
#SBATCH --mem=30gb

cd $SLURM_SUBMIT_DIR

module load gaussian/09-Intel-SSE4_2

. $g09root/g09/bsd/g09.profile

g09 params.com params.log

where params.com is a sample input parameter file that needs to be replaced by the name of the file you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. In this example, the standard output of the g09 command will be saved into a file called params.log.

Please set the --ntasks= variable to be the same number as the number of threads specified in your parameter file (params.com) with the variable %NProcShared, e.g. %NProcShared=4. Please also request as much memory for the job as you set the %Mem keyword in your parameter file.

Submit the job to the queue with

sbatch sub.sh

Gaussian scratch files:

By default g09 jobs generate temporary files called Gau-* in the user's home directory, /home/username. The job automatically deletes these files when it completes successfully. However, if the job crashes (or if you delete a running g09 job), these files are left in your home directory. Please remove leftover temporary files manually so they do not accumulate in your home directory.

Documentation

http://www.gaussian.com

Installation

Built without TCP-Linda, therefore it can only run within one node.

The version for Intel processors is installed in /usr/local/apps/eb/gaussian/09-Intel-SSE4_2

The version for AMD processors is installed in /usr/local/apps/eb/gaussian/09-AMD-SSE4a

System

64-bit Linux