Gaussian16 LINDA

This document provides basic information for using Gaussian software on the Nurion system. Therefore, it does not include instructions on how to use Gaussian software or Nurion/Linux. For information on using Nurion/Linux, please refer to the Nurion user guide available in the resources section of the KISTI website (https://www.ksc.re.kr).

A. Gaussian Introduction

Gaussian is a molecular modeling package used to predict energy, molecular structure, and vibrational frequencies, designed for researchers in chemistry, physics, life sciences, and engineering.

For more detailed information, please visit the Gaussian company's website. Website address: http://gaussian.com

B. Installation version and License

• KISTI Supercomputing Center holds a site license for Gaussian 16/LINDA, and Gaussian16 Rev. A03 is installed.

• To use Gaussian16, your account must be registered in the Gaussian group (gauss group). To register for the Gaussian group, please contact the KISTI website or email [e-mail].

• You can check if your account is part of the Gaussian group as follows:

$ id user ID

※ If your account is included in the Gaussian group, the output should contain "1000009(gauss)."

• Due to security reasons, users do not have access to the program's source code, only to the executable file and basis functions. This does not affect your ability to use the program.

• To use a program linked with Gaussian, you may need access to certain source code or shell files (e.g., Gaussrate). In this case, you should request access through the KISTI website or by emailing [e-mail].

• Both HF and DFT calculations can be performed in parallel.

C. How to Run the Software

1. Settings

Gaussian16 can be loaded using the module command.

$ module load gaussian/g16.a03.linda

2. Writing a scheduler job script file

• On the Nurion system, jobs must be submitted from the login node using the PBS Pro scheduler.

• Example files for using PBS on the Nurion system are available at the path below, and you can refer to them when creating your job file.

※ The following is an example of using Gaussian16 LINDA on the Nurion system.

• File location: /apps/commercial/test_samples/G16/g16_Linda.sh

#!/bin/sh
#PBS -V
#PBS -N gaussian_test
#PBS –q norm_cache          # Specify the PBS queue
#PBS -l select=2:ncpus=64:mpiprocs=1:ompthreads=64
#PBS –l walltime=01:00:00     # Specify the estimated job duration (hh:mm:ss)
#PBS -A gaussian
cd $PBS_O_WORKDIR

module purgemodule load gaussian/g16.a03.linda

nodes=`cat $PBS_NODEFILE`
nodes=`echo $nodes | sed -e 's/ /,/g'`
export GAUSS_SCRDIR="/scratch/${USER}"
export GAUSS_WDEF=${nodes}
export GAUSS_PDEF=$NCPUS

g16 test000.com

exit 0

• After March PM (March 14) in 2019, job submissions will not be accepted without the #PBS -A gaussian option.

• The GAUSS_PDEF variable is equivalent to the %NProcShared option,

• If the input file contains a %NProcShared value, that value will be applied.

  • The value for GAUSS_PDEF or the %NProcShared option should be set according to the compute node—68 cores for Nurion KNL compute nodes and 40 cores for SKL compute nodes—to ensure optimal computational performance.

• Gaussian16 Rev. The maximum number of threads supported by the A03 version is 64. When using KNL compute nodes, please use no more than 64 threads.

• Job submission is only allowed in the scratch directory.

• Each user's scratch directory is located at /scratch/$USER.

• The queue name should be set according to the Nurion user guide, generally to "normal."

• If you create a Gaussian input file on your PC and transfer it via FTP, make sure to transfer it in ASCII mode.

• For other PBS commands and usage instructions, please refer to the Nurion user guide.

3. How to Use GaussView

• GaussView is a GUI-based program and can be run on MyKSC (web service portal) through VNC (remote desktop) (refer to the MyKSC VNC usage guide)

• It is recommended to use GaussView on MyKSC VNC for input data creation and result analysis, given the limitations of allocated computational resources, while full computational jobs should be executed via the batch job scheduler.

GaussView execution screen on MyKSC VNC

D. Reference materials

• For those new to Gaussian, it is recommended to read the following book.

  • James B. Foresman and Aeleen Frisch, "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian", It can be purchased from online bookstores such as www.amazon.com and www.bn.com, or directly from http://gaussian.com.

• All information about Gaussian can be found on the Gaussian company's website (http://gaussian.com)

Last updated on November 06, 2024.