Software: Gaussian on HPCC

FRIDAY, December 16 |  By Chun-Min Chang, Xiaoxing (Adele) Han and Camille Archer

> What is Gaussian?

Gaussian 16 is a popular quantum computational simulation tool among computational chemists. It is widely used for electronic structure simulations and calculations, such as single point energy and properties (electron density, dipole moment, etc.), geometry optimization, frequency and following reaction paths. For a full list of ways Gaussian 16 can help your research visit: http://gaussian.com/relnotes/

> GaussView

GaussView is a graphical interface for Gaussian. With GaussView, users can build molecules or reactive systems, set up Gaussian input files and graphically examine results. To learn more about GaussView, please visit: http://gaussian.com/gaussview6/

> How to use GaussView on MSU’s HPCC

  • Connect to HPCC using either Microsoft Remote Desktop or open a terminal.
  • For a faster graphical interface, please use the Web-based Remote Desktop Protocol to connect to HPCC.
  • ssh to a development node. At the command line, type:

                                          $ module load Gaussian/g16
                                             $ gview

  • Use GaussView to create molecular geometry.

To learn more about using GaussView, please visit:  http://gaussian.com/wp-content/uploads/dl/gv6.pdf

> Using Gaussian 16 on MSU’s HPCC via command lines

There are two ways to use Gaussian 16 at command lines – Interactive mode and Batch mode with job submission. 
1)  Interactive submission: To run your calculations via command lines, type:  

                                             g16 < "input file name" > "output file name"
Note: 

  • Input and output file names can be provided with absolute or relative paths.
  • Gaussian temporary files can be redirected by setting GAUSS_SCRDIR environment variable. For example:

                                GAUSS_SCRDIR=/mnt/scratch/$USER/GAUSS_SCRDIR

2)  Batch mode job submission
With batch mode submission, users do not need to wait in front of the computer for the job to start. Simply write a job script to schedule a job on HPCC. The job will start automatically once the resources are available. Here are some links for writing a job script:

Tips for writing a better Gaussian job script:

  • By default, Gaussian requests only one core, if your calculation requires more cores or more memory, use the Gaussian input file to specify your request. For more details on how to request cores and memory in your Gaussian input file, refer to http://gaussian.com/link0/
  • If you need to submit a job, please request the same number of cores in the job script.  For memory, please request more than in the Gaussian input file to ensure that Gaussian can allocate enough memory for your calculation.

> Using Checkpoint Run

Gaussian’s checkpoint run feature helps users to save results automatically and restart from the place where the last calculation ends.  This feature is helpful for:

  • HPCC users that need calculation time longer than 7 days
  • Non buy-in users who want to break a long job into many short jobs (with walltime less than 4 hours) so they are able to use all computing nodes.

To use Checkpoint run for your job, please follow the instruction below:

  • In the Gaussian input file, specify restart mode for your calculation. For more details please refer to: http://gaussian.com/restart/.
  • If the job does not finish within the walltime, ensure that it will automatically resubmit another job to restart.
  • Keep submitting jobs until the calculation is finished.

We hope this article is helpful for you. If you have any questions about Gaussian, feel free to submit a ticket at http://contact.icer.msu.edu or come to the ICER Open Office Hour from 1 pm to 2 pm on Mondays and Thursdays in:

Institute for Cyber-Enabled Research
Biomedical & Physical Sciences Building
567 Wilson Rd, Room 1440
East Lansing, MI 48824

 

 About the author:

Chun-Min draws on his experience in quantum mechanical and molecular dynamics simulations to help HPCC users hone their research to best utilize ICER’s supercomputing facilities. Contact him>>