Gaussian

Description

gaussian website  
Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 09 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.

Gaussian License

Please note that Gaussian is restricted software. Users who intend to use it must sign the Gaussian Confidentiality Agreement. This form is available in NPB 2335, 2238, or 2148. You may come by during office hours and sign the agreement. Once the form is signed, you will be added to the "gaussian" user group and will have access to the software. See Gaussian License.

Required Modules

modules documentation

Serial

• gaussian

Parallel (Shared memory with OpenMP)

• gaussian

System Variables

• HPC_GAUSSIAN_DIR
• GV_DIR
• g09root
• GAUSS_BSDDIR
• GAUSS_EXEDIR
• _DSM_BARRIER

Additional Information

There are two mechanisms by which you can submit Gaussian Jobs.

1. Command-line batch Job Submission: See the next section.
2. Galaxy Framework: Galaxy can be accessed at: http://galaxy.rc.ufl.edu. Gaussian is listed in the "Tools" pane under "Chemistry". Please refer to Galaxy for more information on how to use this interface. For specific instructions concerning how to submit a Gaussian job using Galaxy, there is also a step-by-step procedure wiki entry: Gaussian Galaxy

Please see the Gaussian_galaxy-input page for a sample input file to run Gaussian using Galaxy.

Example Job Scripts

See the Gaussian Job Scripts page for sample Gaussian job submission scripts.

Considerations

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 across multiple machines on the Research Computing cluster.

This requires a resource request of the form

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=N

where N is constrained by the number of "cores" (i.e. processors) in a single machine. Most of the hipergator nodes have 32 cores per node.

Using Gaussview GUI

When starting gv via a SLURM GUI Session the following steps must be taken:

• Set gv to use MESAGL instead of OpenGL via 'export USE_MESAGL=1'. See http://csc.cnsi.ucsb.edu/docs/gaussview for reference.

Load modules

module load gaussian gui

Start a GUI session

• Example: running Gaussview with 1 CPU, 8gb of memory, 4 hours of run time

gui start -e gv -c 1 -m 8 -t 4

• Note: Give the session from few seconds to a couple of minutes to start if the output is empty.

$ gui show

The output will look similar to the following e.g. with 1 active sessions and real passwords listed instead of 'REDACTED' in the example:

Current GUI sessions:
______________________________________________________________________________
#:  JobID    Application   Type  State       Reason
1: 51019979 gv            gui   RUNNING     
------------------------------------------------------------------------------
Connection URLs:
1: https://gui3.rc.ufl.edu/13132/?password=REDACTED

[[GUI_Programs#Connect_From_a_Client_Computer|Attach to the resulting xpra session from your local computer]]
______________________________________________________________________________

Please copy a connection URL and paste it into a modern web browser's
location bar on your LOCAL computer located on campus or connected via VPN

Connect To GUI Session

• Attach to the job session in your local browser

Copy and paste a session URI into a modern browser (tested on Firefox and Chrome/Chromium) e.g.

https://gui3.rc.ufl.edu/13132/?password=REDACTED

As a result the browser tab becomes a 'desktop canvas' and the GUI program window should be visible and can be resized or maximized to the limits of the browser tab window as normal.

Stop GUI Session

• To the GUI session, do the following, SessionID is the ID listed above, for example "1" in the above example.

gui stop SessionID

• For help with running GUI programs, please refer to: SLURM GUI Session

Citation

If you publish research that uses gaussian you have to cite it as follows:

Gaussian 09, Revision A.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.