Difference between revisions of "Gaussian"
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gui stop SessionID
gui stop SessionID
''For help with running GUI programs, please refer to: [[GUI Programs|SLURM GUI Session]'
''For help with running GUI programs, please refer to: [[GUI Programs|SLURM GUI Session]'''
Revision as of 17:22, 28 April 2020
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.
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.
There are two mechanisms by which you can submit Gaussian Jobs.
- Command-line batch Job Submission: See the next section.
- 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.
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.
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.
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 stop 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: [[GUI Programs|SLURM GUI Session]
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.