CategoryChemistry, Quantum chemistry, DFT
DescriptionGaussian computational chemistry software initially released in 1970 by John Pople and his research group at Carnegie-Mellon University. It is used for electronic structure optimization and for the calculation of atomic and molecular properties.
Available versions (Euler, old software stack)
|Legacy versions||Supported versions||New versions|
Environment modules (Euler, old software stack)
|Version||Module load command||Additional modules loaded automatically|
|09d1||module load gaussian/09d1|
|09d1_nbo31||module load gaussian/09d1_nbo31|
This module works only if you are authorized to use Gaussian on Euler. If not, you will get an error:
ERROR: You are not authorized to use Gaussian on Euler. Please contact 'firstname.lastname@example.org' for assistance.Only after you have agreed to the license agreement, we can add you to the Gaussian user group on Euler.
How to submit a jobYou can submit a Gaussian computation for the input file test000.com in batch mode with the following command.
bsub [LSF options] -R "rusage[scratch=500]" g09 test000
The results of the simulation will be stored in a file called test000.log. LSF options are documented on the wiki page about using the batch system. Please note that you need to request scratch space in any case. The batch system automatically sets
GAUSS_SCRDIR=$TMPDIRwhich forces Gaussian to write temporary file during the calculation into the local scratch of the compute node. Using a local scratch directory offers some significant advantages, as for instance there is no risk to fill up your home directory and you get a very high I/O performance.
Parallel jobsYou can run Gaussian jobs in parallel using the shared-memory model only. Distributed memory is not supported because Linda, the tool used by Gaussian to distribute a computation over multiple nodes, is not available. In order to run a Gaussian computation in parallel on N CPUs, you need to specify the number of cores in the Gaussian input file. Please note that the memory size indicated in Gaussian's input file is for the whole computation, whereas the size indicated in the bsub command is per CPU. This difference does not matter if you are using only one CPU. However, if you are doing a parallel computation, you must adjust the size accordingly. Let's assume that your computation needs 4 CPUs and 8 GB (8192 MB) of memory:
You should therefore request 8192 MB / 4 CPUs + 25% safety margin = 2560 MB / CPU, hence:bsub -n 4 -R "rusage[mem=2560]" ...
ExampleAs a test case, we run a single point calculation for a water molecule using the Hartree-Fock method.
[leonhard@euler04 gaussian]$ cat test000.com # SP, RHF/STO-3G punch=archive trakio scf=conventional Gaussian Test Job 00 Water with archiving 0 1 O H 1 0.96 H 1 0.96 2 109.471221 [leonhard@euler04 gaussian]$ module load gaussian/09d1 [leonhard@euler04 gaussian]$ bsub -n 1 -W 1:00 -R "rusage[mem=512,scratch=2048]" g09 test000 Gaussian job. Job <25727915> is submitted to queue <normal.4h>. [leonhard@euler04 gaussian]$ bjobs JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 25727915 leonhard PEND normal.4h euler04 *9 test000 Aug 25 10:45 [leonhard@euler04 gaussian]$ bjobs JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 25727915 leonhard RUN normal.4h euler04 e1256 *9 test000 Aug 25 10:45 [leonhard@euler04 gaussian]$ bjobs No unfinished job found [leonhard@euler04 gaussian]$ grep "E(RHF)" test000.log SCF Done: E(RHF) = -74.9607232756 A.U. after 7 cycles
The energy is specified in atomic units (1 Hartree = 2625.49962 kJ/mol).
-74.9607232756 A.U. = 196809.35 kJ/molMore information about atomic units can be found in the IUPAC gold book.
License informationCommercial (centrally provided by IT shop).
The use of Gaussian is subject to the following conditions (this is just a summary; the license agreement is several pages long):
Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above.If you want to use Gaussian, simply send a note to Cluster Support stating that you accept these conditions.