Gaussian
Policy
Gaussian is available to users at HPC2N under the condition that published work include citation of the program. See Official Gaussian 09 Literature Citation for instructions.
Note: Please, check which revision you are running in the program output.
General
Gaussian is a connected system of programs for performing a variety of semi-empirical and ab initio molecular orbital calculations.
What is Gaussian for?
Gaussian uses electronic structure theory in computing many properties of molecules and reactions, including the following:
- Molecular energies and structures
- Energies and structures of transition states
- Bond and reaction energies
- Molecular orbitals
- Multipole moments
- Atomic charges and electrostatic potential
- Vibrational frequencies
- NMR properties
- Reaction pathways
Calculations can be carried out on systems in the gas phase or in solutions, and in their ground state or in an excited state.
Availability
Only shared memory parallelism is supported at HPC2N, i.e it is only possible to run Gaussian within a node (using more than one core though). Using distributed memory parallelism (i.e using Linda) is NOT available at HPC2N. Gaussian is installed on Abisko and Akka.
Usage at HPC2N
Gaussian needs an input file which contains information about the aproximation, molucular properties and a list of atoms and their coordinates. An example inputfile is available: jobname.com
Of special interest are:
-
To run on a single node, but using more than one CPU specify:
%NProcShared=<nr of cpus>
where <nr of cpus> is 8 on Akka and 12 on Abisko, for the examples below.
To run Gaussian on 1 node for 1 hour use one of the submit files below. The input file and output file are assumed to be located in the submit directory.
Select number of processors to use on the node by changing NProcShared as per above.
Akka:
#!/bin/sh #PBS -N Gaussian # Change to a valid project account #PBS -A SNICXXX-YY-ZZZ # Using 1 node and all 8 cores of that node #PBS -l nodes=1 # Request all memory on the node. # This has the affect of allocating all processors on the node too. #PBS -l pvmem=16000m #PBS -l pmem=15500m #PBS -l walltime=1:00:00 # module add gaussian/09 # Assume that the job file are located in the submit directory cd $PBS_O_WORKDIR time g09 < jobname.com > jobname.out # # End of script #
Abisko:
#!/bin/sh # Change to a valid project account #SBATCH -A SNICXXX-YY-ZZZ #SBATCH -J some-jobname # Want to run 1 task #SBATCH -n 1 # Using 12 cores per task since gaussian is multi-threaded #SBATCH -c 12 #SBATCH --time=01:00:00 # Set the names for the error and output files #SBATCH --error=job.%J.err #SBATCH --output=job.%J.out module add gaussian # Always use srun to start programs, # including serial and multi-threaded ones. srun time g09 <x.com >x.log
The above submit file will be able to use 12 * 2500MB = 30000MB of memory for that one gaussian job.
