Attention
The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.
Gaussian
Gaussian is a general purpose computational chemistry software package initially released in 1970. It utilizes fundamental laws of quantum mechanics to predict energies, molecular structures, spectroscopic data (NMR, IR, UV) and much more advanced calculations. It provides state-of-the-art capabilities for electronic structure modeling.
Usage
Gaussian versions can be activated loading one of the module files listed below:
module load apps/gaussian_09/e.01/std
module load apps/gaussian_16/c.01/haswell
Warning
Access to Gaussian on ShARC is available to all users from the
Department of Chemistry by default (i.e. user IDs beginning with ch);
other users wishing to access Gaussian will need to contact research-it@sheffield.ac.uk
to request access (i.e. to be added to unix group gaussian09 or Gaussian).
Gaussian utilities
The Gaussian utilities can be accessed by loading the Gaussian module file (see above).
The utilities are executed by typing their name, e.g., formchk and cubegen. The full list of utilities is described at http://gaussian.com/utils.
Hint
The Gaussian 09 command line executuable is g09.
The Gaussian 16 command line executuable is g16.
Batch jobs
Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, to run g09 and which is submitted to the queue by typing qsub my_job.sh.
#!/bin/bash
#$ -cwd
#$ -l h_rt=00:30:00
#$ -l rmem=2G
#$ -pe smp 2
module load apps/gaussian_09/e.01/std
export GAUSS_SCRDIR=$TMPDIR
g09 my_input.gjf
The script requests 2 cores using the shared memory parallel environment smp with a runtime of 30 mins and 2GB of real memory per core. The Gaussian 09 input file is my_input.gjf.
Please note: The above script specifies that the scratch directory for Gaussian 09,
GAUSS_SCRDIR, should be set to $TMPDIR / the highest performance storage on a compute node.
Hint
Gaussian should scale well with increasing core counts with near linear proportional scaling up to 16 cores and diminishing returns at higher core counts.
Installation notes
Gaussian 09 Revision E.01 and 16 Revision C.01 were installed manually
(from the terminal) using appropriately modified commands from the
install_gaussian_09.sh script.
Vendor specified versions of PGI have been selected to maximise solver stability.
Module logic and separated chemistry department specific directories have been created to facilitate multiple group access to binaries correctly as filesystem ACLs are unavailable/undesirable and nested groups unduly affect cluster performance.
Gaussian 09
The Gaussian 09 code was compiled with PGI 12.5
and has no architecutral optimisations that can be utilized. The
make.log file can be found in the $g09root/g09/.
The module file was manually created and can be downloaded:
here.
Gaussian 16
The Gaussian 16 code was compiled with PGI 18.10.
and has architectural optimisations turned on for Haswell processors. The
make.log file can be found in the $g16root/g16/.
The module file was manually created and can be downloaded:
here.
Testing
The Gaussian 09/16 installations were tested by running a batch job using the following text (including a blank line at the end) in an input file and the my_job.sh batch script, above.
%chk=h2o.chk
%nproc=2
%mem=2GB
#n hf/6-31G(d,p) opt freq
H2O
0 1
O
H 1 r1
H 1 r2 2 a1
r1 1.0
r2 1.0
a1 105.0