Information about software packages installed on the ICHEC systems.
Stoney: 09c01 / 09d01
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.
Gaussian is available for use. Please contact the Helpdesk to gain access.
Stoney users can access Gaussian by loading the appropriate environment module:
This module sets all the necessary Gaussian variables and paths in the shell environment without requiring messy additions to .profile or .bashrc files. Users who have added Gaussian related lines to these files should remove them and use the environment module. Note that three ulimit changes are included in the script as these avoid a known problem that we have with Gaussian.
The g09 executable is run via a PBS script:
Please note that some of the nodes on Fionn have SSDs and these will be used as scratch space if the job gets routed to them. Also on Fionn, please use ppn=24.
#PBS -l nodes=1:ppn=24
#PBS -l walltime=48:00:00
#PBS -N my_job_name
#PBS -A project_name
#PBS -r n
#PBS -j oe
#PBS -m bea
#PBS -M me@my_email.ie
module load molmodel gaussian/09d01
ulimit -Ss 1048576
ulimit -Sl 524288
ulimit -c 0
g09 < input.gjf > output.log
For jobs on Stoney use ppn=8.
Gaussian jobs on Fionn and Stoney are run via shared memory (without Linda) on a single compute node. Users should specify 24 processes in their input file for Fionn:
or the following for Stoney:
The Gaussian module sets the GAUSS_SCRDIR to the correct location or redefined to local SSDs in the pbs script as is the case for Fionn outlined above. Jobs can use very large RWF files as the scratch space is provided by a large high-performance shared volume.
Further information can be obtained at www.gaussian.com.
For good performance use the %mem directive. A good compromise I have found to be 50G. If needed at expense of I/O caches one can go as high as 57G, but expect a few percentages lost in performance compared with the 50G case. Of course you can fine tune these values.