Information about software packages installed on the ICHEC systems.
Stokes: 03e01 / 09b01 / 09c01
Stoney: 09a01 / 09a02 / 09b01 / 09c01
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.
Users can access Gaussian by loading the Gaussian 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 two ulimit changes are included in the script as these avoid a known problem that we have with Gaussian on Stokes.
The g09 executable is run via a PBS script:
#PBS -l nodes=1:ppn=12
#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 gaussian
ulimit -Ss 1048576
ulimit -Sl 524288
ulimit -c 0
g09 < input.gjf > output.log
For jobs on Stoney use ppn=8.
Gaussian jobs on Stokes and Stoney are run via shared memory (without Linda) on a single compute node. Users should specify 12 processes in their input file for Stokes:
or the following for Stoney:
Each compute node in Stokes provides 24GB of RAM. Due to Gaussian's use of read-write files (RWF) it's vitally important to leave memory free for block caching by the operating system, otherwise job efficiency will be badly affected. The maximum memory size that can be specified for a Gaussian job on Stokes is 23GB but users should only use 12GB unless more is specifically required. Users with larger memory requirements can use Stoney where much more memory is available for jobs. Example:
The Gaussian module sets the GAUSS_SCRDIR to the correct location so there is no need to set it manually. 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.