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ICHEC Software

Information about software packages installed on the ICHEC systems.

Gaussian

Versions Installed

Fionn: 09b01/09d01

Description

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.

License

Gaussian is available for use. Please contact the Helpdesk to gain access.

Benchmarks

N/A.

Additional Notes

Fionn:

module load molmodel gaussian/09d01

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.

#!/bin/bash
#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

cd $PBS_O_WORKDIR

module load molmodel gaussian/09d01

ulimit -Ss 1048576
ulimit -Sl 524288
ulimit -c 0

source $groot/scratch.sh

g09 < input.gjf > output.log

Gaussian jobs on Fionn are run via shared memory (without Linda) on a single compute node. Users should specify 24 processes in their input file for Fionn:

%nproc=24

Example of script to run on shared memory partition. For each node you select in the -l nodes you get around 120 GiB of RAM for your calculation. Please use %mem inside your gaussian input to specify the amount of memory. Also note that %nproc can be increased in multiples of 8 based on how many nodes you requested.

#!/bin/bash
#PBS -l nodes=3:ppn=8
#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
#PBS -q ShmemQ

cd $PBS_O_WORKDIR

module load molmodel gaussian/09d01

ulimit -Ss 1048576
ulimit -Sl 524288
ulimit -c 0

source $groot/scratch.sh

g09 < input.gjf > output.log

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.

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