Cluster:Gaussian

Web interface: WebMO

Users for WebMo:

• Create an LDAP user.
• Log in using that user's credentials
• Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
• Use Gaussian.

Older notes, c. 2005

• Gaussian environment
• Running Gaussian in parallel
• Sample Gaussian PBS script

Gaussian environment

I use this in my .bashrc:

       export GAUSS_EXEDIR=/cluster/bazaar/software/g03
       export GAUSS_LFLAGS='-nodelist "b0 b1" -opt "Tsnet.Node.lindarsharg: ssh " -mp 2'
       export GAUSS_SCRDIR=/tmp
       export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/cluster/bazaar/software/g03
       export g03root=/cluster/bazaar/software
       export PATH=$PATH:/cluster/bazaar/software/g03

Seems to work, although you might want to tweak the node list.

Running Gaussian in parallel

Understand the distinction between nprocs and nprocl. nprocs is for a shared-memory (single-image) machine, whereas nprocl is for a distributed-memory (cluster) system. You want to use nprocl on all our computing systems. For example, if you want to run on eight processes (four nodes), add a line like this

%nprocl=8

to your input file. You should then specify qsub -l nodes=4:ppn=2 script on the command line to submit your PBS script with a requirement of four dual-processor machines.

Once you have the number of CPUs specified in the input file, make sure that your nodelist in GAUSS_LFLAGS is set properly. See Gaussian environment for details.

If you have a bunch of input files you want to modify, use the add_nproc.pl script in /cluster/generic/bin. First cd to the directory with your input files, and then do:

perl /cluster/generic/bin/add_nproc.pl n

where n is the number proecssors you want to run on.

After that, fire it up with $g03root/bsd/g03l.

Sample Gaussian PBS script

This is a sample PBS script for Gaussian:

#!/bin/sh
#PBS -N gaussian_test061.com_nodes=2:ppn=2
#PBS -o /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.out
#PBS -e /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.err
#PBS -q batch
#PBS -m abe
#PBS -l nodes=2:ppn=2

cd $PBS_O_WORKDIR
/cluster/bazaar/software/g03/bsd/g03l < /cluster/bazaar/software/g03/tests/com_smp4/test061.com > /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.log

exit $!