This script runs a Gaussian 09 quantum chemistry calculation using 2 CPUs on a single compute node. It sets up the environment and scratch directory for Gaussian, runs the formaldehyde2.input calculation, and cleans up files after completion. The calculation is configured to only use one quarter of an 8-core node's resources as a test, even though the methane problem is too small to require that much.

1. formaldehye2.input
formaldehyde2.input
. g09_2.job
#!/bin/csh
# This script runs a 2-cpu (core) Gaussian 09 job
# with the 2 cpus packed onto a single compute node.
# This job uses only one fourth of an 8-core compute
# node (2 cores, 1 quarter memory, 1 quarter scratch disk).
# The methane2.input deck in this directory is configured
# to work with these resources, although this methane
# computation is really too small to make use of even
# one fourth of a node. To increase the resources used
# (cpus memory, or disk) change the '-l select' line here
# and the parameter values at the head of the Gaussian
# input deck.
#PBS -q production_gau
#PBS -N gaussian_job
#PBS -l select=1:ncpus=2:mem=3840mb:lscratch=200gb
#PBS -l place=free
#PBS -V
# Find out name of master execution host (compute node)
echo -n ">>>> PBS Master compute node is: "
hostname

2. # set up G09 environment and scratch directory
setenv g09root /share/apps/gaussian
setenv MY_SCRDIR `whoami;date '+%m.%d.%y_%H:%M:%S'`
setenv MY_SCRDIR `echo $MY_SCRDIR | sed -e 's; ;_;'`
setenv GAUSS_SCRDIR /state/partition1/g09_scr/${MY_SCRDIR}_$$
mkdir -p $GAUSS_SCRDIR
echo $GAUSS_SCRDIR
source $g09root/g09/bsd/g09.login
# You must explicitly change to your working directory under PBS
cd $PBS_O_WORKDIR
$g09root/g09/g09 formaldehyde2.input
# Clean up scratch files by default
/bin/rm -r $GAUSS_SCRDIR
echo 'Job is done!'