Running jobs on Dell Cluster

Introduction

Gaussian 09 software can be used only in parallel mode on the Dell Cluster.

Environmental setup for Dell Cluster :

Gaussian 09 is installed in the directory /home/pkg/lic/g09. To enable the exection of Gaussian 09 jobs, user must set the proper environmental variables depending upon the login shell .

The variable g09root must be set to the installation directory of gaussian 09:

csh:
setenv g09root /home/pkg/lic/g09/em64t

bash/ksh:
export g09root=/home/pkg/lic/g09/em64t

sh:
g09root=/home/pkg/lic/g09/em64t; export g09root

Initialization files to be set up:

csh:
source /home/pkg/lic/g09/em64t/g09/bsd/g09.login

bash/ksh:
. /home/pkg/lic/g09/em64t/g09/bsd/g09.profile

sh:
/home/pkg/lic/g09/em64t/g09/bsd/g09.profile

Setting scratch directory for G09 runs using GAUSS_SCRDIR environmental variable. This should be set to the base directory where scratch files are to be stored.

csh:
setenv GAUSS_SCRDIR /localscratch/loginid
or
setenv GAUSS_SCRDIR /home/dell-scratch/loginid

bash/ksh:
export GAUSS_SCRDIR= /localscratch/loginid
or
export GAUSS_SCRDIR= /home/dell-scratch/loginid

sh:
GAUSS_SCRDIR= /localscratch/loginid
export GAUSS_SCRDIR
or
GAUSS_SCRDIR= /home/dell-scratch/loginid
export GAUSS_SCRDIR

Here, loginid refers to your login id

Note:
  1. Once your job is complete remove all temporary files created by your job in GAUSS_SCRDIR scratch directory.
  2. Files in /home/dell-scratch/loginid older than 7 days are removed automatically
  3. Number of CPUs to be used:
The Gaussian 09 on the Dell Cluster, You may specify the
default number of CPUs to use in the Default.

  • Route file in your current working directory.

For example the following command sets the default number of CPUs to 8:

-P- 8

  • To override the default no of CPUs the following command should be used as the first line in your input file.

%nproc=8

Where %nproc is equal to the number of CPUs.

The above command sets the number of CPUs to be used to 8
Note: Whatever number of CPUs is mentioned in the Default.Route file or using the %nproc directive in the input file, that number should also be specified in the PBS command file using the ncpus directive.

Example PBS Script for a Single Node Parallel Job
#!/bin/csh
#PBS -l ncpus=8
#PBS -S /bin/csh
#PBS -V
setenv g09root /home/pkg/lic/g09/em64t
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /localscratch/loginid
g09<$GAUSS_SCRDIR/benzene.com>$GAUSS_SCRDIR/benzene.log

where benzene.com is the input file to Gaussian 09

Also, add the number of CPUs to the top of the input data file using the following format: %nproc = 8

Where %nproc is equal to the number of CPUs.

Software documentation:

Gaussian 09 online help

Report problems to:

For any problems with respect to G09 software,  contact helpdesk.serc@auto.iisc.ac.in or System Administrator, # 103, SERC.