Guassian 09 – Tesla Cluster

Running jobs on Tesla Cluster

Introduction

G09 software can be used only in parallel mode on the tesla cluster.

Environmental set up for Tesla1:

The Gaussian 09 system includes paths and initialization files to set up user environment for running the program. The paths to be set are

  • The variable g09root must be set to the installation directory of gaussian 09.
    csh:
    setenv g09root /home/pkg/lic/g09/amd64bash/ksh:
    export g09root=/home/pkg/lic/g09/amd64sh:
    g09root=/home/pkg/lic/g09/amd64; export g09root
    •  Initialization files to be set up:

csh:
source /home/pkg/lic/g09/amd64/g09/bsd/g09.login

bash/ksh:
. /home/pkg/lic/g09/amd64/g09/bsd/g09.profile

sh:
/home/pkg/lic/g09/amd64/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 /global/utemp/loginid
or
setenv GAUSS_SCRDIR /home/localscratch/loginid

bash/ksh:
export GAUSS_SCRDIR= /global/utemp/loginid
or
export GAUSS_SCRDIR= /home/localscratch/loginid

sh:
GAUSS_SCRDIR= /global/utemp/loginid;
export GAUSS_SCRDIR
or
GAUSS_SCRDIR= /home/localscratch/loginid ;
export GAUSS_SCRDIR
where, loginid is your login id.

Note:
  1. Once your job is complete remove all temporary files created by your job in /tmp or /global/utemp/loginid.
  2. Files in /home/localscratch/loginid older than 7 days are removed automatic
  3. Number of processors to be used:
The Gaussian 09 on the Tesla cluster, supports parallel processing. You may specify the default number of processors to use in the Default.Route file in your current working directory. For example the following command sets the default number of processors to 4:
-P- 4
To override the default no of processors the following command should be used as the first line in your input file.
%nproc=8
The above command sets the number of processors to be used to 8
Note: Whatever number of processors 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.
    • Running Gaussian 09 jobs in batch mode:
To run the Gaussian 09 jobs in batch mode set up the environment as above,
create a PBS command file as follows:
#!/bin/csh
#PBS -l ncpus=14
#PBS -S /bin/csh
#PBS -V
g09 < /home/localscratch/seccom/benzene.com >
/home/localscratch/benzene.out

where benzene.com is the input file to Gaussian 09

Software documentation:

Gaussian 09 links /help

http://www.gaussian.com/g_tech/g_ur/g09help.html

Report problems to:

For any problems with respect to G09 software send email to helpdesk.serc@auto.iisc.ac.in or contact system administrators at #103, SERC.