How to Run Gaussian03 (g03) via
LoadLeveler or PBS

Introduction

Gaussian can be run in both serial and parallel, via shared memory, through LoadLeveler on the IBM Regatta and IBM SP.

The following sections demonstrate how to run Gaussian03 in parallel and serial in both interactive and batch modes.

IBM Regatta: The Gaussian scratch directory is set automatically on the Regatta. Please DO NOT set the environment variable GAUSS_SCRDIR on the Regatta.

On the IBM SP the scratch directory where Gaussian stores temporary files can be specified in two different ways.

1. Set the environment variable GAUSS_SCRDIR in the .cshrc file or in the LoadLeveler script. This is done by adding the following line to either file:
   setenv GAUSS_SCRDIR scr_directory

   where scr_directory is the directory you want Gaussian to use for the temporary files.

2. Use the qg03 script (described below) to set the scratch directory. If the GAUSS_SCRDIR environment variable has not been set, then the script will create a temporary directory in the scratch space, /scratch1 by default, for Gaussian to use for the temporary files. The temporary directory will be removed when the calculation has finished.

   If the GAUSS_SCRDIR environment variable has been set, then the script will not create a temporary file in the scratch space, rather the predefined scratch location will be used.

Running g03 in serial

• load the g03 module

  module load g03

• launch the executeable

  qg03 [options] input_file

  where input_file is the Gaussian input file and the options for the qg03 script are as follows: (default values in brackets)

  IBM SP:

    -h prints the help menu
    -e [never] email notification (options: end or never)
    -m [300mb] amount of memory (append with mb of gb; ###mb)
    -n [winter] type of node (options: winter or night)
    -p [1] total number of processors (max of 4 proc)
    -r [yes] submit the job? (options: yes or no)
    -s [/scratch1/user] scratch space (options: scratch1 or scratch2)
    -t [5:00:00] the amount of wall clock time (format: hh:mm:ss, max:150:00:00)
  

  IBM Regatta:

    -h prints the help menu
    -e [never] email notification (options: end or never)
    -m [300mb] total amount of memory per processor
    -p [1] total number of processors (max of 16 proc)
    -r [yes] submit the job? (options: yes or no)
    -t [5:00:00] the amount of wall clock time (format: hh:mm:ss)
  

  The qg03 script creates the LoadLeveler file input_file.ll, creates a temporary directory for the Gaussian temporary files (if GAUSS_SCRDIR has not been set), and submits the job to the queue. If the -r flag has been set to "no" then the job will not be submitted; however the LoadLeveler script and the temporary directory (if GAUSS_SCRDIR has not been set) will still be created. The temporary directory is removed when the calculation has finished.

• Examples:
  1. Print out the options menu for qg03

     qg03 -h

• Run the Gaussian job, h2o using the defaults; run serial calculation with a maximum wall clock time of 5 hours and place the temporary files in scratch.

  qg03 h2o

  The output file, h2o.out is created in the current working directory with the input file. The LoadLeveler script, h2o.ll is also placed in the same directory as the input file.

• Run the Gaussian calculation (from the IBM SP), h2o, serially on the nighthawk nodes with maximum wall clock time of 12 hours and place the temporary files in /scratch2.

  qg03 -n night -s scratch2 -t 12:00:00 h2o

• Create the LoadLeveler script, but do not submit the job to the queue.

  qg03 -r no -s scratch2 h2o

  The job, h2o.ll, can be run by typing

  llsubmit h2o.ll

  This command is echoed in the h2o.ll file.

Introduction

Guassian can be run in both serial and parallel (via shared memory) through PBS on the Origin and other Institute machines.

The scratch directory where Gaussian stores temporary files can be specified in two different ways.

1. Set the environment variable GAUSS_SCRDIR in the .cshrc file or in the PBS script. This is done by adding the following line to either file:
   setenv GAUSS_SCRDIR scr_directory

   where scr_directory is the directory you want Gaussian to use for the temporary files.

2. Use the qg03 script (described below) to set the scratch directory. If the GAUSS_SCRDIR environment variable has not been set, then the script will create a temporary directory in the scratch space for Gaussian to use for the temporary files. The temporary directory will be removed when the calculation has finished.

   If the GAUSS_SCRDIR environment variable has been set, then the scripts will not create a temporary file in the scratch space.

Interactive running should be kept to a minimum. Their are a minimum number of interactive processors; therefore any long jobs run interactively on the machine will slow down other users. Running interactively should be used for testing the syntax and command combinations of Gaussian input files only. Any and all production runs should be submitted to the queue so that the jobs run on the larger batch machines. The time limits and memory limits are strictly enforced by the system administrator.

Running g03 in serial:

• load the g03 module

  module load g03

• launch the executable

  g03 < input_file > output_file

  where input_file is the Gaussian input file and output_file is the Gaussian output file. If the GAUSS_SCRDIR environment variable has been set, Gaussian will use the designated directory for the temporary files. If it has not been set Gaussian will use the current working direcotry to store the temporary files.

• Example:
  Run a Gaussian 03 calculation with the input file h2o and return the output file h2o.out to the current working directory.

  g03 < h2o > h2o.out

Running g03 in parallel:

• load the g03 module

  module load g03

• add the line

  %nproc=2

  to the Gaussian input file. This line tells Gaussian that it can use up to 2 processors.

• launch the executable

  g03 < input_file > output_file

  where input_file is the Gaussian input file and ouput_file is the Gaussian output file. If the GAUSS_SCRDIR environment variable has been set, Gaussian will use the designated directory for the temporary files. If it has not been set Gaussian will use the current working direcotry to store the temporary files.

• Example:
  Run a Gaussian 03 calculation with the parallel (%nproc=2) input file h2o-p and return the output file h2o-p.out to the current working directory.

  g03 < h2o-p > h2o-p.out

  Note: the interactive script should only be used for debugging Gaussian input files. The interactive script should not be used for prodcution runs. Any violation of the interactive policies will result in your job being killed by the system administrator.

Running g03 in serial

• load the g03 module

  module load g03

• launch the executeable

  qg03 [options] input_file

  where input_file is the Gaussian input file and the options for the qg03 script is as follows: (default values in brackets)

    -h prints the help menu
    -e [never] email notification (options: end or never)
    -m [300mb] amount of memory (append with mb of gb; ###mb)
    -n [r12k] type of node (options: r10k or r12k)
    -p [1] total number of processors (max of 64 proc)
    -r [yes] submit the job? (options: yes or no)
    -s [/scratch.o3.1/user] scratch space (options: 31, 32, 33)
    -t [5:00:00] the amount of wall clock time (format: hh:mm:ss)
  

  The qg03 script creates the PBS file input_file.pbs, creates a temporary directory for the Gaussian temporary files (if GAUSS_SCRDIR has not been set), and submits the job to the queue. If the -r flag has been set to "no" then the job will not be submitted; however the PBS script and the temporary directory (if GAUSS_SCRDIR has not been set) will still be created. The temporary directory is removed when the calculation has finished.

  Note: When requesting memory, -m flag, make sure to request approximately 200mb more memory than requested with the %mem command in the Gaussian input file.

• Examples:
  1. Print out the options menu for qg03

     qg03 -h

• Run the Gaussian job, h2o using the defaults;

  qg03 h2o

  The output file, h2o.out is created in the current working directory with the input file. The PBS script, h2o.pbs is also placed in the same directory as the input file.