Gaussian FAQ
This is a quick introduction to the usage of the electronic-structure code "Gaussian 03" on the HPCVL SunFire systems. It is meant as an initial pointer to more detailed information, and to get started. It does not replace study of the manual and the Gaussian web page.

Questions:

  1. What does Gaussian do?

  2. Where is the program located?

  3. How do I set up my environment for Gaussian?

  4. How do I run Gaussian?

  5. How do I handle a parallel Gaussian job?

  6. Where can I get detailed help?

  7. How is Gaussian licensed?

Answers:

  1. What does Gaussian do?

    Gaussian is arguably the most-used computational quantum-chemistry program. It does electronic-structure calculations and standard quantum chemical calculations. Among the methods available are simple molecular mechanics (Amber force field and others), semi-empirical methods (such as CNDO), Hartree-Fock (restricted and unrestricted), MPn (Mollar-Plesset perturbation theory of order n=2,3,4), CI (Configuration-Interaction), CC (Coupled-Cluster), Multi-configurational SCF (such as CAS-SCF) and various DFT (Density-Functional Theory) methods. Specific to Gaussian are high-accuracy energy methods (G2, CBS). It can be used to obtain electronic properties, molecular geometries, vibrational frequencies, orbitals, reaction profiles, and much more.
    It does not do molecular dynamics, elaborate calculations on excited states (only single-excitation CI is available), time-dependent calculations and full CI.

    For a more complete list see this Overview

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  2. Where is the program located?

    The program resides in /opt/g03 and is called (you guessed it) g03. We also maintain a copy of the previous release of Gaussian, '98. This is located in /opt/g98.
    In the program directory, there is a series of test jobs, which are very useful to get an idea of how to perform specific types of calculations. The source code of Gaussian is not accessible to the general public, since Gaussian is a licensed product. However, Gaussian grants the permission to alter the code under certain conditions. If you want to do so, contact HPCVL to learn more. You are not allowed to copy the executable or any part of the distribution onto your local machine, unless you hold a proper license yourself. See Question 6.

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  3. How do I set up my environment for Gaussian?

    There is two ways to set up your environment to enable Gaussian.

    • The easy way: The usepackage system has an entry for Gaussian 03 (and another one for Gaussian 98). All you need to do is type use g03 and the proper changes will be made. You can also put this command into your setup (.login or .profile) files.

    • The hard way: You can also do things manually. Include the following lines in your setup files (.login for csh, .profile for ksh or bash):

      For csh: 
      setenv g03root /opt
      source $g03root/g03/bsd/g03.login
      setenv GAUSS_SCRDIR /scratch/hpcxxxx
      
      For ksh, bash, etc:
      g03root=/opt; export g03root
      . $g03root/g03/bsd/g03.profile
      GAUSS_SCRDIR='/scratch/hpcxxxx'; export GAUSS_SCRDIR
    Note that the setting of the environment variable GAUSS_SCRDIR is necessary to redirect the temporary files that Gaussian creates to portion of the disk where they do not interfer with other people's disk space. For the SUN systems, this directory should be /scratch/hpcxxxx (replace the xxxx by your username's numbers). This is done automatically if you use the use. Also note that if for some reason Gaussian does not terminate normally (e.g. a job gets cancelled by hand), it leaves behind large "scratch files" which you should delete by hand. To check if such files exist, type
    ls -lt /scratch/hpcxxxx
    on the Sun Fire cluster where xxxx stands for the numbers in your username. Once you have determined that the scratch files are no longer needed, you can delete them by typing
    rm /scratch/hpcxxxx/Gau-* 
    where, again, xxxx needs to be replaced by the numbers in your username.
    Cleaning up the scratch space is the user's responsibility and cannot be done by the system administrator, since he does not know which files are still in use and which are spurious. If scratch space does not get cleaned up regularly, it can cause jobs to terminate, and much work to be lost. Please do it.
    If you want to run Gaussian on several processors (which is encouraged, since this is a multi-processor machine) on the SUN, you will have to include a line
    %Nproc=number_of_processors
    where number_of_processors is exactly what it says, in your input file for the job you are running (see below).

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  4. How do I run Gaussian?

    To run Gaussian on the SunFire systems of HPCVL, you have to belong to a user group "g98" . You will be entered into the group list when you have read and our license agreement and signed a statement that you have done so (see last question ).
    You will also have to use the load balancing software that HPCVL is using. For the SunFire systems, this is the GridEngine software ( to learn more, check out our GridEngine FAQ)

    Given the complexity of the underlying methods, Gaussian is very simple to use. A given calculation is performed by preparing an input file, piping it to the standard input of the program g03, and catching the standard output in a log-file. We suggest you use the "extension" .g03 for input files and .log for the results.

    Interactively, the command line to invoke Gaussian is thus:

    g03 < test.g03 >test.gout &
    The ampersand & submits the job into the background, so it doesn't block your terminal. This will only work if you are a member of the g98 group and have set the environment correctly (see previous question ). Note that the interactive execution of Gaussian is only meant for test runs. If you use GridEngine (as you are required to do for production jobs), you submit Gaussian jobs under a C-shell via a script. A template for such a script is available here . This script will setup the environment for you, and will also only work if you are a g98 group member. You supply the directory in which you work, the email to which you want to notified, and the name of the input/output files by editing the script. Make the script executable ( chmod 700 g03.sh). Note that you have to replace entries that are enclosed in {} in the script. The script is submitted by the qsub command:
    qsub g03.sh
    This sample script assumes that you run Gaussian with multiple processors. Please refer to the following section of this FAQ about details.

    Gaussian input files have to be set up according to a scheme that is explained in the "User's Reference". It is impossible to give an outline here. The program uses the concept of keywords to describe the method used, the molecule to be described, and the conditions for the calculation (such as basis sets). Sample files can be found under $g03root/g03/bsd/logs.

    Note that it is absolutely essential to have a good idea about the size and complexity of your calculations before you start a Gaussian job. Many of the methods mentioned above have terrible scaling properties, i.e. the computational cost grows very quickly with the number of electrons, degrees of freedom, or number of basis functions used. We suggest you start with a small basis set and a cheap method, and then slowly increase those parameters.

    In the future, HPCVL will be assign a specific queue for Gaussian users on our load-balancing software. This means that if you use Gaussian, you will be doing so on a specific subset of processors to maximize the performance of the program, and minimize the interference with other applications. At this point, contact Hartmut Schmider if you have problems with the submission or execution of Gaussian jobs.

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  5. How do I submit parallel Gaussian jobs?

    Gaussian offers the opportunity to execute major portions of the code on multiple processors. For the SUN computers, this feature is invoked by including a directive

    %Nprocs=number_of_processors
    in the first line of the input file. This line will cause Gaussian to use up to number_of_processors CPU's in the calculation. However, it is not acceptable to start a job like this on the standard serial GridEngine queue for production jobs. If you submit a Gaussian parallel job with the above line in the input file, you must use a special parallel submit script to do so. A sample script for this can be downloaded. In this script, there is a line:
    #$ -pe shm.pe {number of processes}
    where the entry enclosed in {} stands for the number of processors requested, and has to be identical with the number appearing in the input file. Entries in the sample script enclosed in {} must be substituted by specific values. Using this script will assure that the GridEngine knows how many processors are used, and will allocate resources accordingly. You might experience extended waiting times using this method (since the resources must be available first before they can be allocated), but the excution times of your parallel job will scale reasonably well (since you are likely to work on dedicated processors without oversubscription).

    There is an easier way to do this: We are supplying a small perl script called that can be called directly, and will ask a few basic questions, such as the name for the job to be submitted and the number of processes to be used in the job. Simply type

    GaussSubmit
    and answer the questions. The script expects a Gaussian input file with "file extension" .g03 to be present and will do everything else automatically. This is meant for simple Gaussian job submissions. More complex job submissions are better done manually.

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  6. Where can I get more detailed information?

    This is the most important question treated here. To learn the basics about Gaussian input and output, refer to the "Gaussian 03 User's Reference". For templates, and to get many examples, check out /opt/g03/bsd/examples.

    There is a Gaussian web page with lots of information: http://www.gaussian.com There is also a Gaussian user group that has many members who really know what they are talking about (and some who don't). Gaussian also operates a help line for licensed users. Send email to help@gaussian.com , but don't expect the answer to come too quick, they get a lot of requests.

    For hardcore computational chemists, there is the "Gaussian 03 Programmer's Reference" and the IOPs Reference which are useful if you want to tinker with default settings and internal parameters, or even want to write some subroutines of your own.

    If you want to learn about the methods, check out "Exploring Chemistry with Electronic Structure Methods" by J. B. Foresman and Aeleen Frisch, Gaussian Inc. Pittsburgh PA. (This book makes reference to Gaussian 98, but almost all of it applies to Gaussian 03).

    You can also ask Hartmut Schmider about specific technical problems with Gaussian. I am a theoretical chemist by training and have some background in the usage of the program.

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  7. How is Gaussian licensed?

    Gaussian is a licensed program. The license held by HPCVL is limited to the HPCVL-operated computers at Queen's University in Kingston, Ontario, and only covers academic use. That means that any user of HPCVL can use the program for academic research, whether they are located at Queen's or not.

    HPCVL requires users of Gaussian to sign a statement in which they state that they are informed about the terms of the license. Download it, print it out and sign it after reading the license agreement , to be included in the Gaussian user group.

    Non-academic, particularly commercial, users are not allowed to use Gaussian under our license. Neither is it possible for academic users to do contract work using the HPCVL Gaussian installation. Any such use would violate our license agreement. Please abide by those rules.

 
 
   
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