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Gaussian

Description

Gaussian is the latest in the Gaussian series of electronic structure programs. Gaussian 03 & 09 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. Read more here.
Site Version (Latest: G09 B01) Notes
ngs.rl.ac.uk G03 E01 Linda
ngs.rl.ac.uk G09 A02 Linda
ngs.rl.ac.uk G09 B01 Linda

    On this page:

  1. License
  2. Running on the NGS (general)
  3. Compilation Information
  4. Further Information

License

Gaussian is commercial software. On ngs.rl.ac.uk this charge is paid for by STFC eScience Dept SCT group at R.A.L.. Binaries may not be copied from their installed location and the source code is not made available to NGS users.

Users of Gaussian on the NGS should credit the NGS accordingly and STFC eScience Centre (RAL) for providing the code.

In order to access Gaussian on NGS, you should first contact the NGS helpdesk and wait for confirmation that privileges have been setup to run the code.

Running the Application on the NGS (General)

Gaussian may be run from the UI/WMS, from the NGS web portal or from the globus command line. At RAL it can also be directly submitted via the local batch system, as documented below.

The examples below all use example files which can be found and copied from:

gsiftp://ngs.rl.ac.uk:2811/apps/Gaussian/example

Note that although Gaussian is a parallel program, it does not use MPI and RSL 'jobtype' should be left as 'single' with the RSL 'count', changed to reflect the number of parallel processors. You must match the number of processors specified by 'count' with the "%NProcLinda" Link 0 command in the gaussian input file.

Do not exceed 32 processors per Gaussian run, preferably use up to 8 processors per job.

.

  • Submission Using the UI/WMS

    There is a tutorial for running Gaussian via the UI-WMS on the NGS wiki.

    To submit a Gaussian job via the WMS, login to the UI and create a JDL file g09.jdl as below, replacing your ngs ID on the UI for ngsxxxx, then submit using the following command. Output files are automatically returned to your directory on the UI when the job is completed.

    glite-wms-job-submit -o jobIDs -a g09.jdl

    Type = "Job";
JobType = "Normal";
Executable = "/usr/ngs/GAUSSIAN09";
CpuNumber = 8;
StdInput = "g03_Lindatest";
Stdoutput = "Linda_example.out";
StdError = "LindaErr.txt";
Myproxyserver= "myproxy.ngs.ac.uk";
InputSandbox = {"g03_Lindatest"};
InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/gaussian";
OutputSandbox = {"Linda_example.out","LindaErr.txt"};
OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/gaussian/output";
Requirements = (
     member("NGS-UEE-GAUSSIAN09", other.GlueHostApplicationSoftwareRunTimeEnvironment)
);
Rank = other.GlueCEStateFreeCPUs;
ShallowRetryCount = -1;

# Allow user to view output file as the job is running
PerusalFileEnable = true;
# Upload output file changes every 1000 secs (17mins). This is the minimum
PerusalTimeInterval = 1000;
    1. The Perusal settings at the bottom of the JDL file allow, for example, the ouput file Linda_example.out to be viewed in real time. See the Gaussian Tutorial for more details.
    2. Please check that the "%NProcLinda" setting in the Gaussian input deck is the same as the number of processors requested by the "CpuNumber" value in the JDL file.
  • NGS Web Portal Submission

    After logging in to the NGS portal, select the "Gaussian" template under the "Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details about running the job via the portal.

  • Submission Using Globus

    The string 'xxx' in the subsequent commands is to be replaced with your id on NGS.

    You can also create a directory within your home directory (named demo in the following examples) which will be the working directory.

    Any input files required should be copied onto ngs.rl.ac.uk (using gsiscp or gridftp or cp if local to the cluster) into the appropriate directory (/home/ngsxxx/demo in our example).

    The input file for this example is g03_Lindatest , located in /apps/Gaussian/example. To submit a Gaussian job use the following command (one line ignoring the '\'). :

    globus-job-submit ngs.rl.ac.uk/jobmanager-lsf \
    -x '&(jobType=single)(count = 8)(directory=/home/ngsxxx/demo) \
    (stdin=/home/ngsxxx/demo/g03_Lindatest) \
    (stdout=/home/ngsxxx/demo/Linda_example.out) \
    (stderr=/home/ngsxxx/demo/LindErr.txt)' \
    /usr/ngs/GAUSSIAN03

    When this job runs the output file does not appear in the run directory until the job completes. You can check the running output in ~ngsXXX/.lsbatch/ (on ngs.rl.ac.uk only). Alternatively you can use the following command which updates the output file continuously in the run directory:

    globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
    '&(jobType=single)(count = 8)(directory=/home/ngsxxx/demo) \
    (stderr=/home/ngsxxx/demo/LindErr.txt) \
    (arguments= /home/ngsxxx/demo/g03_Lindatest /home/ngsxxx/demo/Linda_example.out) \
    (executable=/usr/ngs/GAUSSIAN03)'

    Please ensure that your certificate proxy does not expire during the run. Use grid-proxy-init -valid 50:00 so that the certificate lasts longer than the maximum batch queue length of 48 hours.

  • Local Batch Submission on ngs.rl.ac.uk (only)

    If all else fails a Gaussian job can be submitted to the local batch queue. However this should only be used for debugging a new job and not for production use. As such, this method of submission is not supported. To submit a job directly to the local batch system use the command:

    bsub < myscript

    where "myscript" contains the following

    #!/bin/csh 
#BSUB -o %J.o
#BSUB -e %J.e
#BSUB -n 8
cd /home/ngsxxx/demo
/usr/ngs/GAUSSIAN03_E_01 < g03_Lindatest > Linda_example.out

    Note that you will have to set the "%NProcLinda" in the gaussian input deck to the same number of processors as in the "#BSUB -n" card.

  • Scratch directory locations

    Gaussian scratch files are directed to the network shared directory /work/scratch/LSF_$LSF_JOBID unless the job is allocated to the processors of one slave host, in which case the scratch files are located locally at /tmp/LSF_$LSF_JOBID if there is >20Gbytes free on /tmp disc on that node.

    If your job will create large .scr or .chk files please create a working directory for the job under /work/scratch (eg mkdir -p /work/scratch/ngs0123/myGaussianJob ) and run the job from there rather than your home directory, then copy any results back to your home directory, as the /work/scratch is not backed up. Jobs which exceed your requested NGS file storage limits on the home directories may be killed by the node administrators at their discretion.

Compilation Information

Gaussian was compiled using Portland Group Compilers on ngs.rl.ac.uk

Further Information

The online Gaussian manuals can be found on the Gaussian web site here :

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