HPC/Applications/g09: Difference between revisions
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* Link0-commands <code>%NProcShared=''ppn''</code> and <code>%LindaWorkers=n123,n124,n125,...</code> are inserted automatically. | * Link0-commands <code>%NProcShared=''ppn''</code> and <code>%LindaWorkers=n123,n124,n125,...</code> are inserted automatically. | ||
* Checkpoint-files named in <code>%chk</code> directives are identified and copied into the compute node's job-specifc <code>$TMPDIR</code>. The <code>%chk</code> specification will be changed to include <code>$TMPDIR</code>. Note that this will be echoed in the g03 output as follows: | * Checkpoint-files named in <code>%chk</code> directives are identified and copied into the compute node's job-specifc <code>$TMPDIR</code>. The <code>%chk</code> specification will be changed to include <code>$TMPDIR</code>. Note that this will be echoed in the g03 output as follows: | ||
%chk=/tmp/12345.mds01. | %chk=/tmp/12345.mds01.carboncluster/test420.chk | ||
: Chk-file processing will be performed only for files within the current directory; to skip processing, specify a relative or absolute path, such as <code>%chk=./name.chk</code> | : Chk-file processing will be performed only for files within the current directory; to skip processing, specify a relative or absolute path, such as <code>%chk=./name.chk</code> | ||
* At the end of the job, chk-files in <code>$TMPDIR</code> are moved to <code>$PBS_O_WORKDIR</code>. | * At the end of the job, chk-files in <code>$TMPDIR</code> are moved to <code>$PBS_O_WORKDIR</code>. | ||
Revision as of 21:43, March 25, 2013
Introduction
Gaussian is an electronic structure program used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.
Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.
Version note
The version on Carbon is 64-bit version with full support for shared memory and Linda parallelization, specifically at time of writing version Gaussian 09: EM64L-G09RevC.01 from 23-Sep-2011.
Status
Available to Argonne employees only.
Job script
- job script template:
$G09_HOME/g09.job
Usage
Copy the template script and use it in one of two ways:
- edit for each job as needed, or
- adapt the script for basic needs of several jobs, and individualize it by the PBS job name.
The job name can be up to 15 characters long and should not contain unusual characters. Set it, along with your project name and the walltime limit on the qsub command line:
qsub -N foo [-l walltime=hhh:mm:ss] g09.job
Operation
Upon job execution, the script reads the input file, interprets and modifies it as follows:
- Link0-commands
%NProcShared=ppnand%LindaWorkers=n123,n124,n125,...are inserted automatically. - Checkpoint-files named in
%chkdirectives are identified and copied into the compute node's job-specifc$TMPDIR. The%chkspecification will be changed to include$TMPDIR. Note that this will be echoed in the g03 output as follows:
%chk=/tmp/12345.mds01.carboncluster/test420.chk
- Chk-file processing will be performed only for files within the current directory; to skip processing, specify a relative or absolute path, such as
%chk=./name.chk
- At the end of the job, chk-files in
$TMPDIRare moved to$PBS_O_WORKDIR.