HPC/Applications/g09

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=ppn and %LindaWorkers=n123,n124,n125,... are inserted automatically.
• Checkpoint-files named in %chk directives are identified and copied into the compute node's job-specifc $TMPDIR. The %chk specification 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 $TMPDIR are moved to $PBS_O_WORKDIR.

Linda errors

You may see messages like these in a job's error stream:

eval server 0 on n019.carboncluster has dropped it's connection.
eval server 0 on n019.carboncluster has dropped it's connection.
subprocess pid = 11505 has exited. status = 0x0000, id = 0, state = 17. command was /opt/soft/g09-D.01.x86_64-1/g09/linda8.2/opteron …
died after signing in successfully
eval server 0 on n019.carboncluster has dropped it's connection.
…

• http://umbc.rnet.missouri.edu/resources/How2RunGAUSSIAN.html says:

These messages are not indicative of a problem. They indicate that the Linda work in a Gaussian link is finished, and that Gaussian is continuing with a new link. They can be ignored.

• Alternatively however, http://www.chm.bris.ac.uk/compres/grendelgauss.html states:

Not all types of calculation are linda parallel. PBC calculations are not, and some others are not, although many are. If a calculation fails because it is not linda parallel you will see a message similar to this on on stderr.

For test job 420, links as they occur in the error log are:

l401.exel  
l906.exel  
l1002.exel 
l703.exel  

l302.exel  
l401.exel  
l502.exel  
l906.exel  
l1002.exel 

• Links as exectuted:

$ grep linda-exe *out
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l302.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l401.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l502.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l906.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l1002.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l701.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l703.exel)

(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l302.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l401.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l502.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l906.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l1002.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l701.exel)
(Enter /opt/soft/g09-D.01.x86_64-1/g09/linda-exe/l703.exel)