General Project

February 28, 2005

Gaussian Notes

Our installation of gaussian resides in /cluster/bazaar/software/g03.
A typical gaussian command line: nohup g03l md.com &
This runs gaussian with linda (g03 is the uniprocessor binary) using the input file md.com. Running g03l with nohup allows gaussian to continue running even if you log off the machine. The stdout and stderr will go to nohup.out. The g03l output will placed in md.log. If you execute the top command and watch gaussian run, it will call specific binaries to perform the molecular dynamics. These binaries are named lxxx.exe where xxx is a number. A list of the calculations each binary performs can be found here.

Gaussian relies on environment variables for most configuration options. Gaussian is packaged with environment setting scripts that should be sourced before running g03l (g03/bsd/g03.profile; it is handy to put this in your .profile). These are set with the export command in bash (export VARIABLE_NAME="value") and setenv in csh (setenv VARIABLE_NAME 'value'). Here are several environment variables that are handy:

  • GAUSS_SCRDIR="/tmp"
    • directory used for scratch files. Using /tmp is a good thing.
  • g03root="dir"
    • The base gaussian directory. Our base directory is /cluster/bazaar/software.
  • LD_LIBRARY_PATH="dir"
    • The path to linda shared libs (just points to $g03root in our setup). This is set in the g03.profile script provided by gaussian.
  • GAUSS_LFLAGS='-option1 "value1" -option2 "value2"'
    • '-nodelist 'b1 b2 b3 b4"' - Set the node list.
    • '-opt "Tsnet.Node.lindarsharg: ssh"' - Set linda to use ssh for authentication (the default is rsh).
    • '-mp 2' - The number of workers per node. [Note: this applies to all nodes in the nodelist. Since this method does not allow much flexibility, we may want to look for a better way to configure this.]

A suite of tests is included with gaussian (g03/tests/com). Running a set of these tests is a good way to test your gaussian environment. Keep in mind that the log file generated by gaussian is going to be placed in the same directory as the run configuration file (e.g. if you run "g03l $g03root/tests/com/test354.com" from your home directory, the test354.log file will be in $g03root/tests/com/).

Posted by mccoyjo at February 28, 2005 01:05 PM
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