GAUSS on Biowulf

The GAUSS executables are not multithreaded or parallel. The advantage of using GAUSS on Biowulf would be to run many GAUSS jobs simultaneously, i.e. a 'swarm' of single-threaded jobs.

Running GAUSS interactively

Typing 'gauss' at the Biowulf prompt will bring up the GAUSS Xwindows interface. You can then type any GAUSS command into the window. This should only be used for testing, or for small development tasks. All other Gauss jobs should be run via batch, as below.

Run as a batch job

Create a batch input file, e.g. /home/username/gaussrun. Example:

#!/bin/tcsh
#PBS -N gauss
#PBS -m be
#PBS -k oe
#
cd /home/username/gauss
/usr/local/bin/gauss -v -b /home/username/gauss.in > gauss.out

Submit this job using the PBS 'qsub' command. Example:

qsub -v np=1 -l nodes=1 gaussrun

Note that there is no need to ask for more than 1 node, since GAUSS is single-threaded.

Running a swarm of GAUSS jobs

The swarm program is designed to submit a group of commands to the Biowulf cluster. Each command is represented by a single line in the swarm command file that you creare, and runs as a separate batch job. See the swarm page for more information.

Create a swarm command file, say, cmdfile, with each line containing a single gauss run. Example:

/usr/local/bin/gauss -v -b /home/username/gauss1.in > gauss1.out
/usr/local/bin/gauss -v -b /home/username/gauss2.in > gauss2.out
/usr/local/bin/gauss -v -b /home/username/gauss3.in > gauss3.out
/usr/local/bin/gauss -v -b /home/username/gauss4.in > gauss4.out
/usr/local/bin/gauss -v -b /home/username/gauss5.in > gauss5.out

Submit this to the batch system with the command:

swarm -f cmdfile

Run on the command line

If you simply log in to Biowulf and type a command, your command will run on the main Biowulf login node. This is not recommended, for obvious reasons. If you really want to run interactively, you can either use one of the interactive nodes (see the user guide for more information) or you can allocate a node for interactive use. Once the node is allocated, you can type commands directly on the command-line. Example:

biowulf% qsub -I -l nodes=1
qsub: waiting for job 2011.biobos to start
qsub: job 2011.biobos ready

p139$ gauss -v -b /home/username/gauss.in > gauss.out
p139$ exit
logout

qsub: job 2011.biobos completed
biobos$ 

GAUSS Documentation

• GAUSS has online help. Typing 'gauss' at the Biowulf prompt will bring up the GAUSS Xwindows interface. Click on the Help button to view the GAUSS help.
• GAUSS links and resources at Aptech.com
• A Short Introduction to GAUSS. PDF, 1997. View as HTML.