Biowulf High Performance Computing at the NIH
GAUSS on Biowulf

gaussThe GAUSS Mathematical and Statistical System is a fast matrix programming language widely used by scientists, engineers, statisticians, biometricians, econometricians, and financial analysts. Designed for computationally intensive tasks, the GAUSS system is ideally suited for the researcher who does not have the time required to develop programs in C or FORTRAN but finds that most statistical or mathematical "packages" are not flexible or powerful enough to perform complicated analysis or to work on large problems.

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.

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ cat > doloop.inp
format /rdn 1,0; 
space = "      "; 
comma = ","; 
i = 1;
do while i <= 4; 
j = 1;
do while j <= 3; print space i comma j;; 
j = j+1;
i = i+1; 

(type Ctrl-D)

[user@cn3144 ~]$ module load gauss
[+] Loading GAUSS  10  on cn3144

[user@cn3144 ~]$ tgauss doloop.inp

GAUSS 10.0.3 (Dec 22 2009, 1346) 64-bit
(C)Copyright 1984-2009 Aptech Systems, Inc.
All Rights Reserved Worldwide.

      1,1      1,2      1,3
      2,1      2,2      2,3
      3,1      3,2      3,3
      4,1      4,2      4,3
(gauss) quit

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:


module load gauss/3.2
cd mydir
gauss -v -b > gauss.out

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#]

Multi-threaded GAUSS jobs

There are several threading programs that can be used to multithread (i.e. run on multiple processors) specific parts of your programs. These are described here . These threading functions can be used to utilize all the processors on an allocated node. It is important to know exactly how many threads you are executing and match this number to the available processors on the node, so that you neither overload the node (very inefficient) or waste processors.

For example, the following sample code from the GAUSS 10 User Guide defines 4 concurrent threads:

ThreadStat n = m'm;    //Thread 1
ThreadBegin;           //Thread 2  
y = x'x;
z = y'y; 
ThreadBegin;          //Thread 3
q = r'r; 
r = q'q;
ThreadStat p = o'o;   //Thread 4

Write a batch script along the following lines:

# ---- this file is called myjobscript -------

module load gauss/10
cd mydir
tgauss multi.inp

This job can be submitted with:

sbatch --cpus-per-task=4  [--mem=#g] myjobscript
This command will submit the job to 2 cores (4 CPUS to match the 4 threads) [and # GB of memory if specified].
Swarm of GAUSS 3.2 Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Note: there are unlimited GAUSS 3.2 licenses, so you can only use v3.2 to run a swarm of jobs.

Create a swarmfile (e.g. GAUSS.swarm). For example:

gauss -v -b > gauss1.out
gauss -v -b > gauss2.out
gauss -v -b > gauss3.out
gauss -v -b > gauss4.out
gauss -v -b > gauss5.out

Submit this job using the swarm command.

swarm -f GAUSS.swarm [-g #] [-t #] --module gauss/3.2
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module GAUSS Loads the GAUSS module for each subjob in the swarm