Octave on Biowulf

Many, but not all, Matlab .m scripts will run in Octave. MEX files (to call custom C or Fortran routines directly from Matlab) can be executed in Octave with some limitations.

Octave was written by John Eaton and others, and is available from the Octave website. Octave on Biowulf is installed courtesy of Tom Holroyd, NIMH. The version of Octave on Biowulf can be determined by typing octave -v at the Biowulf prompt.

Octave runs are typically slower than the equivalent Matlab run. However, Octave is not license-limited, so many more simultaneous runs are possible than with Matlab. Thus, on the Biowulf cluster Octave is most useful for projects which can be split into large numbers of independent simultaneous runs.

Octave Packages (Toolboxes)

Using Octave on Biowulf

1. Create an Octave script. The following sample script takes a single argument from the command line.

   -------------file array.oct-------------------------------
   #!/usr/local/bin/octave -qf
   
   if( nargin != 1 )
       printf( "Usage: %s \n", program_name );
       return;
   endif
   
   len = str2num( argv(){1} );
   printf( "Working with array size %6d\n", len );
   
   clear a; 
   tic(); 
   for i=1:len
       a(i) = i; 
   endfor 
   time1 = toc();
   
   a = [1]; 
   tic(); 
   for i=2:len 
       a = [a i]; 
   endfor
   time2 = toc();
   
   printf( "The time taken for method 1 was %.4f seconds\n", time1 );
   printf( "The time taken for method 2 was %.4f seconds\n", time2 );
   -------------------------------------------------------------------
   

2. Create a batch script for the job. Sample script:

   -------- file array.bat----------------------
   #!/bin/csh
   
   cd /data/user/mydir
   ./array.oct 10000 
   ---------------------------------------------
   

3. Submit this job to the batch system with:

   qsub -l nodes=1 ./array.bat
   

./array.oct 10000 > filename.out

Swarms of Octave jobs

1. Create a swarm command file, with one line for each command you wish to run. Sample file:

   /data/user/mydir/array.oct 1000 > array.out.1000
   /data/user/mydir/array.oct 2000 > array.out.2000
   /data/user/mydir/array.oct 3000 > array.out.3000
   ...
   /data/user/mydir/array.oct 20000 > array.out.20000
   

2. Submit this to the swarm program with swarm -f commandfilename. Sample session:

   [user@biowulf octave]$ swarm -f swarm.cmd
   291383.biobos
   291384.biobos
   [user@biowulf octave]$
   

Interactive use

[susanc@biowulf ~]$ qsub -I -l nodes=1
qsub: waiting for job 290150.biobos to start
qsub: job 290150.biobos ready

p226    job-busy           interactive
[susanc@p226 ~]$ octave
GNU Octave, version 2.9.9 (i686-pc-linux-gnu).
Copyright (C) 2006 John W. Eaton.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to  (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

octave:1> a=1+1
a =  2
octave:2>  sin(x)
ans = -0.27942
octave:3> x=5*pi
x =  15.708
octave:4> sin(x)
ans =  6.1230e-16
octave:6> quit
[susanc@p226 ~]$ exit
logout

qsub: job 290150.biobos completed
[susanc@biowulf ~]$

Documentation