Octave/Matlab#

Octave is a free alternative to Matlab and if you do not use Matlab's toolboxes, your code should work without many changes. For many of Matlab's toolboxes (partial) implementations exist for Octave as well. we have setup a module for Octave:

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module load octave

Octave: Example of a non-interactive batch job (single process)#

SLURM batch script octave-script.slurm

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#!/bin/bash
#SBATCH --partition=common
#SBATCH -t 2:10:00
#SBATCH -J octave
module load octave
octave script.m

The commands that Octave should calculate are in script.m

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n = 1000; 
A = normrnd(0,1, n, n); 
X = A'*A; Y = inv(X); 
a = mean( diag(Y*X) ); 
## should output 1.0: 
a

Octave netcdf toolbox#

To use netcdf in octave the toolbox octcdf has to be installed from octave forge. Note that octcdf is a NetCDF toolbox for Octave which aims to be compatible with the „original“ matlab toolbox.

To install the toolbox do following steps in the frontend and later the package is available in all nodes for your user.

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module load green-spack
module load octave
octave

Inside octave do:

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pkg install -forge -verbose octcdf

You may need to scroll down when necessary and it should complete the compilation successfully. Then you can start using Octcdf in your octave scripts by adding the line

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pkg load octcdf

Matlab#

Matlab is available on the cluster through a campus license. Use

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module avail

to see which version is installed. If a newer is needed, contact us via hpcsupport. Start using it by loading the module

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module load green
module load Matlab/R2018a

Matlab can be used non-interactive (like Octave in the above example).