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==Octave-Forge Package Management== | ==Octave-Forge Package Management== | ||
− | Octave-forge packages are NOT pre-installed on sharcnet systems. Users must therefore download, install then manage the versions needed for their research. An explanation of | + | Octave-forge packages are NOT pre-installed on sharcnet systems. Users must therefore download, install then manage the versions needed for their research. An explanation of how to handle this task is provided within this section: |
<b><u>DOWNLOADING AND INSTALLING PACKAGES</u></b> | <b><u>DOWNLOADING AND INSTALLING PACKAGES</u></b> |
Revision as of 17:59, 13 May 2013
OCTAVE |
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Description: Mostly compatible language with Matlab primarily intended for numerical computations |
SHARCNET Package information: see OCTAVE software page in web portal |
Full list of SHARCNET supported software |
Contents
Introduction
Octave is provided on SHARCNET clusters to allow serial or threaded jobs to be run in the queue as described below.
Usage
Version Selection
To see what versions of Octave are available on sharcnet clusters consult the Availability table on the sharcnet OCTAVE web portal software page OR run the following command directly on a cluster:
module avail octave
Starting with version 3.6.3 its necessary to first unload the intel compiler module (or any other compiler that might be loaded) before loading the Octave module. This is done to ensure any octave-forge packages that are to be downloaded and installed into user space are built with the native gcc compiler which is version 4.4.6 at the time of this writing. Therefore to load octave/3.6.3 one would do:
module unload intel module load octave/3.6.3
Job Submission
On SHARCNET clusters Octave should only be run via the queuing system. Octave serial jobs can be submitted to the serial queue using following sqsub command:
sqsub -r 60m -o ofile.%J octave mycode.m
As of version 3.4.3 the sharcnet octave installation supports multi-threading which based on initial testing lapack/blas intensive octave jobs run in the threaded queue achieve an order of magnitude speedup compared to running single core jobs in the serial queue, without making any changes to your code. Once the optimal number of processors is determined by scaling tests submit the job to the threaded queue for example:
sqsub -r 60m -n 8 -q threaded --mpp=1G -o ofile.%J time octave mycode.m
Example Job
An example job complete with sample .m will be provided here asap. For now please refer to the sqsub command shown in the previous job submission section.
General notes
Matlab Compatibility
The online wiki resources "Octave Wiki":
http://wiki.octave.org/
or "Wikibook":
http://en.wikibooks.org/wiki/MATLAB_Programming/Differences_between_Octave_and_MATLAB
provide good introductory explanations of code compatibility between Octave and Matlab.
Reading/Writing Files
There are two strategies for handling file input and output described in the "Octave manual" viz ...
http://www.gnu.org/software/octave/doc/interpreter/Input-and-Output.html#Input-and-Output
http://www.gnu.org/software/octave/docs.html.
The following stanza demonstrates the "simple file I/O" approach: http://www.gnu.org/software/octave/doc/interpreter/Simple-File-I_002fO.html#Simple-File-I_002fO
save myiofile.dat A B C save ("-text", "myiofile.dat", "A", "B", "C") save ("-binary", "myiofile.dat", "A", "B", "C") load myiofile.dat load ("-text", "myiofile.dat", "A", "B", "C") load ("-binary", "myiofile.dat", "A", "B", "C")
where A, B and C are a potential mix of entities such as scalars, vectors or matrices. Note that for large files the binary format is strongly recommended to both minimize disk space and file read/write wallclock times.
Large Memory Array Allocation Testing
The following command sequence should successfully run on hound or tope. Since tope is recommended for interactive use and has 32gb of memory the test will be demonstrated there:
[mypc ~] ssh tope.sharcnet.ca [tope ~] module load octave/3.4.0 [tope ~] octave GNU Octave, version 3.4.0 octave:3> N=4e8; A=[1:N]; B=[2*(1:N)]; C=A+B; C(1); C(N); 3*N ans = 1.2000e+09 octave:4> exit
Octave-Forge Package Management
Octave-forge packages are NOT pre-installed on sharcnet systems. Users must therefore download, install then manage the versions needed for their research. An explanation of how to handle this task is provided within this section:
DOWNLOADING AND INSTALLING PACKAGES
The "Octave Forge" http://octave.sourceforge.net/ project provides extra packages for use with octave that can be downloaded into a directory such as ~/my_octave_sources then manually installed into your own sharcnet account as will be shown in the follow example. A current list of packages available for download that notable are generally only compatible with the latest major release of octave cat be found here http://octave.sourceforge.net/packages.php.
In the event where the major version of octave on sharcnet you are using (for instance 3.4.x) is not the same as latest major version (at the time of writing 3.6.x) and there were programming api changes between the two versions that effect the package you want to use, then you probably will need to download an older version of a package from http://sourceforge.net/projects/octave/files/Octave%20Forge%20Packages/Individual%20Package%20Releases/. for it to work.
To help estimate the package version required as a starting point, consider the major release dates of recent which are octave-3.4.3 (10/10/11), octave-3.6.0 (01/15/12), octave-3.6.1 (02/22/12) and finally octave-3.6.2 (05/31/12). Next consider you want to download the latest geometry package that was compatible with octave-3.4.3 at the time of its release, then simply display all the archived versions as shown in the following stanza and pick the last available geometry release date before the next major release octave-3.6.0 (01/15/12). To show a list of all archived geometry versions, do the following steps:
http://octave.sourceforge.net/ Click Packages on top menu menu bar Scroll down to the miscellaneous package row and click details Click (older versions) located below "Download Package" Click Octave Forge Packages Click Individual Package Releases Please wait for the page to load ... Click "Name" at the top of first colum to sort packages alphabetically Scroll down you will find all available archived geometry packages: geometry-1.0.1.tar.gz 2011-09-27 geometry-1.1.1.tar.gz 2011-10-06 geometry-1.1.2.tar.gz 2011-10-09 geometry-1.1.3.tar.gz 2011-10-13 geometry-1.1.tar.gz 2011-10-04 geometry-1.2.0.tar.gz 2011-10-22 geometry-1.2.1.tar.gz 2011-11-02 geometry-1.2.2.tar.gz 2011-11-04 geometry-1.4.0.tar.gz 2012-01-25 geometry-1.4.1.tar.gz 2012-03-24 geometry-1.5.0.tar.gz 2012-06-05
Therefore you will download geometry-1.2.2.tar.gz (2011-11-04) since the next release geometry-1.4.0.tar.gz (2012-01-25) and then install it into octave 3.4.3 as follows:
[roberpj@tope:~/my_octave_sources] octave GNU Octave, version 3.4.3 octave:1> pkg install geometry-1.2.2.tar.gz octave:2> pkg list Package Name | Version | Installation directory ---------------+---------+----------------------- geometry | 1.2.2 | /home/roberpj/octave/geometry-1.2.2 octave:15> pkg load geometry octave:16> pkg describe geometry --- Package name: geometry Version: 1.2.2 Short description: Library for geometric computing extending MatGeom functions. Useful to create, transform, manipulate and display geometric primitives. Status: Loaded
Note: Any questions regarding package version compatibility with major or minor octave release should be referred to the developers.
ADDITIONAL EXAMPLES OF PACKAGE COMMANDS
For demonstration purpose linear-algebra will first be downloaded:
[roberpj@iqaluk:~] mkdir my_octave_sources [roberpj@iqaluk:~] cd my_octave_sources wget http://downloads.sourceforge.net/octave/general-1.3.2.tar.gz wget http://downloads.sourceforge.net/octave/linear-algebra-2.2.0.tar.gz
[myusername@orc-login1:~]octave octave:1> help pkg
To install a package such as linear-algebra do:
octave:2> cd ~/my_octave_sources octave:3> pkg install general-1.3.2.tar.gz octave:4> pkg install linear-algebra-2.2.0.tar.gz
To remove a package, from a terminal first do:
cd ~/octave rm -rf linear-algebra-2.2.0
... then from within octave do:
octave:5> pkg uninstall linear-algebra
To list all installed packages do:
octave:6> pkg list
To add a named packages to your path:
octave:7> pkg load name
To remove a named package from your path:
octave:8> pkg unload
To list all functions provided by a package:
octave:9> pkg describe -verbose all
To list functions provide by extra odepkg package:
octave:10> pkg describe odepkg
To list functions details for extra financial package:
octave:11> pkg describe financial -verbose
To get documentation for a topic such as sin do:
octave:12> doc sin
To get help using the doc command do:
octave:13> help doc
To get documentation for a topic such as matrix do:
octave:14> doc matrix
To get documentation for any topic run the doc command alone:
octave:15> doc
A COMPLETE PACKAGE EXAMPLE
This example assumes you first create two directories in your home account one being named
~/my_octave_packages
and the other
~/my_octave_sources
then download the required three tar.gz files into the latter from
http://octave.sourceforge.net/packages.php ...
[roberpj@orc-login1:~] module unload octave [roberpj@orc-login1:~] module load octave [roberpj@orc-login1:~] octave GNU Octave, version 3.4.3 octave:1> pkg prefix ~/my_octave_packages ans = /home/roberpj/my_octave_packages octave:2> cd my_octave_sources octave:3> ls miscellaneous-1.0.11.tar.gz optim-1.0.17.tar.gz struct-1.0.9.tar.gz octave:4> pkg install miscellaneous-1.0.11.tar.gz optim-1.0.17.tar.gz struct-1.0.9.tar.gz octave:5> pkg list Package Name | Version | Installation directory ---------------|---------|----------------------- miscellaneous *| 1.0.11 | /home/roberpj/my_octave_packages/miscellaneous-1.0.11 optim *| 1.0.17 | /home/roberpj/my_octave_packages/optim-1.0.17 struct *| 1.0.9 | /home/roberpj/my_octave_packages/struct-1.0.9</PRE>
References
o Octave Homepage
http://www.gnu.org/software/octave/
o Octave 725 Page Manual (Version 3.4.0)
http://www.gnu.org/software/octave/doc/interpreter/
o Statistic Package Function Reference
http://octave.sourceforge.net/doc/funref_statistics.html
o GNU Octave Wiki
http://wiki.octave.org/
o Matlab-Like Tools for HPC (article)
http://www.admin-magazine.com/HPC/Articles/Matlab-Like-Tools-for-HPC