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− | The Graham national system uses the Slurm scheduler which is different from the Torque Moab scheduler that is typical to the majority of other SHARCNET systems. In order to submit a simple " | + | The Graham national system uses the Slurm scheduler which is different from the Torque Moab scheduler that is typical to the majority of other SHARCNET systems. In order to submit a simple "Hello World!" process to Graham the user would first need to create a submit script as follows. |
$ cat oct_serial.sh | $ cat oct_serial.sh |
Revision as of 13:34, 8 May 2018
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.
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
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
Similarly, to load the default Octave module (currently version 3.8.1) one would do:
module unload intel module load octave
On the Graham national system
The module setup on the new national systems general purpose systems Graham and Cedar are slightly different from other SHARCNET systems. The module loading procedures introduce more automation of dependency interactions.
On the Graham system the user simply needs to call the "module load" command without manually unloading conflicting packages.
$ module load octave/4.2.1
To obtain information about the package's dependencies the "spider" action can be included in the call to "module":
$ module spider octave --------------------------------------------------------------------------------------------------------------------------------------------------------- octave: --------------------------------------------------------------------------------------------------------------------------------------------------------- Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. - Homepage: http://www.gnu.org/software/octave/ Versions: octave/4.2.1 --------------------------------------------------------------------------------------------------------------------------------------------------------- For detailed information about a specific "octave" module (including how to load the modules) use the module's full name. For example: $ module spider octave/4.2.1 --------------------------------------------------------------------------------------------------------------------------------------------------------- [jdesjard@gra-login1 ~]$ module spider octave/4.2.1 --------------------------------------------------------------------------------------------------------------------------------------------------------- octave: octave/4.2.1 --------------------------------------------------------------------------------------------------------------------------------------------------------- Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. - Homepage: http://www.gnu.org/software/octave/ Properties: Tools for development / Outils de développement You will need to load all module(s) on any one of the lines below before the "octave/4.2.1" module is available to load. nixpkgs/16.09 gcc/5.4.0 nixpkgs/16.09 intel/2016.4 nixpkgs/16.09 intel/2017.1 Help: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. - Homepage: http://www.gnu.org/software/octave/
Job Submission
On SHARCNET clusters for production work 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
On the Graham national system
The Graham national system uses the Slurm scheduler which is different from the Torque Moab scheduler that is typical to the majority of other SHARCNET systems. In order to submit a simple "Hello World!" process to Graham the user would first need to create a submit script as follows.
$ cat oct_serial.sh #!/bin/bash #SBATCH -t 0-00:01 #SBATCH --mem=400 octave --eval 'disp("Hello World! from Octave")'
Then pass this submit script to "sbatch" to be entered into the queue:
$ sbatch --account=accountname oct_serial.sh
... where "accountname" is the name of the accounting group to submit to (e.g. def-groupname, rgg-projectname).
Example Job
This section shows howto submit a sample.m file to the serial queue that accepts command line arguments.
[roberpj@hnd20:~/samples/octave/args] cat sample.m #! /bin/octave -qf printf ("%s", program_name ()); arg_list = argv (); for i = 1:nargin printf (" %s", arg_list{i}); endfor printf ("\n");
To eliminate exatraneous verbosity in the output file two switches are passed:
[roberpj@hnd20:~/samples/octave/args] sqsub -r 60m -o ofile.%J octave -qf --no-window-system sample.m arg1 arg2 arg3 etc WARNING: no memory requirement defined; assuming 2GB per process. submitted as jobid 6937872
The output file from the job appears as:
[roberpj@hnd20:~/samples/octave/args] cat ofile.6937872.hnd50 sample.m arg1 arg2 arg3 etc
Running in the development nodes
Besides running production work in Octave via the scheduler on SharcNET systems it is also possible to use Octave interactively on systems' development nodes.
To start Octave from a development node one can login to a system with trusted X11 forwarding enabled:
ssh -Y username@kraken.sharcnet.ca
Then login to one of the development nodes with trusted X11 forwarding enabled:
ssh -Y kraken-devel1
Once logged into the development node one can load the Octave modules and launch the program:
module unload intel module load octave octave
GNU Octave, version 3.8.1 Copyright (C) 2014 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type 'warranty'. Octave was configured for "x86_64-unknown-linux-gnu". 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/get-involved.html Read http://www.octave.org/bugs.html to learn how to submit bug reports. For information about changes from previous versions, type 'news'. octave:1>
With X11 forwarding enabled in the development node interactive work with Octave can include figure generation.
One the Graham nation system
Rather than dedicated development as it typical on some of the other SHARCNET systems the national systems have nodes that prioritize interactive jobs allocated by call to "salloc" of the Slurm scheduler.
To use Octave interactively on Graham you can do the following:
Use salloc to request a single task for one hour:
$ salloc --account=def-roxa88 --time=1:0:0 --ntasks=1
Then you will receive notification when the reservation is granted (including jobid), for example:
salloc: Granted job allocation 12345
Then use srun to start a terminal to work in on the reservation:
$ srun --wait 0 --pty bash
Once running the terminal in the allocation you can start your work with Octave by loading the module and starting the program:
$ module load octave $ octave octave: X11 DISPLAY environment variable not set octave: disabling GUI features GNU Octave, version 4.2.1 Copyright (C) 2017 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type 'warranty'. Octave was configured for "x86_64-pc-linux-gnu". 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/get-involved.html Read http://www.octave.org/bugs.html to learn how to submit bug reports. For information about changes from previous versions, type 'news'. octave:1>
... Then once you have the "octave:#>" prompt the terminal will behave like the Matlab command line.
Once you are finished with Octave use "quit" to exit the program, then "exit" to logout of the compute node (terminate srun), then "exit" again to terminate the allocation (relinquishing the allocate resources).
Running on a visualization system
Once logged in to a visualization system an instance of Octave can be launched from Applications Menu > Eduction > GNU Octave.
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.
In order to run Octave so that it interprets scripts as closely as possible to Matlab, use the --traditional flag. Taking from the above sqsub example the maximum Matlab compatible submission would be:
sqsub -r 60m -o ofile.%J octave --traditional mycode.m
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.
Octave-Forge
Octave-forge packages are not pre-installed on SHARCNET clusters since none are available at this time for the operating system. Therefore any required packages must be downloaded, manually installed from source and then managed in local user accounts (as described below).
However 16 of approximately 95 octave-forge packages are installed on some sharcnet visualization workstations including viz1,2,3-uwaterloo, viz2-uwo, viz6-uoguelph under /usr/share/octave/packages. As a word of caution however, all package versions will likely be significantly old since they are tied to the operating system fedora /etc/redhat-release major version and hence not contain recent critical bug fixes (which could be numerical in nature). Users are therefore strongly recommended to likewise download and install the latest version similarly as would be done on the clusters.
Sharing Packages
Note that packages installed by a single sharcnet user in their home account can be shared out to other research group members or even among general SHARCNET users. To do this simply set access permissions for group or global read access accordingly. For details on how to change the permissions see: https://www.sharcnet.ca/help/index.php/Knowledge_Base#How_do_I_give_other_users_access_to_my_files_.3F
Managing 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.
Package Commands
Additional examples of package commands are shown in this section. 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
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