Tool/Resource: Pipeline system for Octave and Matlab - News

PSOM release 1.2.0

pbellec@stage.nitrcce.org (Pierre Bellec) — Tue, 07 Jul 2015 13:00:01 GMT

Main new features are:
* Improved, more concise verbose. Three levels are now supported for opt.flag_verbose: 0: minimal verbose. 1: default (concise) verbose. 2: extensive verbose, suitable for debugging.
* Figures are generated in the background.
* Killing the pipeline manager (i.e. deleting PIPE.lock) will now kill all active jobs, regardless of the execution mode.
* Jobs that become inactive are automatically detected and counted as failed.

This release should work on Octave and *nix systems, and likely on OSX as well. As not been tested much on matlab, and not at all on windows. But it may work. Feeback welcome.

PSOM website

pbellec@stage.nitrcce.org (Pierre Bellec) — Tue, 30 Sep 2014 14:48:43 GMT

The PSOM website has just gone live, featuring a fully revamped documentation.

http://psom.simexp-lab.org/

PSOM now on github

pbellec@stage.nitrcce.org (Pierre Bellec) — Thu, 17 Jul 2014 1:34:44 GMT

The PSOM code repository has moved to https://github.com/SIMEXP/psom

The wiki can now be found at https://github.com/SIMEXP/psom/wiki

PSOM release 1.0.2

pbellec@stage.nitrcce.org (Pierre Bellec) — Tue, 27 Aug 2013 15:10:58 GMT

Bug fix for the 1.0.1, the update feature was broken for jobs with Inf (or -Inf) values in their options.

PSOM release 1.0.1

pbellec@stage.nitrcce.org (Pierre Bellec) — Tue, 27 Aug 2013 15:10:47 GMT

New PSOM release 1.0.1. This release adds a few minor features:
* Support of a new field DEP in a job description. This field can be used to explicitly list a list of dependencies (cell of strings with job names). The field DEP is dealt with appropriately by PSOM_MERGE_PIPELINE.
* In qsub/msub modes, job names are now truncated to 8 characters before submission to qsub/msub. This was implemented because long job names crash some flavors of qsub/msub.
* PSOM_CMP_VAR now work on structures with similar fields names but where the field names have not been built in the same order (i.e. the function is insensitive to the order of field names). This impacts only octave, as in matlab fields are ordered alphabetically, independently of the order of creation.
* PSOM_CMP_VAR now has options to control the level of tolerable numerical noise as well as the ability to compare only the fields found in one of the variables (when comparing structures).
* In qsub/msub mode, the subprocesses initiated by PSOM to quickly submit jobs are now terminated cleanly (before it left some zombie jobs behind).
* Minor bug fixes and doc improvement.

PSOM presentation at HBM 2013

pbellec@stage.nitrcce.org (Pierre Bellec) — Sun, 16 Jun 2013 4:33:22 GMT

There will be presentation on PSOM given tomorrow by Christian Dansereau at the educational course of the Human Brain Mapping conference 2013, entitled "Neuroimaging ‘Big Data’ Challenges and Computational Workflow Solutions" and organized by Ivo Dinov. The pdf of the presentation has been posted on the download section.

PSOM 1.0 released

pbellec@stage.nitrcce.org (Pierre Bellec) — Thu, 13 Dec 2012 15:42:16 GMT

After over a year of test, it is finally time to release PSOM 1.0. This is a stable, production release that includes all of the features planned on the initial roadmap (and a few more).

New logo

pbellec@stage.nitrcce.org (Pierre Bellec) — Mon, 18 Jun 2012 18:46:22 GMT

PSOM has new logo, that was designed to avoid any confusion between PSOM and a popular (although rather old) video game.

PSOM paper published

pbellec@stage.nitrcce.org (Pierre Bellec) — Wed, 04 Apr 2012 13:59:17 GMT

There is now a published paper providing an overview of PSOM features and implementations:
Bellec P, Lavoie-Courchesne S, Dickinson P, Lerch JP, Zijdenbos AP and Evans AC (2012) The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front. Neuroinform. 6:7. doi: 10.3389/fninf.2012.00007

http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2012.00007/abstract

PSOM release 0.9

pbellec@stage.nitrcce.org (Pierre Bellec) — Thu, 01 Dec 2011 15:49:30 GMT

PSOM r0.9 had just been released and can be downloaded from here:
http://www.nitrc.org/frs/?group_id=316

This is the PSOM candidate release, with all the features planned for PSOM 1.0 available. A paper of PSOM has also been submitted for publication, with a detailed description of the PSOM design and implementation. This will be made avaiable on the PSOM website upon acceptance. If you are using PSOM and find it useful, it is now an excellent time to show your support by filling in an evaluation on the NITRC website:
http://www.nitrc.org/rating/show_results.php?group_id=316

The main changes since PSOM 0.8.8 are:
* The PSOM has now been tested on a variety of operating systems (Linux, Windows, Mac OSX), with both Matlab and Octave and with different configurations. So far, the only issue that was found was the 'background'/'batch' modes for Octave on Cygwin (Windows).
* A new function PSOM_CONFIG. It will test step-by-step that the submission of jobs is successful, and provide context-dependent error messages and suggestions if an issue is detected. This function should help a lot setting up the configuration of PSOM.
* A new wiki page providing [http://code.google.com/p/psom/wiki/CodingGuidelines coding guidelines] for PSOM users.
* A new execution mode : 'background'. In this mode jobs run in the background, and they will get interrupted if the initial matlab/octave session is interrupted (which is not the case in 'batch' mode). The default mode is now 'session' for the pipeline manager, and 'background' for the jobs.
* The [http://code.google.com/p/psom/wiki/ConfigurationPsom PSOM configuration tutorial] has been updated to reflect the changes made in release 0.9.
* The [http://code.google.com/p/psom/wiki/HowToUsePsom PSOM tutorial] has been updated to match the reflect made to `psom_demo_pipeline` in release 0.9.
* Many minor bug fixes and improvements.
A more detailed list of changes can be found in the [http://code.google.com/p/psom/wiki/ReleaseNotes release notes].