Singularity mode improvement and bugfixes

• Create /tmp script on the fly for qsub
• psom_console handle psom_gb_local_var.m path and loading process
• psom_console.m will load a psom.conf file that is in the same directory

Singularity support with bug fixes

Add support to run on hpc with singularity containers (http://singularity.lbl.gov/)

Singularity support

Add support to run on hpc with singularity containers (http://singularity.lbl.gov/)

alpha release 2.0.1

Bug fixes for Matlab.

alpha release of PSOM 2.0

The 2.0 release of PSOM is almost ready. Changes visible to the users are minor:

• more compact verbose,
• better error messages,
• better handling of figures.

Major changes under the hood: the execution engine has been completely redesigned. If PSOM is using up to 100 parallel processes, only 100 instances (at most) of Matlab/Octave will be started. PSOM will distribute the jobs to these "workers", independently of the number of jobs. This process is more efficient and scalable than the one implemented in PSOM 1.0, and will handle smoothly tens of thousands of jobs and hundreds of execution nodes. Probably scales to thousands of execution nodes, but has not been tested yet in these conditions. PSOM 2.0 will also be very reactive on a multicore laptop or workstation.

Disclaimer: This version is a pre (alpha) release, which lacks some features in terms of fault tolerance and resource optimization. Not to use in production.

PSOM version 1.2.0

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 version 1.0.4

• Keep figures in the background while processing pipelines.
• Better catching of warnings inside the logs. Cleaner verbose.
• Default execution mode is now background for both the jobs and the pipeline manager.

PSOM version 1.0.3

• Support for condor.
• Better handling of warning/error message.
• Figures are now kept in the background.

Version 1.0.2

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