[phenixbb] parallel phenix.phaser on SGE cluster

Nathaniel Echols nechols at lbl.gov
Wed Jul 10 11:18:59 PDT 2013

On Wed, Jul 10, 2013 at 7:16 AM, L. Costenaro (IBB)
<lionel.costenaro at bioinf.uab.es> wrote:
> I am trying to run phaser in a SGE cluster (qsub) using multiple proc
> (either phenix.phaser from the command line or phaser-MR from the GUI), but
> the jobs do not parallelize. When I run the phaser-MR locally (same
> executable) it does parallelize (multiple python threads).

I'm a little confused - what parameters are you using and what
behavior do you expect?  As distributed, Phaser itself (i.e. the
Phaser-MR or Phaser-EP GUIs, or phenix.phaser) will not run in
parallel, regardless of whether you're running the jobs on a cluster
or locally.  If you want to use the OpenMP compiler extensions to
parallelize single jobs, you need to build from source *without the
Phenix GUI*, because OpenMP does not play nicely with Python
multiprocessing (or vice-versa, I guess).  I'm not sure what makes you
think it's being run in parallel locally, but I suspect you're being
confused by the fact that executing a job from the GUI starts a
separate process.

The MR programs that run in parallel are a) phaser.MRage, Gabor's
automated system which is designed to try many different models
(including different model preparation protocols), and b) my somewhat
obsolete "parallel Phaser" GUI, which is a much more minimalist
approach.  These can both execute on a cluster, but the individual
jobs will still be single-processor.  (Currently both are still
flagged as "alpha" features in the GUI, although MRage will hopefully
be a fully supported program in the near future.)


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