[phenixbb] parallel phenix.phaser on SGE cluster

L. Costenaro (IBB) lionel.costenaro at bioinf.uab.es
Thu Jul 11 07:14:31 PDT 2013

Thanks for your replies Nat and Jon,

Given the answer of Nat, phenix.phaser is not (by default) OpenMP, which
explains the non-parallel behaviour of my phenix.phaser.
I think I have been misleading by the GUI behaviour that actually show 3
threads for python (1 for phenix and apparently -for some reason- 2 for the
phaser gui, one of those disappearing quickly).

As I want to run phaser with a few different model, but as quick as
possible, I switched to the ccp4 phaser that parralelize and run well on
the cluster.

Best regards,

2013/7/10 Nathaniel Echols <nechols at lbl.gov>

> 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.)
> -Nat
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