[phenixbb] OpenMP incompatible with Phenix GUI?
nechols at lbl.gov
Wed Apr 7 10:21:36 PDT 2010
On Wed, Apr 7, 2010 at 10:03 AM, Donnie Berkholz <dberkholz at gentoo.org>wrote:
> I would really like to use OpenMP parallelization and also use the
> Phenix GUI. When I attempted a source build with OpenMP support, I was
> informed that the two were incompatible. My understanding is that this
> used to work fine with the old wizards. Would it be possible to fix
The OpenMP incompatibility has to do with the way the GUI used to run every
process - some weird conflict with Python threading, we think. Now that it
is possible to run fully "detached" jobs from the GUI, I think it should be
possible to turn OpenMP on for just these jobs. I will look into this.
However, I think you're confusing the different kinds of parallelization we
use. OpenMP works at the level of C++ 'for' loops, and is used in the FFT
for phenix.refine, and some parts of Phaser, so you'll get a little speed
boost on those apps - but in our experience this is rarely better than 2x,
if that, regardless of # of CPUs. AutoBuild (and related programs) actually
spawns several parallel jobs, which do most of the work independently, and
this scales very well (and potentially over multiple machines). This is
also supported in the GUI (and it tries to detect how many cores you have
and set the 'nproc' parameter appropriately).
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