[phenixbb] OpenMP incompatible with Phenix GUI?

Donnie Berkholz dberkholz at gentoo.org
Wed Apr 7 13:12:32 PDT 2010

On 10:21 Wed 07 Apr     , Nathaniel Echols wrote:
> 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.  

Dear Nat,

Thanks for looking into it! I am aware of the different types of 
parallization and would like to use the OpenMP support. A 2x difference 
may seem negligible to you, but I've got refinement jobs that can take 8 
hours on my dual-core laptop so any improvement is welcome.

(It seems that 12x NCS + 16 TLS groups per chain makes phenix.refine a 
sad boy, at least on my protein, whereas Refmac completes in minutes.)


Donald S. Berkholz, Postdoctoral research fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905

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