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.) -- Thanks, Donnie 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 612-991-1321