Thanks for pointing out that link. The graph makes the point I was going to mention, i.e. that you notice a big difference in using up to about 4 processors for typical jobs, but after that point the non-parallelisable parts of the code start to dominate and there's less improvement. This is very useful if you have one MR job to run on a typical modern workstation (2-8 cores), but if you have several separate jobs to run then you're better off submitting them simultaneously, each using a subset of the available cores. Of course, that assumes you have enough memory for several simultaneous separate jobs!
Regards, Randy Read On 9 Nov 2011, at 07:21, Ed Pozharski wrote: > See page 3 of this > > http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf > > > > On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote: >> Hello, >> >> How faster is the OpenMP version of Phaser >> versus number of cores used? >> >> In the past I have been quite badly surprised by >> the no-acceleration I gained when using OpenMP >> with some of my programs... :( >> >> Regards, >> F. >> >> On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote: >>> Hi Ed, >>> >>> in the CCP4 distribution, openmp is not enabled by default, and there >>> seems to be no easy way to enable it (i.e. by setting a flag at the >>> configure stage). >>> >>> On the other hand, you can easily create a separate build for phaser >>> that is openmp enabled and use phaser from there. To do this, create a >>> new folder, say "phaser-build", cd into it, and issue the following >>> commands (this assumes you are using bash): >>> >>> $ python $CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py >>> --repository=$CCP4/src/phaser/source phaser >>> --build-boost-python-extensions=False --enable-openmp-if-possible=True >>> >>> $ . ./setpaths.sh ("source ./setpaths.csh" with csh) $ libtbx.scons (if >>> you have several CPUs, add -jX where X is the number of CPUs you want to >>> use for compilation) >>> >>> This will build phaser that is openmp-enabled. You can also try passing >>> the --static-exe flag (to configure.py), in which case the executable is >>> static and can be relocated without any headaches. This works with >>> certain compilers. >>> >>> Let me know if there are any problems! >>> >>> BW, Gabor >>> >>> On Nov 8 2011, Ed Pozharski wrote: >>> >>>> Could anyone point me towards instructions on how to get/build >>>> parallelized phaser binary on linux? I searched around but so far found >>>> nothing. The latest updated phaser binary doesn't seem to be >>>> parallelized. >>>> Apologies if this has been resolved before - just point at the relevant >>>> thread, please. >>>> >>>> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
