aiko, in particular, grep on HAVE_OPENMP in the c files in dev/utils. eg gcamorph.c., also dev/mri_ca_register/mri_ca_register.c. we havent done anything with em reg, but welcome any improvements you can make per what you see with how ca_reg was done.
this is the pattern of speed improvements we've seen with openmp: https://surfer.nmr.mgh.harvard.edu/fswiki/CaRegTimings note that the nehalem/sandybridge/(newest) architecture is essential for this improvement, as it accesses scattered memory structures much more efficiently. nick > Hi Akio > > we have made some progress on this, but it is different for different > algorithms. If you get the current dev codebase you'll find some examples > of MPI pragmas. > > cheers > Bruce > On Mon, 25 Jun 2012, Akio Yamamoto wrote: > >> FreeSurfer experts, >> >> I need to make the process of each one brain 10-20 times faster somehow >> - one way should be parallelization approach. >> >> Currently I'm trying to add OpenMP parallelization to time-consuming >> part of the source code, especially mri_ca_register and mri_em_register. >> >> Not completed yet, but at this point of time, I can not see the speed-up >> in proportion to the number of CPU cores; it's just x2.5 speed-up using >> 8 or 16 cores. >> >> I'm afraid there might be fundamental limitations in algorithm and/or >> implementation of the code. >> Should I proceed with this work? >> >> Any advice, help or comment would be appreciated. >> >> Akio >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
