Akio, the results of our dev tree will be different from the stable branch (as we are continually incorporating improvements in the dev tree which eventually make their way into the public stable release). The new OpenMP code will also change the results, but we have found not significant differences.
To enable usage of more than one thread (currently just in mri_ca_register), you must add the flag -openmp <numthreads> to the recon-all command line (where numthreads is, say, 8, to use 8 cores). Nick On Tue, 2012-06-12 at 18:25 +0900, Akio Yamamoto wrote: > Hi all, > > I'm attempting to build FreeSurfer with OpenMP enabled. > > After checking out a copy of the main dev trunk from the CVS repository, > I did the configuration with "--enable-openmp" option and run 'make'. > Compilation successfully finished and all of 'make check' tests passed. > > Now I have two questions. > > (1) Although 'recon-all' finished without error, the results are > slightly different from those obtained by the binary distribution > (stable v5.1.0). I also find that the message format in a log file > (recon-all.log) is not the same as that of the stable version, so I > wonder if the source code in the main dev trunk is modified/updated from > the stable version... > Is it okay to ignore the slight difference of the results? > > (2) Despite the openmp option being enabled, it looks like the program > runs as a single-thread mode. I actually find the message "NUMBER OF > OPENMP THREADS = 1" in a log file. > Do I need to specify some option when running 'recon-all' script? > > > Any suggestion and/or help would be appreciated. > > Best, > Akio Yamamoto > > > _______________________________________________ > 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.
