Hi Malcolm in collaboration with IBM we are also looking at MPI and pthreads.
cheers Bruce On Fri, 13 Jan 2012, Malcolm Tobias wrote: > > Is there a standard benchmark for FreeSurfer? > I've been using the data under subjects (Bert?/Ernie?) and running a recon- > all: > > recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz -all > > On our hardware using the 5.1 distributed binary (freesurfer-Linux- > centos4_x86_64-stable-pub-v5.1.0.tar.gz) it takes about 12 hours. > > I was surprised that 5.1 was running so much faster than 5.0. With 5.0 > (freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.tar.gz) it was taking about > 18 hours. Did anyone else notice a big speed-up from 5.0 to 5.1? Maybe it's > a difference between centos5 vs. centos4? If so, wouldn't you expect the > former to be faster? > > If I back-port the changes Nick made to configure.in for the dev branch to the > stable release of 5.1 and build from source on our systems, I'm able to run in > ~10 hours. I'm guessing this is mostly due to the difference in the versions > of gcc used on our system (4.1.2) vs. those used for the centos4 distributed > binary? > > For the dev release, it's taking about ~11 hours. I'm guessing the dev branch > is mostly focused on features/bug-fixes and performance is only looked at > before a release? > > Besides GPUs, what else are people doing to increase performance? > > Cheers, > Malcolm > > _______________________________________________ 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.
