OpenMP (depending how efficiently FreeSurfer can be parallelized) would be a great benefit here.
I have no idea what's causing the centos4 vs. 5 results, but it might be interesting to start collecting some performance data if enough people are interested. All the benchmark numbers I've mentioned have been run on Nehalem based x5550 CPUs. I only run 1 job/node, so the Turbo-mode is probably kicking in. Cheers, Malcolm On Wednesday 18 January 2012 12:09:32 Nick Schmansky wrote: > Malcolm, > > actually, they (IBM) are looking at openmp (to allow multiple threads to > process for-loops) and SSE3 instructions (better vectorization). > > recon-all --help contains some timings for an AMD processor. centos4 > vs. centos5 itself should not account for any speed differences, but it > is true that our centos5 build was built with gcc 4.1 while our centos4 > build uses gcc 3.4.7, so those compiler difference likely account for > speed differences. > > another major factor that affects runtime is whether the Intel Nahalem > architecture exists on your system. this memory controller is much > better at handling the wide memory layout of freesurfer structures > (minimizing cache-line hits). > > Nick > > On Fri, 2012-01-13 at 09:13 -0500, Bruce Fischl wrote: > > 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. -- Malcolm Tobias 314.362.1594 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
