I think IBM has a better compiler. Better than gcc and slightly slower than intel compiler
Sent from my iPad On Jan 18, 2012, at 16:09, Nick Schmansky <ni...@nmr.mgh.harvard.edu> 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 >> >> > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
