Hi Nick- I was explicitly told by you there was not stable centos5 release of 5.1. And unless it is located elsewhere, it is not located in:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/ Can you please clarify this? Thanks, Wil |-----Original Message----- |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] |Sent: Wednesday, January 18, 2012 10:10 AM |To: Bruce Fischl |Cc: freesurfer@nmr.mgh.harvard.edu; Malcolm Tobias |Subject: Re: [Freesurfer] Performance questions | |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.
