Wil, this is correct, we do not officially support a centos5 build, because the centos4 build works on centos5, and we want to make public distributions and maintenance as simple as possible.
in future, we will start releasing a centos6 build, because we will begin using openmp in our builds, but openmp is only supported in gcc 4.2 and later, which centos4 and centos5 do not have, but centos6 does. N. On Thu, 2012-01-19 at 23:49 +0000, Irwin, William wrote: > 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.
