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
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