On 07/12/2013 12:15 PM, Dorian P. wrote:

Dear list,

We are buying a computer dedicated mostly to Freesurfer. Initially we thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good choice. However, I noticed that Freesurfer seem better tuned to use CUDA. Many of the messages I read are from 2010 so I am not sure whether this is the case.

In sum is it better to focus on CUDA gpu or on Intel I7?

Second, does the CUDA speeds matter a lot?

Go with the I7 3770k Ivy Bridge. Spec'ing out a system to run Freesurfer with CUDA is not recommended for a long term solution. The reasons being that first and foremost we actually no longer support CUDA development at this time. We distribute the libraries with freesurfer and some users have reported success running recon-all with CUDA but we no longer support it. It has become too cumbersome to keep up with all the versions of the graphics cards and libraries and their respective compatibilities.

Third, is it true that I will not be able to run multiple instances of Freesurfer with CUDA, which is possible with I7? Will it still be faster using CUDA rather than running a Freesurfer instance on each I7 core?

Yes, its true that you will not be able to run multiple instances of Freesurfer with CUDA. When running a recon using CUDA you are only allowed a single subject to run with the GPU. All other subjects must be run against the CPU and if a request is made to the GPU while in use, a very cryptic error message is received.

Fourth, is the OS important, for example can we just continue on Ubuntu or is it better Debian/CentOS etc.?

Freesurfer is built against CentOS4, CestOS6 (as well as various MacOSX platforms) and advertised as such. However we have many users who successfully run Freesurfer on Ubuntu platforms.

-Zeke