Hi Richard,

That information was a lot helpful. At this point I'm currently trying to reduce the recon-all processing time as much as possible and for this reason I was looking to get the -use-gpu flag working. I'm currently running a freesurfer v6 beta version on Ubuntu 14.04.4. With regard to the graphic card it is a dual K2200 configuration (I guess they are running in sli configuration - although I'm not completely sure).

When you mentioned you compiled everything, I believe you were referring to compiling CUDA 7.5 for Ubuntu 14.04. Because after seeing the link - https://developer.nvidia.com/cuda-gpus

- we settled for CUDA 5 since it was the compatible version mentioned for K2200. Does that mean CUDA 7.5 is backwards compatible with a slight tinkering and can be used with freesurfer 6.0 ?

I however tried to setup CUDA 5 following the instructions in the link - http://www.unixmen.com/how-to-install-cuda-5-0-toolkit-in-ubuntu/ - however, I'm not able to get it running. I keep getting the following error "Unable to acquire CUDA device". Does this sound familiar ?

If you can share some more information in setting this up it will be great since the amount of time recon-all takes is quite too long for running multiple datasets. Most importantly we are concerned about the hippocampal segmentation in freesurfer 6 rather than recon-all and so speeding this up would be extremely helpful.

Thank you,

Tyson

On Thu, Mar 3, 2016 at 2:23 PM, R Edgar <freesurfer.rge@gmail.com> wrote:

On 3 March 2016 at 13:22, Francis Tyson Thomas
<francistthomas@email.arizona.edu> wrote:

> Also, it looks like development for GPU usage has been halted for now and so
> I was trying to use the CUDA 5 for getting it working under ubuntu 14.04. I
> have been not successful that as the cuda device isn't getting selected. Do
> you have any recommendations on that?

I have recently started looking at the CUDA port again, although I'm
making no promises as to the amount of time I'll have to spend on it.
This said I've got mri_ca_register running with CUDA 7.5 on my
machine. On my E3 Xeon with a K1200, I can run mri_ca_register with
the test dataset in about 9 minutes.

Are you compiling from source? I had to tamper a bit with the
configure script before compiling CUDA was enabled again. I don't have
access to the right machine at the moment, but as I recall, there was
a line
with_cuda=""
which I had to comment out, since it was overriding the path to the
machine's CUDA installation which I was passing on the command line.
There are a few other minor bug fixes and performance improvements for
GPU code which I've submitted for Zeke; no new kernels yet, I'm
afraid.

If you could give me some more details about what you're doing, I may
be able to help.

Just the standard warning: the GPU results will be different from the
CPU results on the same inputs. We've been kicking around some ideas
recently to quantify how different (and to devise input datasets where
the correct answers are unambiguous).

Regards,

Richard
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