Hi,
Has all of the GPU code also been updated in the new FS6.0 version or the code is still from the old 5.x but can be compiled with new cuda toolkits?
Best regards,
--
Shahid.
On Mon, Nov 27, 2017 at 9:29 PM, Meij, Henk hmeij@wesleyan.edu wrote:
Well, it looks the *_cuda files for mri_glmfit and mri_robust_register and some others were dropped from the repository. Downloaded fresh copy today but the files are not there. So no errors.
-Henk
*From:* Meij, Henk *Sent:* Monday, November 27, 2017 11:02:44 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* GPU compile cuda8/centos7
Just wanted to report back a success. I had to do some fixes so hope this helps anybody.
My gpus are GTX1080Ti and the CPU involved is E5-2620 dual 10 core on this server.
The vanilla cpu recon-all finished in 7 hours, the gpu run finished in 4.3 hours.
Q: I seem to not have any errors or indications why mri_glmfit or mri_robust_register cuda binaries did not compile. Any ideas?
-Henk
In configure file (from previous post) comment out the with_cuda="" line https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2016-June/046236.html CUDA_DIR="" with_cuda=""
In utils/mrifilter.c uncomment line defining 'int width, weight, height' above the test if (width <=1 || height <=1 || depth <=1) on line 3005
then find Makefiles with incorrect gpu arch for the gpu packages change architecture from sm_?? to sm_61 (multiple times per file)
which nvcc
export PATH=/usr/local/cuda/bin:$PATH locate libcuda.so export LD_LIBRARY_PATH=/usr/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH
./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda make clean make -j 4 make install
yields
./bin/mris_flatten_cuda ./bin/mris_sphere_cuda ./bin/mris_fix_topology_cuda ./bin/mri_segstats_cuda ./bin/mri_em_register_cuda ./bin/mri_vol2vol_cuda ./bin/mris_inflate_cuda ./bin/mri_ca_register_cuda
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