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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