External Email - Use Caution Hello Christian,
I have not checked 'make check' procedure, 'recon-all' with my compiled binary was finished without error and segmentation results looks nice. It may be OK for my environment. Using '-use-gpu' and '-openmp 8' flag, the time of 'recon-all' reduced to around 4 hours from 12 hours without flag in my PC environment (Xenon E5-2620 [2.00GHz/15M/6Core-12Thread] x 2 + Tesla C2075 6GB x2 ). At the first time in build freesurfer, I have not known my Tesla GPU (fermi-architecture of sm_20) was not supported in CUDA 9.1 (distribution in Ubuntu 18.04 package). I have tried to configure with '--with-cuda = /usr'. 'make -j4 'was completely finished but cuda related binary (such as 'mri_em_register_cuda') have not compiled and not installed. Then I made '/usr/local/cuda' directory and include and library path was linked in '/usr/local/cuda' directory cd /usr/local/cuda sudo ln -s /usr/include include sudo ln -s /usr/lib/x86_64-linux-gnu lib sudo ln -s /usr/bin bin and NVIDIA_ARCH in 'configure.in' was edited to sm_11 to sm_30, configure with '--with-cuda=/usr/local/cuda' flag. It can compiled cuda related binary. However my GPU architecture does not support sm_30, 'recon-all' was stopped with error of ---------------------------------------------------------------------------------- CUDA Error in file '../include/ctfactory.hpp' on line 96 : invalid texture reference. Abort (core dumped) --------------------------------------------------------------------------------- After that, I did extract cuda_cluster_pkgs_8.0.61_ubuntu1604.tar.gz and compiled freesufer binary again. GPU architecture and related CUDA version was reffered in the following URL http://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/ >P.S. Kazuhiro, I tried your 8-step procedure above, but on step 2 I got an >error building vxl that it could not find the '-lgeotiff' flag used in one of >the cmake commands. I tried debugging but found no help online. Any advice? I remeber ubuntu 18.04 package of libgeotiff-dev was installed after vxl compilation error appeared. You might require sudo apt install libgeotiff-dev. -------------------------------------------------------------- Kazuhiro Nakamura, Ph.D. Research Institute for Brain and Blood Vessels-Akita 6-10 Senshukubota machi, Akita 010-0874 JAPAN phone +81-18-833-0115 ext 769, fax +81-18-833-2104 E-mail: k...@akita-noken.jp _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer