And that ofcourse was the partial answer, as listed on wiki page, I need to apply a data dir,, these links are pointing to missing files. Will retry Monday.
-Henk
[hmeij@n78 freesurfer-gpu.git]$ find . -name *glnxa64* -exec ls -l {} ; lrwxrwxrwx 1 hmeij its 195 Nov 17 08:14 ./scripts/fs_spmreg.glnxa64 -> ../.git/annex/objects/9g/2q/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a lrwxrwxrwx 1 hmeij its 196 Nov 17 08:14 ./fsfast/bin/fast_selxavg3b.glnxa64 -> ../../.git/annex/objects/5P/qx/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce lrwxrwxrwx 1 hmeij its 194 Nov 17 08:14 ./fsfast/bin/mkcontrast2m.glnxa64 -> ../../.git/annex/objects/P7/77/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Meij, Henk hmeij@wesleyan.edu Sent: Friday, November 17, 2017 6:35:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] cuda compile help
I should have mentioned, i did not do any data dirs step, confused on this, just hoping to compile gpu code
-Henk
----- Reply message ----- From: "Meij, Henk" hmeij@wesleyan.edu To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] cuda compile help Date: Fri, Nov 17, 2017 6:24 PM
cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env recap:
999 cd /usr/local/freesurfer-gpu.git/ 1001 export PATH=/usr/local/cuda-8.0/bin:$PATH 1002 export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64 1004 make clean 1008 ./setup_configure | tee -a setup_configure.log 1011 ./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda-8.0 | tee -a configure.log 1012 time make -j4 | tee -a make.log 1013 make install
[hmeij@n78 freesurfer-gpu.git]$ grep nvcc Makefile NVCC = /usr/local/cuda-8.0/bin/nvcc
Q1 what causes this and how to fix, make install fails /bin/install -c fs_spmreg.glnxa64 irepifitvol.glnx64 /usr/local/freesurfer-6.0.0/bin /bin/install: cannot stat â_spmreg.glnxa64âNo such file or directory /bin/install: cannot stat âepifitvol.glnx64âNo such file or directory make[2]: *** [install-data-local] Error 1 make[2]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make: *** [install-recursive] Error 1
Q2 no cuda packages, maybe related to Q1
[hmeij@n78 freesurfer-gpu.git]$ ls /usr/local/freesurfer-6.0.0/bin/*cuda* /usr/local/freesurfer-6.0.0/bin/cuda_setup
Thanks for any help. -Henk