To close this thread, on centos7 'git annex' is an invalid command. That can be
fixed with
yum install epel-release
yum install git-annex
git-annex get --metadata fstags=makeinstall .
Now the 'make install' finishes without errors.
-Henk
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Meij, Henk
<hm...@wesleyan.edu>
Sent: Saturday, November 18, 2017 11:28:09 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] cuda compile help
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Meij, Henk
<hm...@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" <hm...@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
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