[Neurodebian-devel] Could you enable fls-5.0-gpu package by default?

[Michael Hanke]

Hey,

On Sun, May 29, 2016 at 01:21:56PM +0200, Michal Hocko wrote:
> > There was no attachment -- please resend.
> 
> Sorry about that. See attached.

Thanks!

> I guess so. nifti and newmat headers have to be specified in the build
> env.
> Please also note 5.0.7 needs one more fix to address sqrt nvcc linking
> issue. This seems to be fixed in 5.0.9 version. I have attached this one
> as well (workaround-nvidia-linkage-issue).

I will not worry about older version and start with the latest 5.0.9.

I have applied your patches to the current source package version
(sources are here:
http://anonscm.debian.org/cgit/pkg-exppsy/fsl.git/log/?h=gpu). This is
how far I get:


g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_LIBFREETYPE -fPIC -I/usr/include/nifti -I/usr/include/gifti -I/usr/include/newmat -I/home/mih/debian/fsl/fsl/extras/src/libprob -I/home/mih/debian/fsl/fsl/extras/src/libcprob -I/home/mih/debian/fsl/fsl/src        -I/usr/include/newmat -I -I/home/mih/debian/fsl/fsl/extras/include/libcprob -I/home/mih/debian/fsl/fsl/extras/include/libprob -I/usr/include/boost -I/usr/include -I/usr/include/nifti -I. -I/home/mih/debian/fsl/fsl/include -I/home/mih/debian/fsl/fsl/include -Wl,-z,relro -Wl,--no-undefined -L/usr/lib/fsl/lib -L/usr/lib -L -L/home/mih/debian/fsl/fsl/extras/lib -L/home/mih/debian/fsl/fsl/extras/lib -L/usr/lib -L. -L/home/mih/debian/fsl/fsl/lib -L/home/mih/debian/fsl/fsl/lib -o xfibres_gpu xfibres_gpu.o xfibresoptions.o diffmodels.o Bingham_Watson_approx.o -lwarpfns -lbasisfield -lmeshclass -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lfslio -lniftiio -lznz -lprob -lm -lz -lcudart -lcuda -lcurand -lbedpostx_cuda -LCUDA -L/usr/lib64 -L/usr/lib
xfibres_gpu.o: In function `main':
/home/mih/debian/fsl/fsl/src/fdt/xfibres_gpu.cc:177: undefined reference to `xfibres_gpu(NEWMAT::Matrix, NEWMAT::Matrix, NEWMAT::Matrix, NEWMAT::Matrix, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/home/mih/debian/fsl/fsl/src/fdt/xfibres_gpu.cc:196: undefined reference to `xfibres_gpu(NEWMAT::Matrix, NEWMAT::Matrix, NEWMAT::Matrix, NEWMAT::Matrix, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::string_to_T(std::string&, std::string const&)'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::string_to_T(bool&, std::string const&)'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::string_to_T(float&, std::string const&)'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::string_to_T(int&, std::string const&)'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::BaseOption::long_form() const'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::BaseOption::short_form() const'
/home/mih/debian/fsl/fsl/lib/libbedpostx_cuda.so: undefined reference to `Utilities::Option<bool>::set_value(std::string const&)'
collect2: error: ld returned 1 exit status
Makefile:181: recipe for target 'xfibres_gpu' failed
make[1]: *** [xfibres_gpu] Error 1
make[1]: Leaving directory '/home/mih/debian/fsl/fsl/src/fdt'



Looking at the logs it seems to have built the CUDA bits prior just
fine. I am on CUDA 7.0 with an amd64 Debian (somewhat close to unstable
and very similar to the actual build environment that we need to
target).

Does that look familiar to you?

Thanks in advance,

Michael







-- 
Michael Hanke
http://mih.voxindeserto.de