On Sat, May 11, 2013 at 2:07 AM, salehi <[email protected]> wrote: > I was trying to install gromacs 4.6.1 with CUDA and have a weird problem. > My system is as the following > new iMAC OS x 10.8.3 > GPU : FTX 650 M 512 MB > I also installed the open-mpi libraries into the /usr/local/lib folder > before installation. I have got to say I'm by no means a UNIX expert. > although I have installed gromacs 4.6.1 with float double and mpi options > but they were all without GPU options. SO when I started installing 4.6.1 > version with GPU I ran into problems. So I figured it has got to have sth > to > do with the GPU! I don't know what environment variables I needed have > changed before installation with CMAKE, So I would appreciate it if the > experts here help me out. > > Firstly, I have installed FFTW3.3.3 with these options: > > ./configure --prefix /usr/local/fftw3 --enable-sse2 --enable-float > --enable-shared > make $$ make install > > so the fftw3 installation folder is /usr/local/fftw3. > my cuda source directory is located at : /usr/local/cuda > and for the cmake options to install the gromacs.Then, > in the build folder within the gromacs root folder > cmake -DGMX_FFT_LIBRARY=fftw3 > -DFFTW_LIBRARY='/usr/local/fftw3/lib/libfftw3f.a' > -DFFTW_INCLUDE_DIR='/usr/local/fftw3/include/' -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.1 ../ > > First of all I get the error which says the libfftw3f can not be found. > The following is my fftw3 installation folder : > drwxr-xr-x 3 root 102 26 Apr 22:04 pkgconfig > -rwxr-xr-x 1 root 899 26 Apr 22:04 libfftw3f.la > -rw-r--r-- 1 root 2421656 26 Apr 22:04 libfftw3f.a > > As you can see the file libfftw3f.a is in the folder I have netered in the > cmake options. I don't know if there is any CMAKE variables I needed have > changed here, So I worked around that by copying the contents of the > fftw3/lib folder to the usr/local/lib and since cmake looked into that > folder it found the fftw file and thus ignored my manual addresses for fftw > library.
http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprogramsdescribes a better approach. > This time, the cmake command with the same options as above ran > successfully. However when I run the make I get: > sudo make > > [ 0%] Building NVCC (Device) object > > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o > clang: error: unsupported option '-dumpspecs' > clang: error: no input files > CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 > (message): > Error generating > > > /Users/salehi/Downloads/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o > > > make[2]: *** > > [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o] > Error 1 > make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 > make: *** [all] Error 2 > > > I don't know if there is anything wrong with the installation of CUDA but I > could confirm that all the files that needed be there were there after > following CUDA's own web site. > I understand clang is not functional as a back-end compiler for CUDA's nvcc. You need to set up a different back-end compiler. Mark > Thank you so much in advance. > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Problem-with-Installing-Gromacs-4-6-1-with-GPU-tp5008119.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
