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. 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. 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
