[gmx-users] Problem with Installing Gromacs 4.6.1 with GPU

[Mark Abraham]

On Sat, May 11, 2013 at 2:07 AM, salehi <salehi at umich.edu> 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    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>