[gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X

[Mark Abraham]

Hi,

This list is for discussion of GROMACS development; please keep it that
way. I will answer your question on gmx-users.

Mark

On Wed, Mar 26, 2014 at 12:14 AM, xraynano <mancini at anl.gov> wrote:

> We have had a similar problem as described below. We have tried various
> work
> arounds that force use of clang correctly with CUDA, or that try to
> substitute gcc47 for clang. Then, we can get everything to compile, but
> when
> trying to run anything in the final installation, it fails with the error:
> Malformed Mach-o file
>
>

> One would think someone by now would have figured out how to get the GPU
> version of GROMACS to properly compile for current Mac OSX. We are running
> 10.9.2 on a 12 core with Geforce 680 GPU.
>
>
> salehi 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. 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.
>
>
>
> --
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