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

Wed Mar 26 15:09:33 CET 2014

On OS X the CUDA compiler only supports the official OS X toolchain,
Xcode. Hence you'll have to use as CUDA_HOST_COMPILER either
gcc(-llvm) or clang from Xcode. NVIDIA actually has pretty decent docs
on this:
http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-mac-os-x/

The forwarded error was caused by the fact that nvcc uses clang as a
host-compiler while the standard C/C++ compiler you used is probably
gcc. Hence, as the gcc C++ compiler flags are propagated to clang and
this chokes on it. To work around this issue you can:
- use clang as your C/C++ compiler (but this will leave you without OpenMP) or
- set CUDA_PROPAGATE_HOST_FLAGS=OFF.

Cheers,
--
Szilárd

On Wed, Mar 26, 2014 at 11:10 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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
>>
>
> I haven't the faintest idea what a Mach-o file is.
>
> Since you can get things to compile, you no longer have any problems
> related to the email you forwarded below. Why did you want to ask me to
> spend my time reading that?
>
>
>> 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.
>>
>
> Maybe they have, and haven't shared it. Asking people if they have solved
> it might get a more useful response than expressing frustration that they
> haven't shared it yet ;-)
>
> On Mac, you need a CUDA-compatible compiler that can compile correct SIMD
> intrinsics (ie. can use a functioning assembler), and preferably support
> OpenMP. That's an extremely small set, and I don't even know if it is
> non-zero. You can make do with something CUDA-compatible without SIMD or
> OpenMP support, so long as the assembler works - there's various
> discussions on http://redmine.gromacs.org about known problems.
>
> Mark
>
> 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.
>>
>>
>>
>> --
>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/Problem-in-compiling-Gromacs-4-6-1-with-GPU-on-MAC-OS-X-tp5008204p5015382.html
>> Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.
>> --
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