[gmx-users] [gmx-developers] Problem in compiling Gromacs 4.6.1 with GPU on MAC OS X
mark.j.abraham at gmail.com
Wed Mar 26 14:58:01 CET 2014
Guessing: some version of icc probably works; some gcc (perhaps needs to be
hand rolled) probably works (perhaps with low SIMD support); maybe some
clang works with CUDA (if so, the result without OpenMP will still be lower
performance than your hardware could deliver).
On Mar 26, 2014 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
>> 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
>> 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.
> salehi wrote
>> > I was trying to install gromacs 4.6.1 with CUDA and have a weird
>> > 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
>> > but they were all without GPU options. SO when I started installing
>> > version with GPU I ran into problems. So I figured it has got to have
>> > to do with the GPU! I don't know what environment variables I needed
>> > 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
>> > cmake options. I don't know if there is any CMAKE variables I needed
>> > 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
>> > ran successfully. However when I run the make I get:
>> > sudo make
>> > [ 0%] Building NVCC (Device) object
>> > 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
>> > make: ***
>> > Error 1
>> > make: *** [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
>> > 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:
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