<div dir="ltr">Hi,<div><br></div><div>This list is for discussion of GROMACS development; please keep it that way. I will answer your question on gmx-users.<br><div class="gmail_extra"><br></div><div class="gmail_extra">Mark<br>
<br><div class="gmail_quote">On Wed, Mar 26, 2014 at 12:14 AM, xraynano <span dir="ltr"><<a href="mailto:mancini@anl.gov" target="_blank">mancini@anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
We have had a similar problem as described below. We have tried various work<br>
arounds that force use of clang correctly with CUDA, or that try to<br>
substitute gcc47 for clang. Then, we can get everything to compile, but when<br>
trying to run anything in the final installation, it fails with the error:<br>
Malformed Mach-o file<br></blockquote><div>></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
One would think someone by now would have figured out how to get the GPU<br>
version of GROMACS to properly compile for current Mac OSX. We are running<br>
10.9.2 on a 12 core with Geforce 680 GPU.<br>
<br>
<br>
salehi wrote<br>
> I was trying to install gromacs 4.6.1 with CUDA and have a weird problem.<br>
> My system is as the following<br>
> new iMAC OS x 10.8.3<br>
> GPU : FTX 650 M 512 MB<br>
> I also installed the open-mpi libraries into the /usr/local/lib folder<br>
> before installation. I have got to say I'm by no means a UNIX expert.<br>
> although I have installed gromacs 4.6.1 with float double and mpi options<br>
> but they were all without GPU options. SO when I started installing 4.6.1<br>
> version with GPU I ran into problems. So I figured it has got to have sth<br>
> to do with the GPU! I don't know what environment variables I needed have<br>
> changed before installation with CMAKE, So I would appreciate it if the<br>
> experts here help me out.<br>
><br>
> Firstly, I have installed FFTW3.3.3 with these options:<br>
><br>
> ./configure --prefix /usr/local/fftw3 --enable-sse2 --enable-float<br>
> --enable-shared<br>
> make && make install<br>
><br>
> so the fftw3 installation folder is /usr/local/fftw3.<br>
> my cuda source directory is located at : /usr/local/cuda<br>
> and for the cmake options to install the gromacs.Then,<br>
> in the build folder within the gromacs root folder<br>
> cmake -DGMX_FFT_LIBRARY=fftw3<br>
> -DFFTW_LIBRARY='/usr/local/fftw3/lib/libfftw3f.a'<br>
> -DFFTW_INCLUDE_DIR='/usr/local/fftw3/include/' -DGMX_GPU=ON<br>
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda<br>
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.1 ../<br>
><br>
> First of all I get the error which says the libfftw3f can not be found.<br>
> The following is my fftw3 installation folder :<br>
> drwxr-xr-x 3 root 102 26 Apr 22:04 pkgconfig<br>
> -rwxr-xr-x 1 root 899 26 Apr 22:04 <a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a><br>
> -rw-r--r-- 1 root 2421656 26 Apr 22:04 libfftw3f.a<br>
><br>
> As you can see the file libfftw3f.a is in the folder I have netered in the<br>
> cmake options. I don't know if there is any CMAKE variables I needed have<br>
> changed here, So I worked around that by copying the contents of the<br>
> fftw3/lib folder to the usr/local/lib and since cmake looked into that<br>
> folder it found the fftw file and thus ignored my manual addresses for<br>
> fftw library. This time, the cmake command with the same options as above<br>
> ran successfully. However when I run the make I get:<br>
> sudo make<br>
><br>
> [ 0%] Building NVCC (Device) object<br>
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o<br>
> clang: error: unsupported option '-dumpspecs'<br>
> clang: error: no input files<br>
> CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206<br>
> (message):<br>
> Error generating<br>
><br>
> /Users/salehi/Downloads/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o<br>
><br>
><br>
> make[2]: ***<br>
> [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o]<br>
> Error 1<br>
> make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2<br>
> make: *** [all] Error 2<br>
><br>
><br>
> I don't know if there is anything wrong with the installation of CUDA but<br>
> I could confirm that all the files that needed be there were there after<br>
> following CUDA's own web site.<br>
> Thank you so much in advance.<br>
<br>
<br>
<br>
--<br>
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