[gmx-users] Problem with Installing Gromacs 4.6.1 with GPU
mark.j.abraham at gmail.com
Sat May 11 10:33:33 CEST 2013
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
> 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
> 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_INCLUDE_DIR='/usr/local/fftw3/include/' -DGMX_GPU=ON
> -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
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
> clang: error: unsupported option '-dumpspecs'
> clang: error: no input files
> CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206
> 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 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.
> Thank you so much in advance.
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