[gmx-users] Message-ID: <CANnYEw4dDD9YKA=MaMQaNAeU5dKdaPGBKJHSxM2_O7Uc3pBzvQ at mail.gmail.com> Content-Type: text/plain; charset=UTF-8

[Mark Abraham]

Hi,

On Mon, Oct 12, 2015 at 3:31 PM Kim Jessica Novacek <
Kim.J.Novacek at campus.lmu.de> wrote:

> Although I did let out the Xeon Phi Command there is still the same make
> error.
> Greetings
> Kim
>
>
> /usr/bin/ld: cannot find -lcudart
> /usr/bin/ld: cannot find -lmpi
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/gmx_mpi] Fehler 1
> make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2
> make[1]: *** Auf noch nicht beendete Prozesse wird gewartet …
> /usr/bin/ld: cannot find -lcudart
> /usr/bin/ld: cannot find -lmpi
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Fehler 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2
> make: *** [all] Fehler 2
>
>
> cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc
> -DGMX_MPI=ON -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit
> -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3
> -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG
> -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static"
> -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda
> -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so
> -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml
>

Setting CMAKE_LIBRARY_PATH to an actual file, which is then the one that
can't be found seems like a bad thing to do. That path is a standard system
path, so if you want to find that library, you can probably leave it alone.
But you will get this library via the CUDA toolkit you already asked for,
if the toolkit is installed correctly and you're using it the way the
sysadmins intended you to use it.

Your system should have an MPI wrapper compiler - find out what it is and
use it. Maybe there's even a documented way to compile for MPI+CUDA :-)

Mark


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