[gmx-users] Issue building 5.0.2 release for GPU

[Roland Schulz]

Hi,

this seems to be the boost bug https://svn.boost.org/trac/boost/ticket/10420
. Please file a Gromacs redmine issue. As a temporary solution use
gcc>=4.7. It should be as fast as ICC at least when used with GPU.

Roland

On Fri, Oct 17, 2014 at 2:23 AM, Éric Germaneau <germaneau at sjtu.edu.cn>
wrote:

> Dear all,
>
> I'm building the 5.0.2 release the same way as the 4.6.x releases but
> can't compile it for GPU.
> I use CUDA 6.5 and icc/14.0.2 and impi/4.1.3.048.
>
> Here is my cmake command:
>
>     CC=mpiicc CXX=mpiicpc
>
> CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
>     \
>        $CMAKE \
>         -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
>         -DFFTW_LIBRARY=$FFTW3DIR/lib\
>         -DGMX_MPI=ON \
>         -DGMX_GPU=ON [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
>         -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
>         -DGMX_X11=OFF ../$APP \
>         -DGMX_THREADS=OFF \
>         -DBUILD_SHARED_LIBS=OFF \
>         -DGMX_PREFER_STATIC_LIBS=ON
>
> Here is the kind of errors I get:
>
>
> /tmp/tmpxft_000088e3_00000000-9_copyrite_gpu.compute_20.cudafe1.stub.c(6):
>     remark #82: storage class is not first
>        static void __nv_cudaEntityRegisterCallback(void **__T20){{
>     volatile static void * *__ref __attribute__((unused)); __ref =
>     (volatile void * *)__T20;
>     };__nv_save_fatbinhandle_for_managed_rt(__T20);}
>     ^
>     In file included from
>     /path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config.hpp(35),
>                       from
>
> /path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/smart_ptr/scoped_ptr.hpp(14),
>                       from
>
> /path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/scoped_ptr.hpp(14),
>                       from
>     /path/to/gromacs/gromacs-5.0.2/src/gromacs/utility/common.h(50),
>                       from
>     /path/to/gromacs/gromacs-5.0.2/src/gromacs/mdlib/nbnxn_cuda/
> nbnxn_cuda_data_mgmt.cu(63):
>
> /path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config/compiler/intel.hpp(40):
>     warning #47: incompatible redefinition of macro "BOOST_COMPILER"
>     (declared at line 11 of
>
> "/path/to/gromacs/gromacs-5.0.2/src/external/boost/boost/config/compiler/nvcc.hpp")
>        #define BOOST_COMPILER "Intel C++ version "
>     BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION)
>                ^
>
> Do I have to install Boost?
> I actually just tried but it's horrible with Intel MPI.
> Any suggestions?
> Thanks,
>
>                           Éric.
>
> --
> Éric Germaneau (艾海克), Specialist
> Center for High Performance Computing
> Shanghai Jiao Tong University
> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
> M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
> --
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