[gmx-users] Issue building 5.0.2 release for GPU

[Éric Germaneau]

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