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 <german...@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:german...@sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.