[gmx-users] Issue building 5.0.2 release for GPU

[Éric Germaneau]

Hey Roland,

Thank you for your reply.
I'll do that.
Hopefully this will fixed in the next release.

               Éric.

On 10/17/2014 03:02 PM, Roland Schulz wrote:
> 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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>
>

-- 
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