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 <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
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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:german...@sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
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