Hello,
I want to compile relion2-beta on Ubuntu 16.04 but I get following error:
# cmake ..
-- BUILD TYPE set to the default type: 'Release'
-- Setting fallback CUDA_ARCH=35
-- Setting cpu precision to double
-- Setting gpu precision to single
-- Using cuda wrapper to compile....
-- Cuda version is >= 7.5 and single-precision build, enable double
usage warning.
-- MPI_INCLUDE_PATH :
/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
-- MPI_LIBRARIES :
/usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH :
/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
-- MPI_CXX_LIBRARIES :
/usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so
-- X11 and FLTK were found
-- FLTK_LIBRARIES:
fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found FFTW: fftw3
-- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3.so
-- Building shared libs (smaller build size and binaries)
-- CMAKE_BINARY_DIR:/usr/local/src/relion/relion2-beta/build
-- added autopick...
-- added autopick_mpi...
-- added display...
-- added find_tiltpairs...
-- added helix_toolbox...
-- added image_handler...
-- added maingui...
-- added manualpick...
-- added mask_create...
-- added particle_polish...
-- added particle_polish_mpi...
-- added particle_reposition...
-- added particle_sort...
-- added particle_sort_mpi...
-- added particle_symmetry_expand...
-- added pipeliner...
-- added postprocess...
-- added postprocess_mpi...
-- added preprocess...
-- added preprocess_mpi...
-- added project...
-- added reconstruct...
-- added refine...
-- added refine_mpi...
-- added run_ctffind...
-- added run_ctffind_mpi...
-- added run_motioncorr...
-- added run_motioncorr_mpi...
-- added stack_create...
-- added star_combine...
-- added star_compare...
-- added tiltpair_plot...
-- Configuring done
-- Generating done
-- Build files have been written to:
/usr/local/src/relion/relion2-beta/build
# make
[ 0%] Built target copy_scripts
[ 1%] Building NVCC (Device) object
src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o
/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
void*, size_t)’:
/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
return (char *) memcpy (__dest, __src, __n) + __n;
^
CMake Error at relion_gpu_util_generated_helper.cu.o.cmake:266 (message):
Error generating file
/usr/local/src/relion/relion2-beta/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/./relion_gpu_util_generated_helper.cu.o
src/apps/CMakeFiles/relion_gpu_util.dir/build.make:1359: recipe for
target
'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o'
failed
make[2]: ***
[src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o]
Error 1
CMakeFiles/Makefile2:758: recipe for target
'src/apps/CMakeFiles/relion_gpu_util.dir/all' failed
make[1]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
Any hints how to fix this error?
Thanks!
Regards,
Alexander
|