{"action":"opened","issue":{"url":"https://api.github.com/repos/3dem/relion/issues/358","repository_url":"https://api.github.com/repos/3dem/relion","labels_url":"https://api.github.com/repos/3dem/relion/issues/358/labels{/name}","comments_url":"https://api.github.com/repos/3dem/relion/issues/358/comments","events_url":"https://api.github.com/repos/3dem/relion/issues/358/events","html_url":"https://github.com/3dem/relion/issues/358","id":321479404,"number":358,"title":"Error in make","user":{"login":"Zhengyanglee","id":39117815,"avatar_url":"https://avatars3.githubusercontent.com/u/39117815?v=4","gravatar_id":"","url":"https://api.github.com/users/Zhengyanglee","html_url":"https://github.com/Zhengyanglee","followers_url":"https://api.github.com/users/Zhengyanglee/followers","following_url":"https://api.github.com/users/Zhengyanglee/following{/other_user}","gists_url":"https://api.github.com/users/Zhengyanglee/gists{/gist_id}","starred_url":"https://api.github.com/users/Zhengyanglee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Zhengyanglee/subscriptions","organizations_url":"https://api.github.com/users/Zhengyanglee/orgs","repos_url":"https://api.github.com/users/Zhengyanglee/repos","events_url":"https://api.github.com/users/Zhengyanglee/events{/privacy}","received_events_url":"https://api.github.com/users/Zhengyanglee/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-09T08:35:00Z","updated_at":"2018-05-09T08:35:00Z","closed_at":null,"author_association":"NONE","body":"Dear all,\r\nI have the similar error with issue #187 , however, I have no idea how to solve it. \r\nMy system is Ubuntu 16.04 LTS, cuda version is 9.1, g++ version is 5.4.\r\nHere is terminal output when I run cmake and make.\r\n$ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/relion -DCMAKE_C_COMPILER=/usr/bin/gcc-5 -DCMAKE_CXX_COMPILER=/usr/bin/g++-5 -DCUDA_ARCH=52 ..\r\n-- The C compiler identification is GNU 5.4.0\r\n-- The CXX compiler identification is GNU 5.4.0\r\n-- Check for working C compiler: /usr/bin/gcc-5\r\n-- Check for working C compiler: /usr/bin/gcc-5 -- works\r\n-- Detecting C compiler ABI info\r\n-- Detecting C compiler ABI info - done\r\n-- Detecting C compile features\r\n-- Detecting C compile features - done\r\n-- Check for working CXX compiler: /usr/bin/g++-5\r\n-- Check for working CXX compiler: /usr/bin/g++-5 -- works\r\n-- Detecting CXX compiler ABI info\r\n-- Detecting CXX compiler ABI info - done\r\n-- Detecting CXX compile features\r\n-- Detecting CXX compile features - done\r\n-- BUILD TYPE set to the default type:  'Release'\r\n-- Using provided CUDA_ARCH=52\r\n-- Setting cpu precision to double\r\n-- Setting gpu precision to single\r\n-- Looking for pthread.h\r\n-- Looking for pthread.h - found\r\n-- Looking for pthread_create\r\n-- Looking for pthread_create - not found\r\n-- Looking for pthread_create in pthreads\r\n-- Looking for pthread_create in pthreads - not found\r\n-- Looking for pthread_create in pthread\r\n-- Looking for pthread_create in pthread - found\r\n-- Found Threads: TRUE  \r\n-- Found CUDA: /usr (found version \"7.5\") \r\n-- Using cuda wrapper to compile....\r\n-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.\r\n-- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so  \r\n-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so  \r\n-- 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\r\n-- MPI_LIBRARIES : /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so\r\n-- 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\r\n-- MPI_CXX_LIBRARIES : /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so\r\n-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so\r\n-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found\r\n-- Looking for gethostbyname\r\n-- Looking for gethostbyname - found\r\n-- Looking for connect\r\n-- Looking for connect - found\r\n-- Looking for remove\r\n-- Looking for remove - found\r\n-- Looking for shmat\r\n-- Looking for shmat - found\r\n-- Looking for IceConnectionNumber in ICE\r\n-- Looking for IceConnectionNumber in ICE - found\r\n-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so\r\n-- Found FLTK: fltk_images;fltk_forms;fltk  \r\n-- X11 and FLTK were found\r\n-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libSM.so;/usr/lib/x86_64-linux-gnu/libICE.so;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libm.so\r\n-- Found FFTW: fftw3\r\n-- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3.so\r\n-- Looking for sincos\r\n-- Looking for sincos - found\r\n-- Looking for __sincos\r\n-- Looking for __sincos - not found\r\n-- Building shared libs (smaller build size and binaries)\r\n-- CMAKE_BINARY_DIR:/home/lilab202/relion/build\r\n-- added particle_reposition...\r\n-- added manualpick...\r\n-- added run_ctffind_mpi...\r\n-- added preprocess...\r\n-- added run_ctffind...\r\n-- added localsym_mpi...\r\n-- added pipeliner...\r\n-- added particle_sort...\r\n-- added mask_create...\r\n-- added particle_symmetry_expand...\r\n-- added particle_sort_mpi...\r\n-- added refine_mpi...\r\n-- added run_motioncorr...\r\n-- added localsym...\r\n-- added prepare_subtomo...\r\n-- added refine...\r\n-- added stack_create...\r\n-- added run_motioncorr_mpi...\r\n-- added display...\r\n-- added reconstruct...\r\n-- added tiltpair_plot...\r\n-- added postprocess_mpi...\r\n-- added maingui...\r\n-- added helix_toolbox...\r\n-- added star_combine...\r\n-- added find_tiltpairs...\r\n-- added ctf_toolbox...\r\n-- added project...\r\n-- added preprocess_mpi...\r\n-- added postprocess...\r\n-- added autopick...\r\n-- added particle_polish_mpi...\r\n-- added star_compare...\r\n-- added particle_polish...\r\n-- added autopick_mpi...\r\n-- added image_handler...\r\n-- Configuring done\r\n-- Generating done\r\n-- Build files have been written to: /home/lilab202/relion/build\r\n---------------------------------------------------------------------------------------------------------------------------------\r\n$ make -j4\r\nScanning dependencies of target copy_scripts\r\n[  1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o\r\n[  2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_projector_plan.cu.o\r\n[  3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_benchmark_utils.cu.o\r\n[  3%] Built target copy_scripts\r\n[  3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_backprojector.cu.o\r\n/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const void*, size_t)’:\r\n/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope\r\n   return (char *) memcpy (__dest, __src, __n) + __n;\r\n                                          ^\r\n/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const void*, size_t)’:\r\n/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope\r\n   return (char *) memcpy (__dest, __src, __n) + __n;\r\n                                          ^\r\n/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const void*, size_t)’:\r\n/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope\r\n   return (char *) memcpy (__dest, __src, __n) + __n;\r\n                                          ^\r\nCMake Error at relion_gpu_util_generated_cuda_benchmark_utils.cu.o.cmake:266 (message):\r\n  Error generating file\r\n  /home/lilab202/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o\r\n\r\n\r\nsrc/apps/CMakeFiles/relion_gpu_util.dir/build.make:70: recipe for target 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_benchmark_utils.cu.o' failed\r\nmake[2]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_benchmark_utils.cu.o] Error 1\r\nmake[2]: *** Waiting for unfinished jobs....\r\nCMake Error at relion_gpu_util_generated_cuda_backprojector.cu.o.cmake:266 (message):\r\n  Error generating file\r\n  /home/lilab202/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/./relion_gpu_util_generated_cuda_backprojector.cu.o\r\n\r\n\r\nsrc/apps/CMakeFiles/relion_gpu_util.dir/build.make:77: recipe for target 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_backprojector.cu.o' failed\r\nmake[2]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_backprojector.cu.o] Error 1\r\nCMake Error at relion_gpu_util_generated_helper.cu.o.cmake:266 (message):\r\n  Error generating file\r\n  /home/lilab202/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/./relion_gpu_util_generated_helper.cu.o\r\n\r\n\r\nsrc/apps/CMakeFiles/relion_gpu_util.dir/build.make:112: recipe for target 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o' failed\r\nmake[2]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o] Error 1\r\n/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const void*, size_t)’:\r\n/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope\r\n   return (char *) memcpy (__dest, __src, __n) + __n;\r\n                                          ^\r\nCMake Error at relion_gpu_util_generated_cuda_projector_plan.cu.o.cmake:266 (message):\r\n  Error generating file\r\n  /home/lilab202/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/./relion_gpu_util_generated_cuda_projector_plan.cu.o\r\n\r\n\r\nsrc/apps/CMakeFiles/relion_gpu_util.dir/build.make:63: recipe for target 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_projector_plan.cu.o' failed\r\nmake[2]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_generated_cuda_projector_plan.cu.o] Error 1\r\nCMakeFiles/Makefile2:1151: recipe for target 'src/apps/CMakeFiles/relion_gpu_util.dir/all' failed\r\nmake[1]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2\r\nMakefile:138: recipe for target 'all' failed\r\n-------------------------------------------------------------------------------------------------------------------------------\r\nLooking forward to your reply. Thank you very much.\r\nBest wishes!\r\n\r\n"}}
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