Неопределенная ссылки на __cxa_atexit с Matlab/CUDA MEX

Question

Я компиляция некоторых CUDA/C для работы в качестве библиотеки MEX в Matlab, и я получаю следующее сообщение об ошибке:

Error using mex 
/usr/lib/x86_64-linux-gnu/libc_nonshared.a(atexit.oS): In function `atexit': 
(.text+0x12): undefined reference to `__cxa_atexit' 
collect2: error: ld returned 1 exit status 

Я предполагаю, что это означает, Мне нужно связать в какой-то дополнительной библиотеке, но что?

Моя текущая команда компиляции является:

mex -L/usr/local/cuda/lib64 -lcudart -I./ A.cpp B.cpp C.cu D.cpp 

У меня есть несколько ядер для компиляции в Mex, и интересно некоторые из них работают, а некоторые из них не делают. Я не сразу вижу, какая разница между ними - я, конечно, не звоню atexit нигде в моем источнике.

Вот выход из многословной Mex:

Verbose mode is on. 
Neither -compatibleArrayDims nor -largeArrayDims is selected. 
    Using -compatibleArrayDims. In the future, MATLAB will require the use of 
    -largeArrayDims and remove the -compatibleArrayDims option. 
    For more information: 
    http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html. 
... Looking for compiler 'nvcc' ... 
... Looking for environment variable 'MW_NVCC_PATH' ...Yes ('/usr/local/cuda-6.5/bin/nvcc'). 
... Looking for folder '/usr/local/cuda-6.5/bin' ...Yes. 
... Looking for file '/usr/local/cuda-6.5/bin/nvcc' ...Yes. 
... Executing command 'which g++' ...Yes ('/usr/bin/g++'). 
... Executing command 'g++ -print-file-name=libstdc++.so' ...Yes ('/usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so'). 
Found installed compiler 'nvcc'. 
Options file details 
------------------------------------------------------------------- 
    Compiler location: /usr/local/cuda-6.5/bin/nvcc 
    Options file: /home/nick/Documents/FrameLab/matlab/mex/source codes/mex_CUDA_glnxa64.xml 
    CMDLINE2 : /usr/bin/g++ -pthread -Wl,--no-undefined -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5 -o Atx_fan_mf.mexa64 
    CXX : /usr/local/cuda-6.5/bin/nvcc 
    DEFINES : -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE 
    MATLABMEX : -DMATLAB_MEX_FILE 
    NVCCFLAGS : -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS 
    CXXFLAGS : --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread 
    INCLUDE : -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" 
    CXXOPTIMFLAGS : -O -DNDEBUG 
    CXXDEBUGFLAGS : -g 
    LDXX : /usr/bin/g++ 
    LDFLAGS : -pthread -Wl,--no-undefined 
    LDTYPE : -shared 
    LINKEXPORT : -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" 
    LINKLIBS : -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5 
    LDOPTIMFLAGS : -O 
    LDDEBUGFLAGS : -g 
    OBJEXT : .o 
    LDEXT : .mexa64 
    NVCC : /usr/local/cuda-6.5/bin/nvcc 
    GCC : /usr/bin/g++ 
    CPPLIB_DIR : /usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so 
    MATLABROOT : /usr/local/MATLAB/R2014a 
    ARCH : glnxa64 
    SRC : "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp" 
    OBJ : /tmp/mex_86382821022260_3849/Atx_fan_mf.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o;/tmp/mex_86382821022260_3849/find_l.o;/tmp/mex_86382821022260_3849/find_area.o 
    OBJS : /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o 
    SRCROOT : /home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf 
    DEF : /tmp/mex_86382821022260_3849/Atx_fan_mf.def 
    EXP : Atx_fan_mf.exp 
    LIB : Atx_fan_mf.lib 
    EXE : Atx_fan_mf.mexa64 
    ILK : Atx_fan_mf.ilk 
    MANIFEST : Atx_fan_mf.mexa64.manifest 
    TEMPNAME : Atx_fan_mf 
    EXEDIR : 
    EXENAME : Atx_fan_mf 
    OPTIM : -O -DNDEBUG 
    LINKOPTIM : -O 
    CMDLINE1_0 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf.o 
    CMDLINE1_1 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o 
    CMDLINE1_2 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o 
    CMDLINE1_3 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o 
    CMDLINE1_4 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o 
    CMDLINE1_5 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp" -o /tmp/mex_86382821022260_3849/find_l.o 
    CMDLINE1_6 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp" -o /tmp/mex_86382821022260_3849/find_area.o 
    CMDLINE3_0 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf.o 
    CMDLINE3_1 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o 
    CMDLINE3_2 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o 
    CMDLINE3_3 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o 
    CMDLINE3_4 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o 
    CMDLINE3_5 : rm -f /tmp/mex_86382821022260_3849/find_l.o 
    CMDLINE3_6 : rm -f /tmp/mex_86382821022260_3849/find_area.o 
------------------------------------------------------------------- 
Building with 'nvcc'. 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp" -o /tmp/mex_86382821022260_3849/find_l.o 
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp" -o /tmp/mex_86382821022260_3849/find_area.o 
/usr/bin/g++ -pthread -Wl,--no-undefined -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5 -o Atx_fan_mf.mexa64 

мне интересно, если я должен попытаться использовать другую версию г ++ или C++ библиотеки? Я не уверен, как изменить переменную CPPLIB_DIR ... Matlab усложнил настройку mex в 2014a.

Спасибо за любые мысли!

Answer 1

Я получил ту же ошибку, используя Matlab 2015 Prerelease на Ubuntu 14.04 с CUDA 6.5 и g ++ 4.8. Благодаря поддержке Matlab мы выяснили, что ручная привязка делает трюк. Вот моя компиляция сценарий для MatLab примера MEX/GPU:

myArch = computer('arch'); pathToOpts = fullfile(matlabroot, ... 'toolbox', 'distcomp', 'gpu', ... 'extern', 'src', 'mex', myArch,'gcc',... ['mex_CUDA_' myArch '.xml']); copyfile(pathToOpts,'.','f') 

mex -v -largeArrayDims mexGPUExample.cu -lstdc++ -lc