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Undefined symbol errors in MEX compilation

This is a discussion on Undefined symbol errors in MEX compilation within the C Programming forums, part of the General Programming Boards category; Hi there! I am currently trying to run someone else's code on my machine ( Link) . The precompiled MEX ...

  1. #1
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    Undefined symbol errors in MEX compilation

    Hi there!

    I am currently trying to run someone else's code on my machine (Link).
    The precompiled MEX files are available for a Linux 64-bit machine. However, I am trying to run it on a Mac using MATLAB 2012b.

    I adapted the makefile by adjusting the MATLAB directory. However, I still get some compilation errors.
    It seems that certain libraries cannot be located.


    mycomputer:mpi_kmeans-1.5 username$ make matlab
    ar rc libmpikmeans.a mpi_kmeans.o
    ranlib libmpikmeans.a
    g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o libmpikmeans.so mpi_kmeans.cxx
    gcc mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex
    Undefined symbols:
    "_mxGetM", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxGetN", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxIsDouble", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    "___gxx_personality_v0", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    CIE in mpi_kmeans_mex.o
    comp_randperm(void const*, void const*)in libmpikmeans.a(mpi_kmeans.o)
    remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    compute_distance(double const*, double const*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    randperm(unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    kmeans_error(char*) in libmpikmeans.a(mpi_kmeans.o)
    remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in libmpikmeans.a(mpi_kmeans.o)
    compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in libmpikmeans.a(mpi_kmeans.o)
    assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in libmpikmeans.a(mpi_kmeans.o)
    kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
    _kmeans in libmpikmeans.a(mpi_kmeans.o)
    CIE in libmpikmeans.a(mpi_kmeans.o)
    "_mxCreateNumericArray_730", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxIsComplex", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxGetNumberOfDimensions_730", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxIsInf", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    "_mxIsSingle", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    "_mxIsNaN", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    "_mxGetPr", referenced from:
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    _mexFunction in mpi_kmeans_mex.o
    "_mxCreateDoubleScalar", referenced from:
    _mexFunction in mpi_kmeans_mex.o

    ld: symbol(s) not found
    collect2: ld returned 1 exit status
    make: *** [mpi_kmeans_mex.mexmaci64] Error 1

    Any ideas where the problem could be?

  2. #2
    and the hat of wrongness Salem's Avatar
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    > g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o libmpikmeans.so mpi_kmeans.cxx
    So why are you overwriting your library with the result of a module compilation?

    In fact, the whole sequence seems wrong - you create the library, then build the source.

    Try
    g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o mpi_kmeans.o mpi_kmeans.cxx
    ar rc libmpikmeans.a mpi_kmeans.o
    ranlib libmpikmeans.a


    > gcc mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex
    If you're compiling separate files using g++, then the final executable needs to be linked by invoking g++ as well.
    Seeing ___gxx_personality_v0 is a sign you've mixed up the C and C++.
    stahta01 likes this.
    If you dance barefoot on the broken glass of undefined behaviour, you've got to expect the occasional cut.
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  3. #3
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    Hey Salem!

    Thanks for your willingness to help!

    I've removed the .so file command and changed g++ to gcc. Unfortunately though, I still seem to be getting an error on the g++ reference:

    ar rc libmpikmeans.a mpi_kmeans.o
    /usr/bin/ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
    ranlib libmpikmeans.a
    ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
    ranlib: empty library: libmpikmeans.a (no table of contents added)
    gcc -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx

    Undefined symbols:
    "___gxx_personality_v0", referenced from:
    comp_randperm(void const*, void const*)in ccWhobPa.o
    remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccWhobPa.o
    add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccWhobPa.o
    compute_distance(double const*, double const*, unsigned int)in ccWhobPa.o
    randperm(unsigned int*, unsigned int)in ccWhobPa.o
    kmeans_error(char*) in ccWhobPa.o
    remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in ccWhobPa.o
    compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in ccWhobPa.o
    compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in ccWhobPa.o
    assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in ccWhobPa.o
    assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in ccWhobPa.o
    init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in ccWhobPa.o
    kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in ccWhobPa.o
    _kmeans in ccWhobPa.o
    CIE in ccWhobPa.o
    ld: symbol(s) not found
    collect2: ld returned 1 exit status
    make: *** [libmpikmeans] Error 1


  4. #4
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    Here's an edit from my side:

    I tried what you recommended, i.e. I used a different order for the 3 compile commands and replaced g++ with gcc
    Code:
    gcc -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64  -DKMEANS_VERBOSE=0  -o mpi_kmeans.o   mpi_kmeans.cxx
    ar rc libmpikmeans.a mpi_kmeans.o
    ranlib libmpikmeans.a
    Unfortuntely though, I still get some error!
    Undefined symbols:
    "___gxx_personality_v0", referenced from:
    comp_randperm(void const*, void const*)in ccs3czSH.o
    remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccs3czSH.o
    add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccs3czSH.o
    compute_distance(double const*, double const*, unsigned int)in ccs3czSH.o
    randperm(unsigned int*, unsigned int)in ccs3czSH.o
    kmeans_error(char*) in ccs3czSH.o
    remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in ccs3czSH.o
    compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in ccs3czSH.o
    compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in ccs3czSH.o
    assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in ccs3czSH.o
    assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in ccs3czSH.o
    init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in ccs3czSH.o
    kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in ccs3czSH.o
    _kmeans in ccs3czSH.o
    CIE in ccs3czSH.o
    ld: symbol(s) not found
    collect2: ld returned 1 exit status
    make: *** [libmpikmeans] Error 1
    I have not seen the ccs3czSH.o file ever before?

  5. #5
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    I change the gcc command in the first line to g++. The references error vanished, but now I seem to have library connection problem! :-(
    The code in the Makefile is bold and the errors are highlighted in red.

    Code:
    gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64  -DKMEANS_VERBOSE=0   -c -o mpi_kmeans.o mpi_kmeans.cxx
    g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64  -DKMEANS_VERBOSE=0  -o mpi_kmeans.o   mpi_kmeans.cxx
    ar rc libmpikmeans.a mpi_kmeans.o
    /usr/bin/ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
    ranlib libmpikmeans.a
    ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
    ranlib: empty library: libmpikmeans.a (no table of contents added)
    gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64  -I/Applications/MATLAB_R2012b.app/extern/include -DKMEANS_VERBOSE=0   -c mpi_kmeans_mex.cxx -o mpi_kmeans_mex.o
    g++ mpi_kmeans_mex.o -shared -m64 -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex 
    ld: warning: in libmpikmeans.a, file was built for unsupported file format which is not the architecture being linked (x86_64)
    Undefined symbols:
      "_mxGetM", referenced from:
          _mexFunction in mpi_kmeans_mex.o
    ........

  6. #6
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    IIRC, The "-shared" means make a dynamic library/object file.

    I have no idea if you want a dynamic or static library.

    The "-static" should make a static library/object file.

    http://gcc.gnu.org/onlinedocs/gcc/Link-Options.html

    Tim S.
    Last edited by stahta01; 12-06-2012 at 01:54 PM.
    "Programming today is a race between software engineers striving to build bigger and better idiot-proof programs, and the universe trying to produce bigger and better idiots. So far, the Universe is winning." Rick Cook

  7. #7
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    Hey stahta01!

    Thanks for the heads-up!

    I did try that too. Unfortunately though, I still get errors:
    gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -c -o mpi_kmeans.o mpi_kmeans.cxx
    g++ -static -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx
    ld: warning: in /usr/lib/gcc/i686-apple-darwin10/4.2.1/libgcc_static.a, file was built for unsupported file format which is not the architecture being linked (x86_64)

    Undefined symbols:
    "___assert_rtn", referenced from:
    -----
    I understand that there is an incompatibility problem, but which library must be rebuilt and how?

  8. #8
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    Doing both makes no sense to me "-static -shared". I could be wrong on this.

    The "-m64" means 64 bit; "x86_64" means 64 bit.
    The i686-apple-darwin10 implies 32 bit.

    You might try adding "-shared-libgcc" in case your compiler only has 64 bit Dynamic of libgcc.


    Tim S.
    Last edited by stahta01; 12-06-2012 at 03:07 PM.
    "Programming today is a race between software engineers striving to build bigger and better idiot-proof programs, and the universe trying to produce bigger and better idiots. So far, the Universe is winning." Rick Cook

  9. #9
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    Hey Tim!

    There is still some issue here.

    gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -c -o mpi_kmeans.o mpi_kmeans.cxx
    g++ -shared-libgcc -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx

    Undefined symbols:
    "_main", referenced from:
    start in crt1.10.6.o
    ld: symbol(s) not found
    collect2: ld returned 1 exit status
    make: *** [libmpikmeans] Error 1
    I used the library path on my system to be '/usr/lib/gcc/i686-apple-darwin10/4.2.1/'
    Could this be an issue?

  10. #10
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    Quote Originally Posted by in_ship View Post
    Hey Tim!

    There is still some issue here.

    Code:
    Undefined symbols:
    "_main", referenced from:
    start in crt1.10.6.o
    I used the library path on my system to be '/usr/lib/gcc/i686-apple-darwin10/4.2.1/'
    Could this be an issue?
    I am guessing your code is missing the main function.

    If your code is not supposed to have a main you might need to add another option.
    I can not remember the right option; not even sure I ever know about the right option.

    Tim S.
    "Programming today is a race between software engineers striving to build bigger and better idiot-proof programs, and the universe trying to produce bigger and better idiots. So far, the Universe is winning." Rick Cook

  11. #11
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    mpi_kmeans does not really have a main-file.
    However, mpi_kmeans_main.cxx does!
    Can I somehow link them together?


    Here's the Makefile (compile with make matlab)
    Code:
    #
    # Choose your compiler
    #
    # 
    
    CC = gcc
    CPP = g++
    CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -m64 #-Werror
    
    
    
    
    
    #
    # MPI KMEANS FLAGS
    #
    VERBOSEFLAG=-DKMEANS_VERBOSE=0 # 0: silent, 1:iteration counter, 2:everything
    #PRECISION=-DINPUT_TYPE=0 # 0: double, 1:float 
    
    #
    # MATLAB
    #
    
    MATLABDIR=/Applications/MATLAB_R2012b.app
    MATLAB_INCLUDE=-I$(MATLABDIR)/extern/include
    
    
    
    
    #
    # ARCHITECURE
    # 
    
    
    
    # 64 bit
    
    
    SUFFIX=mexmaci64
    MATLAB_LIB=-L$(MATLABDIR)/bin/maci64 -lmex
    
    LIBS=/usr/lib/gcc/i686-apple-darwin10/4.2.1/ /usr/lib/
    
    
    matlab:     mpi_kmeans_mex.$(SUFFIX) mpi_assign_mex.$(SUFFIX)
    
    
    mpi_kmeans.o:    mpi_kmeans.cxx mpi_kmeans.h
        $(CC) $(CFLAGS) $(VERBOSEFLAG) $(PRECISION) -c -o $@ mpi_kmeans.cxx
    
    
    mpi_kmeans_main.o:    mpi_kmeans_main.cxx
        $(CC) $(CFLAGS) $(BOOST_INCLUDE) -c -o mpi_kmeans_main.o mpi_kmeans_main.cxx 
    
    libmpikmeans:    mpi_kmeans.o
        ar rc libmpikmeans.a mpi_kmeans.o
        ranlib libmpikmeans.a
        $(CPP) -shared-libgcc -fPIC $(CFLAGS) $(VERBOSEFLAG) -o libmpikmeans.so $(VERBOSEFLAGS) $(PRECISION) mpi_kmeans.cxx
    
    mpi_assign_main.o:    mpi_assign_main.cxx
        $(CC) $(CFLAGS) $(BOOST_INCLUDE) -c -o mpi_assign_main.o mpi_assign_main.cxx 
    
    mpi_kmeans_main:    libmpikmeans mpi_kmeans_main.o
        $(CC) mpi_kmeans_main.o  $(CFLAGS) -L/usr/lib/ -static -o mpi_kmeans -lm libmpikmeans.a \
            $(BOOST_LIB) $(LIBS)
    
    mpi_assign_main:    libmpikmeans mpi_assign_main.o
        $(CC) mpi_assign_main.o  $(CFLAGS) -L/usr/lib/ -static -o mpi_assign -lm libmpikmeans.a \
            $(BOOST_LIB) $(LIBS)
    
    
    mpi_kmeans_mex.$(SUFFIX):    libmpikmeans mpi_kmeans_mex.o 
        $(CPP) mpi_kmeans_mex.o -shared -m64 -o mpi_kmeans_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB) 
    
    mpi_assign_mex.$(SUFFIX):    libmpikmeans mpi_assign_mex.o
        $(CC) mpi_assign_mex.o -shared -o mpi_assign_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB)
    Last edited by in_ship; 12-07-2012 at 12:30 PM.

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