c - Matlab 2013b generated code produces Undefined symbols for architecture x86_64 error in mex

Question

I have a C-Code generated by the Simulink Coder that I need to use in a C S-function.

This may sound a bit strange but I need this Code to be executed multiple times within the s-function before writing the outputs of the s-function (it's an evolutionary algorithm that needs to simulate a prediction for a lot of individuals before evaluation and ranking...but those details do not really matter).

The Problem is that I seem to have a problem with the 64bit instruction set when trying to mex my code.

I am taking the generated erg_main.c as an example on how to interact with the generated code:

/*
 * File: ert_main.c
 *
 * Code generated for Simulink model 'Peltier_model'.
 *
 * Model version                  : 1.14
 * Simulink Coder version         : 8.5 (R2013b) 08-Aug-2013
 * C/C++ source code generated on : Thu Apr  3 18:01:46 2014
 *
 * Target selection: ert.tlc
 * Embedded hardware selection: 32-bit Generic
 * Emulation hardware selection:
 *    Differs from embedded hardware (MATLAB Host)
 * Code generation objective: Debugging
 * Validation result: Passed (0), Warning (1), Error (0)
 */

#include <stdio.h>                     /* This ert_main.c example uses printf/fflush */
#include "Peltier_model.h"             /* Model's header file */
#include "rtwtypes.h"

/*
 * Associating rt_OneStep with a real-time clock or interrupt service routine
 * is what makes the generated code "real-time".  The function rt_OneStep is
 * always associated with the base rate of the model.  Subrates are managed
 * by the base rate from inside the generated code.  Enabling/disabling
 * interrupts and floating point context switches are target specific.  This
 * example code indicates where these should take place relative to executing
 * the generated code step function.  Overrun behavior should be tailored to
 * your application needs.  This example simply sets an error status in the
 * real-time model and returns from rt_OneStep.
 */
void rt_OneStep(void)
{
  static boolean_T OverrunFlag = 0;

  /* Disable interrupts here */

  /* Check for overrun */
  if (OverrunFlag) {
    rtmSetErrorStatus(Peltier_model_M, "Overrun");
    return;
  }

  OverrunFlag = TRUE;

  /* Save FPU context here (if necessary) */
  /* Re-enable timer or interrupt here */
  /* Set model inputs here */

  /* Step the model */
  Peltier_model_step();

  /* Get model outputs here */

  /* Indicate task complete */
  OverrunFlag = FALSE;

  /* Disable interrupts here */
  /* Restore FPU context here (if necessary) */
  /* Enable interrupts here */
}

/*
 * The example "main" function illustrates what is required by your
 * application code to initialize, execute, and terminate the generated code.
 * Attaching rt_OneStep to a real-time clock is target specific.  This example
 * illustates how you do this relative to initializing the model.
 */
int_T main(int_T argc, const char *argv[])
{
  /* Unused arguments */
  (void)(argc);
  (void)(argv);

  /* Initialize model */
  Peltier_model_initialize();

  /* Attach rt_OneStep to a timer or interrupt service routine with
   * period 0.01 seconds (the model's base sample time) here.  The
   * call syntax for rt_OneStep is
   *
   *  rt_OneStep();
   */
  printf("Warning: The simulation will run forever. "
         "Generated ERT main won't simulate model step behavior. "
         "To change this behavior select the 'MAT-file logging' option.
");
  fflush((NULL));
  while (rtmGetErrorStatus(Peltier_model_M) == (NULL)) {
    /*  Perform other application tasks here */
  }

  /* Disable rt_OneStep() here */

  /* Terminate model */
  Peltier_model_terminate();
  return 0;
}

/*
 * File trailer for generated code.
 *
 * [EOF]
 */

For now I am just trying to initialize my model using the Peltier_model_initialize(); and including those headers from the erg_main.c

trying to mex this results in the following:

**************************************************************************
  Warning: 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, see:
           http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html
**************************************************************************

-> mexopts.sh sourced from directory (DIR = $PREF_DIR)
   FILE = /Users/JoachimSA/.matlab/R2013b/mexopts.sh
----------------------------------------------------------------
->    MATLAB                = /Applications/MATLAB_R2013b.app
->    CC                    = xcrun  -sdk macosx10.9  clang
->    CC flags:
         CFLAGS             = -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions
         CDEBUGFLAGS        = -g
         COPTIMFLAGS        = -O2 -DNDEBUG
         CLIBS              = -L/Applications/MATLAB_R2013b.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    CXX                   = xcrun  -sdk macosx10.9  clang++
->    CXX flags:
         CXXFLAGS           = -fno-common -fexceptions -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9
         CXXDEBUGFLAGS      = -g
         CXXOPTIMFLAGS      = -O2 -DNDEBUG
         CXXLIBS            = -L/Applications/MATLAB_R2013b.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    FC                    = gfortran
->    FC flags:
         FFLAGS             = -fexceptions -m64 -fbackslash
         FDEBUGFLAGS        = -g
         FOPTIMFLAGS        = -O
         FLIBS              = -L/Applications/MATLAB_R2013b.app/bin/maci64 -lmx -lmex -lmat -L -lgfortran -L -lgfortranbegin
         arguments          =  -DMX_COMPAT_32
->    LD                    = xcrun -sdk macosx10.9 clang
->    Link flags:
         LDFLAGS            = -arch x86_64 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013b.app/extern/lib/maci64/mexFunction.map
         LDDEBUGFLAGS       = -g
         LDOPTIMFLAGS       = -O
         LDEXTENSION        = .mexmaci64
         arguments          = 
->    LDCXX                 = 
->    Link flags:
         LDCXXFLAGS         = 
         LDCXXDEBUGFLAGS    = 
         LDCXXOPTIMFLAGS    = 
         LDCXXEXTENSION     = 
         arguments          = 
----------------------------------------------------------------

-> xcrun  -sdk macosx10.9  clang -c  -I/Applications/MATLAB_R2013b.app/rtw/c/src -I/Users/JoachimSA/Documents/WICHTIG/Diplomarbeit/Matlab_FIles/Peltier_Codegen/Peltier_model_ert_rtw -I/Applications/MATLAB_R2013b.app/extern/include -I/Applications/MATLAB_R2013b.app/simulink/include -DMATLAB_MEX_FILE -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions  -DMX_COMPAT_32 -O2 -DNDEBUG  "CC_IMEA.c"

-> xcrun  -sdk macosx10.9  clang -c  -I/Applications/MATLAB_R2013b.app/rtw/c/src -I/Users/JoachimSA/Documents/WICHTIG/Diplomarbeit/Matlab_FIles/Peltier_Codegen/Peltier_model_ert_rtw -I/Applications/MATLAB_R2013b.app/extern/include -I/Applications/MATLAB_R2013b.app/simulink/include -DMATLAB_MEX_FILE -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions  -DMX_COMPAT_32 -O2 -DNDEBUG  "CC_Opt_Objectives.c"

-> xcrun  -sdk macosx10.9  clang -c  -I/Applications/MATLAB_R2013b.app/rtw/c/src -I/Users/JoachimSA/Documents/WICHTIG/Diplomarbeit/Matlab_FIles/Peltier_Codegen/Peltier_model_ert_rtw -I/Applications/MATLAB_R2013b.app/extern/include -I/Applications/MATLAB_R2013b.app/simulink/include -DMATLAB_MEX_FILE -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions  -DMX_COMPAT_32 -O2 -DNDEBUG  "CC_System_Utils.c"

-> xcrun  -sdk macosx10.9  clang -c  -I/Applications/MATLAB_R2013b.app/rtw/c/src -I/Users/JoachimSA/Documents/WICHTIG/Diplomarbeit/Matlab_FIles/Peltier_Codegen/Peltier_model_ert_rtw -I/Applications/MATLAB_R2013b.app/extern/include -I/Applications/MATLAB_R2013b.app/simulink/include -DMATLAB_MEX_FILE -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions  -DMX_COMPAT_32 -O2 -DNDEBUG  "CC_Opt_SystemCabin.c"

-> xcrun  -sdk macosx10.9  clang -c  -I/Applications/MATLAB_R2013b.app/rtw/c/src -I/Users/JoachimSA/Documents/WICHTIG/Diplomarbeit/Matlab_FIles/Peltier_Codegen/Peltier_model_ert_rtw -I/Applications/MATLAB_R2013b.app/extern/include -I/Applications/MATLAB_R2013b.app/simulink/include -DMATLAB_MEX_FILE -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9  -fexceptions  -DMX_COMPAT_32 -O2 -DNDEBUG  "CC_Optimiser.c"

-> xcrun -sdk macosx10.9 clang -O -arch x86_64 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013b.app/extern/lib/maci64/mexFunction.map -o  "CC_Optimiser.mexmaci64"  CC_IMEA.o CC_Opt_Objectives.o CC_System_Utils.o CC_Opt_SystemCabin.o CC_Optimiser.o  -L/Applications/MATLAB_R2013b.app/bin/maci64 -lmx -lmex -lmat -lstdc++

Undefined symbols for architecture x86_64:
  "_Peltier_model_initialize", referenced from:
      _CC_Opt_SystemCabin in CC_Opt_SystemCabin.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

    mex: link of ' "CC_Optimiser.mexmaci64"' failed.

Unable to complete successfully.

Error in build_mex_files (line 6)
mex -v ...

Error in run (line 63)
evalin('caller', [script ';']);

Do I really have a problem with my 6bit version or am I just not handling the code right ?

Thanks a lot for the help !

Answer 1

The OP discovered that all source files need to be specified on the mex command.

This can cause compilation to succeed, but linking to fail, if all the necessary declarations are included by the main source file.

Here is some additional information from the Linking Multiple Files section of "Building MEX-Files" on the MathWorks website:

You can combine multiple source files, object files, and file libraries to build a binary MEX-file. To do this, list the additional files, with their file extensions, separated by spaces. The name of the MEX-file is the name of the first file in the list.

The following command combines multiple files of different types into a binary MEX-file called circle.ext, where ext is the extension corresponding to the current platform:

mex circle.c square.obj rectangle.c shapes.lib

As it says above, put the file with mexFunction as the first in the list so that the MEX-file gets the name from that file.

The mex help page has a section "Build MEX-File from Multiple Source Files" with a similar example, although with Fortran source:

mex -largeArrayDims fulltosparse.F loadsparse.F

The MEX-file name is fulltosparse because fulltosparse.F is the first file on the command line.