Error with codegen/mex (error status code 2)

Hi, I am trying to compile code that I know has compiled successfully on another computer. I am running Matlab 2014b on Ubuntu 12.04. Any ideas on how to fix this?

I am running the following code:

t = coder.typeof(0, [1e6 3],1);
C = coder.typeof(0, [1e6 3],1);
vt = coder.typeof(0, [1e6 3],1);
R = coder.typeof(0, [1e6 9],1);
EV = coder.typeof(0, [1e6 3 3],1);
codegen CalRigidEnergy3d -args { EV,t,vt,C,R }

This refers to the file CalRigidEnergy3d:

 function E=CalRigidEnergy3d(EV,t,U,C,R)
 E=0;
 Eij = zeros(3,1);
 for i=1:size(t,1)
    rot=reshape(R(i,:),[3 3]);
    for j=0:2
        j1=j+1;
        j2=mod(j+1,3)+1;
        j3=mod(j+2,3)+1;
        idx2=t(i,j2);
        idx3=t(i,j3);
        Uij=U(idx3,:)-U(idx2,:);
        Eij(1,1)=EV(i,j1,1);
        Eij(2,1)=EV(i,j1,2);
        Eij(3,1)=EV(i,j1,3);
        E=E+C(i,j1)*norm(Uij'-rot*Eij)^2;
    end 
 end

Running mex -setup returns the following:

 MEX configured to use 'gcc' for C language compilation.
 Warning: The MATLAB C and Fortran API has changed to support MATLAB
    variables with more than 2^32-1 elements. In the near future
    you will be required to update your code to utilize the
   new API. You can find more information about this at:
   http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
 To choose a different language, select one from the following:
 mex -setup C++ 
 mex -setup FORTRAN

The error given is:

 ??? Build error: Compilation returned error status code 2. See the target build log in the  report for further details.
 Error in ==> CalRigidEnergy3d Line: 1 Column: 1
 Code generation failed: Open error report.
 Error using codegen (line 146)

The Build Log is:

    1   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "CalRigidEnergy3d_data.c"
    2   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "CalRigidEnergy3d_initialize.c"
    3   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "CalRigidEnergy3d_terminate.c"
    4   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "CalRigidEnergy3d.c"
    5   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "interface/_coder_CalRigidEnergy3d_api.c"
    6   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "CalRigidEnergy3d_emxutil.c"
    7   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "interface/_coder_CalRigidEnergy3d_mex.c"
    8   /usr/bin/gcc -c -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE  -DMX_COMPAT_32  -O -DNDEBUG  -I "/usr/local/MATLAB/R2014b/simulink/include" -I "/usr/local/MATLAB/R2014b/toolbox/shared/simtargets" -I "/home/ari" -I "/home/ari/codegen/mex/CalRigidEnergy3d" -I "/home/ari/codegen/mex/CalRigidEnergy3d/interface" -I "/usr/local/MATLAB/R2014b/extern/include" -I "." "interface/_coder_CalRigidEnergy3d_info.c"
    9   /usr/bin/gcc -Wl,--version-script,CalRigidEnergy3d_mex_mex.map -pthread -Wl,--no-undefined -Wl,-rpath-link,/usr/local/MATLAB/R2014b/bin/glnxa64 -shared -L/usr/local/MATLAB/R2014b/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++    -o CalRigidEnergy3d_mex.mexa64  CalRigidEnergy3d_data.o CalRigidEnergy3d_initialize.o CalRigidEnergy3d_terminate.o CalRigidEnergy3d.o _coder_CalRigidEnergy3d_api.o CalRigidEnergy3d_emxutil.o _coder_CalRigidEnergy3d_mex.o _coder_CalRigidEnergy3d_info.o   -lemlrt -lcovrt -lut -lmwmathutil -lmwblas 
   10   _coder_CalRigidEnergy3d_api.o: In function `c_emlrt_marshallIn':
   11   _coder_CalRigidEnergy3d_api.c:(.text+0xb0): undefined reference to `mxGetData'
   12   _coder_CalRigidEnergy3d_api.o: In function `CalRigidEnergy3d_api':
   13   _coder_CalRigidEnergy3d_api.c:(.text+0x2cb): undefined reference to `mxGetData'
   14   _coder_CalRigidEnergy3d_api.c:(.text+0x427): undefined reference to `mxGetData'
   15   _coder_CalRigidEnergy3d_mex.o: In function `mexFunction':
   16   _coder_CalRigidEnergy3d_mex.c:(.text+0x3e): undefined reference to `mexAtExit'
   17   _coder_CalRigidEnergy3d_info.o: In function `b_emlrt_marshallOut':
   18   _coder_CalRigidEnergy3d_info.c:(.text+0x62): undefined reference to `mxGetData'
   19   _coder_CalRigidEnergy3d_info.o: In function `emlrtMexFcnProperties':
   20   _coder_CalRigidEnergy3d_info.c:(.text+0x8cac): undefined reference to `mxCreateStructMatrix_700'
   21   _coder_CalRigidEnergy3d_info.c:(.text+0x8cc7): undefined reference to `mxCreateStructMatrix_700'
   22   _coder_CalRigidEnergy3d_info.c:(.text+0x8cd9): undefined reference to `mxCreateLogicalMatrix_700'
   23   _coder_CalRigidEnergy3d_info.c:(.text+0x8ce8): undefined reference to `mxCreateString'
   24   _coder_CalRigidEnergy3d_info.c:(.text+0x8cfd): undefined reference to `mxSetFieldByNumber_700'
   25   _coder_CalRigidEnergy3d_info.c:(.text+0x8d0a): undefined reference to `mxCreateDoubleScalar'
   26   _coder_CalRigidEnergy3d_info.c:(.text+0x8d1f): undefined reference to `mxSetFieldByNumber_700'
   27   _coder_CalRigidEnergy3d_info.c:(.text+0x8d2c): undefined reference to `mxCreateDoubleScalar'
   28   _coder_CalRigidEnergy3d_info.c:(.text+0x8d41): undefined reference to `mxSetFieldByNumber_700'
   29   _coder_CalRigidEnergy3d_info.c:(.text+0x8d56): undefined reference to `mxSetFieldByNumber_700'
   30   _coder_CalRigidEnergy3d_info.c:(.text+0x8d62): undefined reference to `mxCreateString'
   31   _coder_CalRigidEnergy3d_info.c:(.text+0x8d77): undefined reference to `mxSetFieldByNumber_700'
   32   _coder_CalRigidEnergy3d_info.c:(.text+0x8d91): undefined reference to `mxSetFieldByNumber_700'
   33   _coder_CalRigidEnergy3d_info.c:(.text+0x8da6): undefined reference to `mxSetFieldByNumber_700'
   34   collect2: ld returned 1 exit status
   35   gmake: *** [CalRigidEnergy3d_mex.mexa64] Error 1

Answer 1

[Ryan Livingston]

The version of GCC shipped with Ubuntu is not compatible with the Makefile generated by MATLAB Coder. You can edit the template for this Makefile in your MATLAB installation to work around this by following the answer:

http://www.mathworks.com/matlabcentral/answers/163264#answer_159475

[Ari Kapusta]

Thank you very much!

The method in that link fixes the issue.