MATLAB: Symbol error using mex in Yosemite

When running a compiled mex-fortran file, I get a "Symbol not found" error. I think it's a linking error, but i don't know how to fix it. Any suggestions? Here is the error:

Invalid MEX-file '/Users/scott/Documents/Code/Mfiles-other/mex/band/band.mexmaci64':
dlopen(/Users/scott/Documents/Code/Mfiles-other/mex/band/band.mexmaci64, 6): Symbol not
found: __gfortran_transfer_integer_write
  Referenced from: /Users/scott/Documents/Code/Mfiles-other/mex/band/band.mexmaci64
  Expected in: /Applications/MATLAB_R2014b.app/sys/os/maci64/libgfortran.3.dylib
 in /Users/scott/Documents/Code/Mfiles-other/mex/band/band.mexmaci64

I'm compiling using the "mex" command within MATLAB 2014b, using fortran 4.9.1, installed as part of homebrew gcc 4.9.1, on Max OS Yosemite. The fortran file seems to compile fine, and I've copied the output of "mex -v band.F" below.

>> mex -v band.F
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.
No MEX options file identified; looking for an implicit selection.
... Looking for compiler 'gfortran' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... Executing command 'which gfortran' ...No.
... Looking for file '/usr/local/bin/gfortran' ...Yes.
... Looking for folder '/usr/local/bin' ...Yes.
... Executing command 'which gfortran' ...No.
... Looking for file '/usr/local/bin/gfortran' ...Yes.
... Executing command '/usr/local/bin/gfortran -print-file-name=libgfortran.dylib' ...Yes ('/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1/libgfortran.dylib').
... Looking for folder '/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1' ...Yes.
... Executing command 'which gfortran' ...No.
... Looking for file '/usr/local/bin/gfortran' ...Yes.
... Executing command '/usr/local/bin/gfortran -print-file-name=libgfortranbegin.a' ...Yes ('/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1/libgfortranbegin.a').
... Looking for folder '/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1' ...Yes.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...Yes.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...Yes.
... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.9').
Found installed compiler 'gfortran'.
Options file details
-------------------------------------------------------------------
  Compiler location: /usr/local/bin
  Options file: /Applications/MATLAB_R2014b.app/bin/maci64/mexopts/gfortran.xml
  CMDLINE1 : /usr/local/bin/gfortran -c -DMX_COMPAT_32    -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -fexceptions -m64 -fbackslash  -O /Users/scott/Documents/Code/Mfiles-other/mex/band/band.F -o /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o
  CMDLINE2 : xcrun -sdk macosx10.9 clang -Wl,-twolevel_namespace -undefined error -mmacosx-version-min=10.9 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/fexport.map" -O /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o   -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortran -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortranbegin -o band.mexmaci64
  CMDLINE3 : rm -f /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o
  FC : /usr/local/bin/gfortran
  FDEFINES : -DMX_COMPAT_32   
  FFLAGS : -fexceptions -m64 -fbackslash 
  INCLUDE : -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include"
  FOPTIMFLAGS : -O
  FDEBUGFLAGS : -g
  LDF : xcrun -sdk macosx10.9 clang
  LDFLAGS : -Wl,-twolevel_namespace -undefined error -mmacosx-version-min=10.9 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/fexport.map"
  LDBUNDLE : -bundle 
  LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/fexport.map"
  LINKLIBS : -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortran -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortranbegin
  LDOPTIMFLAGS : -O
  LDDEBUGFLAGS : -g
  OBJEXT : .o
  LDEXT : .mexmaci64
  DEVELOPER_DIR_CHECK : 
  GFORTRAN_INSTALLDIR : /usr/local/bin
  GFORTRAN_LIBDIR : /usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1
  GFORTRANBEGIN_LIBDIR : /usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1
  ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
  SDKVER : 10.9
  MATLABROOT : /Applications/MATLAB_R2014b.app
  ARCH : maci64
  SRC : /Users/scott/Documents/Code/Mfiles-other/mex/band/band.F
  OBJ : /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o
  OBJS : /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o 
  SRCROOT : /Users/scott/Documents/Code/Mfiles-other/mex/band/band
  DEF : /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.def
  EXP : band.exp
  LIB : band.lib
  EXE : band.mexmaci64
  ILK : band.ilk
  MANIFEST : band.mexmaci64.manifest
  TEMPNAME : band
  EXEDIR : 
  EXENAME : band
  OPTIM : -O
  LINKOPTIM : -O
-------------------------------------------------------------------
Building with 'gfortran'.
/usr/local/bin/gfortran -c -DMX_COMPAT_32    -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -fexceptions -m64 -fbackslash  -O /Users/scott/Documents/Code/Mfiles-other/mex/band/band.F -o /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o
xcrun -sdk macosx10.9 clang -Wl,-twolevel_namespace -undefined error -mmacosx-version-min=10.9 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/fexport.map" -O /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o   -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortran -L"/usr/local/Cellar/gcc/4.9.1/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1" -lgfortranbegin -o band.mexmaci64
rm -f /var/folders/_2/cdmj3bs94gx6r569mvsqqblm0000gn/T//mex_11838655149306_12289/band.o
MEX completed successfully.

Best Answer

Scott - I observed a similar error when I tried to run a Fortran-based MEX function that included some code to write data to the console (via mexPrintf). To get around this problem, I had to move my copy of libgfortran.3.dylib, substituting a different version using a symbolic link.

In my /Applications/MATLAB_R2014a.app/sys/os/maci64 folder, I did the following

 cd /Applications/MATLAB_R2014a.app/sys/os/maci64
 mv libgfortran.3.dylib libgfortran.3.dylib.old
 ln -s /usr/local/gfortran/lib/libgfortran.3.dylib libgfortran.3.dylib

I then quit MATLAB, restarted it, and was able to run the MEX function with no errors.

Best Answer

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