Basti's Scratchpad on the Internet
20 Oct 2012

Matlab, Mex, Homebrew and OS X 10.8 Mountain Lion

Now that I am a student again, I have to use Matlab again. Among the many joys of Matlab is the compilation of mex files.

Because it does not work. So angry.

Basically, mex does not work because it assumes that you have OS X 10.6 installed. In OS X 10.6 you had gcc-4.2 and your system SDK was stored in \/Developer\/SDKs\/MacOSX10.6.sdk. However, as of 10.7 (I think), the \/Developer directory has been deprecated in favor of distributing the whole development environment within the App package of XCode. Also, gcc has been deprecated in favor of clang. While a gcc binary is still provided, gcc-4.2 is not. Of course, that is what mex relies on. Lastly, mex of course completely disregards common system paths such as, say, \/usr\/local\/bin, so compiling against some homebrew library won't work.

At least these things are rather easy to fix, since all these settings are saved in a file called, which is saved to ~\.matlab\/R2012a\// by default. The relevant section on 64-bit OS X begins after maci64) and should look like this: (changes are marked by comments)

            # StorageVersion: 1.0
            # CkeyName: GNU C
            # CkeyManufacturer: GNU
            # CkeyLanguage: C
            # CkeyVersion:
            CC='gcc' # used to be 'gcc-4.2'

            # used to be '/Developer/SDKs/MacOSX10.6.sdk'
            MACOSX_DEPLOYMENT_TARGET='10.8' # used to be '10.5'
            CFLAGS="-fno-common -no-cpp-precomp -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            CFLAGS="$CFLAGS  -fexceptions"
            CFLAGS="$CFLAGS -I/usr/local/include" # Homebrew include path
            COPTIMFLAGS='-O2 -DNDEBUG'
            CLIBS="$CLIBS -lstdc++"
            # C++keyName: GNU C++
            # C++keyManufacturer: GNU
            # C++keyLanguage: C++
            # C++keyVersion:
            CXX=g++ # used to be 'g++-4.2'
            CXXFLAGS="-fno-common -no-cpp-precomp -fexceptions -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            CXXLIBS="$MLIBS -lstdc++"
            # FortrankeyName: GNU Fortran
            # FortrankeyManufacturer: GNU
            # FortrankeyLanguage: Fortran
            # FortrankeyVersion:
            FFLAGS='-fexceptions -m64 -fbackslash'
            FC_LIBDIR=`$FC -print-file-name=libgfortran.dylib 2>&1 | sed -n '1s/\/*libgfortran\.dylib//p'`
            FC_LIBDIR2=`$FC -print-file-name=libgfortranbegin.a 2>&1 | sed -n '1s/\/*libgfortranbegin\.a//p'`
            FLIBS="$MLIBS -L$FC_LIBDIR -lgfortran -L$FC_LIBDIR2 -lgfortranbegin"
            LDFLAGS="-Wl,-twolevel_namespace -undefined error -arch $ARCHS -Wl,-syslibroot,$SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            LDFLAGS="$LDFLAGS -bundle -Wl,-exported_symbols_list,$TMW_ROOT/extern/lib/$Arch/$MAPFILE"
            LDFLAGS="$LDFLAGS -L/usr/local/lib" # Homebrew library path

To summarize:

With those settings, the mex compiler should work and it should pick up any libraries installed by homebrew.

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