Mex -setup does not show gcc 4.7.3 compiler with Matlab 2013b + (ubuntu) Linux 64 bit

When I run 'mex -setup' I get:

>> mex -setup

      Options files control which compiler to use, the compiler and link command
      options, and the runtime libraries to link against.

      Using the 'mexsh -setup' command selects an options file that is
      placed in /home/wouter/.matlab/R2013b and used by default for 'mexsh'. An options 
      file in the current working directory or specified on the command line 
      overrides the default options file in /home/wouter/.matlab/R2013b.

      To override the default options file, use the 'mexsh -f' command
      (see 'mexsh -help' for more information).

The options files available for mexsh are:

    1: /usr/local/MATLAB/R2013b/bin/mexopts.sh : 
        Template Options file for building MEX-files

    0: Exit with no changes

Enter the number of the compiler (0-1):

Where is my gcc compiler? When I look in /usr/bin/ the binary/executable/link of gcc is clearly there which as far as I read on the web should be located there.

Answer 1

[Walter Roberson]

Which gcc is it? gcc 4.7.x is what is supported in R2013b

http://www.mathworks.com/support/compilers/R2013b/index.html?sec=glnxa64

[Wouter]

Yes gcc 4.7.3 to be exact.

Do you have any idea?

[Walter Roberson]

If you go to the Linux shell, and give the commands

gcc --version
which gcc

does it find gcc? In which directory? Inside MATLAB, if you give the command

getenv('PATH')

then does the directory with gcc in it show up on the list ?

[Wouter]

Output

$ gcc --version
gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ which gcc
/usr/bin/gcc

PATH variable

/usr/local/texlive/2013/bin/x86_64-linux/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/wouter/.local/bin

so yes "/usr/bin" is included...

When I look in mexopts.sh I see the following below. I see at line 59 something about gcc...? (Do not know if this helps?)

#
# mexopts.sh  Shell script for configuring MEX-file creation script,
#               mex.  These options were tested with the specified compiler.
#
# usage:        Do not call this file directly; it is sourced by the
#               mex shell script.  Modify only if you don't like the
#               defaults after running mex.  No spaces are allowed
#               around the '=' in the variable assignment.
#
# Note: For the version of system compiler supported with this release,
#       refer to the Supported and Compatible Compiler List at:
#       http://www.mathworks.com/support/compilers/current_release/
#
#
# SELECTION_TAGs occur in template option files and are used by MATLAB
# tools, such as mex and mbuild, to determine the purpose of the contents
# of an option file. These tags are only interpreted when preceded by '#'
# and followed by ':'.
#
#SELECTION_TAG_MEX_OPT: Template Options file for building MEX-files
#
# Copyright 1984-2011 The MathWorks, Inc.
# $Revision: 1.78.4.18 $  $Date: 2012/11/15 06:22:54 $
#----------------------------------------------------------------------------
#
    TMW_ROOT="$MATLAB"
    MFLAGS=''
    if [ "$ENTRYPOINT" = "mexLibrary" ]; then
        MLIBS="-L$TMW_ROOT/bin/$Arch -lmx -lmex -lmat -lmwservices -lut"
    else  
        MLIBS="-L$TMW_ROOT/bin/$Arch -lmx -lmex -lmat"
    fi
    case "$Arch" in
        Undetermined)
#----------------------------------------------------------------------------
# Change this line if you need to specify the location of the MATLAB
# root directory.  The script needs to know where to find utility
# routines so that it can determine the architecture; therefore, this
# assignment needs to be done while the architecture is still
# undetermined.
#----------------------------------------------------------------------------
            MATLAB="$MATLAB"
            ;;
        glnx86)
#----------------------------------------------------------------------------
echo "Error: Did not imbed 'options.sh' code"; exit 1 #imbed options.sh glnx86 12
#----------------------------------------------------------------------------
            ;;
        glnxa64)
#----------------------------------------------------------------------------
            RPATH="-Wl,-rpath-link,$TMW_ROOT/bin/$Arch"
            # StorageVersion: 1.0
            # CkeyName: GNU C
            # CkeyManufacturer: GNU
            # CkeyLanguage: C
            # CkeyVersion:
            # CkeyLinkerName: GNU ld
            # CkeyLinkerVersion:
            CC='gcc'
            CFLAGS='-ansi -D_GNU_SOURCE'
            CFLAGS="$CFLAGS  -fexceptions"
            CFLAGS="$CFLAGS -fPIC -fno-omit-frame-pointer -pthread"
            CLIBS="$RPATH $MLIBS -lm"
            COPTIMFLAGS='-O -DNDEBUG'
            CDEBUGFLAGS='-g'
            CLIBS="$CLIBS -lstdc++"
#
            # C++keyName: GNU C++
            # C++keyManufacturer: GNU
            # C++keyLanguage: C++
            # C++keyVersion:
            # C++keyLinkerName: GNU ld
            # C++keyLinkerVersion:  
            CXX='g++'
            CXXFLAGS='-ansi -D_GNU_SOURCE'
            CXXFLAGS="$CXXFLAGS -fPIC -fno-omit-frame-pointer -pthread"
            CXXLIBS="$RPATH $MLIBS -lm"
            CXXOPTIMFLAGS='-O -DNDEBUG'
            CXXDEBUGFLAGS='-g'
#
            # FortrankeyName: gfortran
            # FortrankeyManufacturer: GNU
            # FortrankeyLanguage: Fortran
            # FortrankeyVersion:
            # FortrankeyLinkerName: GNU ld
            # FortrankeyLinkerVersion:  
#
            FC='gfortran'
            FFLAGS='-fexceptions -fbackslash'
            FFLAGS="$FFLAGS -fPIC -fno-omit-frame-pointer"
            FLIBS="$RPATH $MLIBS -lm"
            FOPTIMFLAGS='-O'
            FDEBUGFLAGS='-g'
#
            LD="$COMPILER"
            LDEXTENSION='.mexa64'
            LDFLAGS="-pthread -shared -Wl,--version-script,$TMW_ROOT/extern/lib/$Arch/$MAPFILE -Wl,--no-undefined"
            LDOPTIMFLAGS='-O'
            LDDEBUGFLAGS='-g'
#
            POSTLINK_CMDS=':'
#----------------------------------------------------------------------------
            ;;
        sol64)
#----------------------------------------------------------------------------
echo "Error: Did not imbed 'options.sh' code"; exit 1 #imbed options.sh sol64 12
#----------------------------------------------------------------------------
            ;;
        mac)
#----------------------------------------------------------------------------
echo "Error: Did not imbed 'options.sh' code"; exit 1 #imbed options.sh mac 12
#----------------------------------------------------------------------------
            ;;
        maci)
#----------------------------------------------------------------------------
echo "Error: Did not imbed 'options.sh' code"; exit 1 #imbed options.sh maci 12
#----------------------------------------------------------------------------
            ;;
        maci64)
#----------------------------------------------------------------------------
            # StorageVersion: 1.0
            # CkeyName: Clang
            # CkeyManufacturer: Apple
            # CkeyLanguage: C
            # CkeyVersion:
            # CkeyLinkerName:
            # CkeyLinkerVersion:
            CC='xcrun  -sdk macosx10.7  clang'
## workaround clang defect temporarily use line below           SDKROOT='/Developer/SDKs/MacOSX10.6.sdk'
# compute SDK root on the fly
# target 10.7 
            MW_SDKROOT_TMP="find `xcode-select -print-path` -name MacOSX10.7.sdk"
      MW_SDKROOT=`$MW_SDKROOT_TMP`
            MACOSX_DEPLOYMENT_TARGET='10.7'
            ARCHS='x86_64'
            CFLAGS="-fno-common -arch $ARCHS -isysroot $MW_SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            CFLAGS="$CFLAGS  -fexceptions"
            CLIBS="$MLIBS"
            COPTIMFLAGS='-O2 -DNDEBUG'
            CDEBUGFLAGS='-g'
#
            CLIBS="$CLIBS -lstdc++"
            # C++keyName: Clang++
            # C++keyManufacturer: Apple
            # C++keyLanguage: C++
            # C++keyVersion:
            # C++keyLinkerName:
            # C++keyLinkerVersion:
            CXX='xcrun  -sdk macosx10.7  clang++'
            CXXFLAGS="-fno-common -fexceptions -arch $ARCHS -isysroot $MW_SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            CXXLIBS="$MLIBS -lstdc++"
            CXXOPTIMFLAGS='-O2 -DNDEBUG'
            CXXDEBUGFLAGS='-g'
#
            # FortrankeyName: GNU Fortran
            # FortrankeyManufacturer: GNU
            # FortrankeyLanguage: Fortran
            # FortrankeyVersion: 
            # FortrankeyLinkerName: 
            # FortrankeyLinkerVersion:
            FC='gfortran'
            FFLAGS='-fexceptions -m64 -fbackslash'
            FC_LIBDIR=`$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"
            FOPTIMFLAGS='-O'
            FDEBUGFLAGS='-g'
#
            LD="$CC"
            LDEXTENSION='.mexmaci64'
            LDFLAGS="-arch $ARCHS -Wl,-syslibroot,$MW_SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            LDFLAGS="$LDFLAGS -bundle -Wl,-exported_symbols_list,$TMW_ROOT/extern/lib/$Arch/$MAPFILE"
            LDOPTIMFLAGS='-O'
            LDDEBUGFLAGS='-g'
#
            POSTLINK_CMDS=':'
#----------------------------------------------------------------------------
            ;;
    esac
#############################################################################
#
# Architecture independent lines:
#
#     Set and uncomment any lines which will apply to all architectures.
#
#----------------------------------------------------------------------------
#           CC="$CC"
#           CFLAGS="$CFLAGS"
#           COPTIMFLAGS="$COPTIMFLAGS"
#           CDEBUGFLAGS="$CDEBUGFLAGS"
#           CLIBS="$CLIBS"
#
#           FC="$FC"
#           FFLAGS="$FFLAGS"
#           FOPTIMFLAGS="$FOPTIMFLAGS"
#           FDEBUGFLAGS="$FDEBUGFLAGS"
#           FLIBS="$FLIBS"
#
#           LD="$LD"
#           LDFLAGS="$LDFLAGS"
#           LDOPTIMFLAGS="$LDOPTIMFLAGS"
#           LDDEBUGFLAGS="$LDDEBUGFLAGS"
#----------------------------------------------------------------------------
#############################################################################

[Walter Roberson]

I notice that the dialog talks about selecting an options file, rather than about selecting a compiler. It appears that a proper options file has been created and selected, so you should be able to go ahead and mex files.

[Wouter]

You are totally correct. The problem was within a toolbox that I downloaded. When installing the toolbox it was saying that 'mex -setup' was not configured correctly. Thats why I thought something was a miss.