OS X 10.9 - Compilation error

[andreadelprete]

I'm experiencing a problem when trying to run any simulink controller using the WBI-Toolbox. I installed CoDyCo-superbuild on Mac OS X 10.9 and I'm using Matlab 2013a. When I try to run (e.g.) controllerWithHandControl.slx (located in the folder torqueBalancing) I get the following error:

Making simulation target "WBCLibrary_sfun", ... 

/Applications/MATLAB_R2013a.app/bin/mex -c -O  -DMATLAB_MEX_FILE    -I/Applications/MATLAB_R2013a.app/stateflow/c/mex/include -I/Applications/MATLAB_R2013a.app/stateflow/c/debugger/include   WBCLibrary_sfun.c
In file included from WBCLibrary_sfun.c:3:
In file included from ./WBCLibrary_sfun.h:6:
In file included from /Applications/MATLAB_R2013a.app/stateflow/c/mex/include/sfc_sf.h:33:
In file included from /Applications/MATLAB_R2013a.app/simulink/include/mwmathutil.h:23:
/Applications/MATLAB_R2013a.app/extern/include/tmwtypes.h:819:9: error: unknown type
      name 'char16_t'
typedef char16_t CHAR16_T;
        ^
1 error generated.
    mex: compile of ' "WBCLibrary_sfun.c"' failed.
gmake: *** [WBCLibrary_sfun.o] Error 1

With the help of @francesco-romano I tried to solve it by modifying the Matlab's configuration file mexopts.sh so as to force the use of the c++11 standard library (because char16t has been introduced in c++11):

maci64)
#----------------------------------------------------------------------------
            # StorageVersion: 1.0
            # CkeyName: Clang
            # CkeyManufacturer: Apple
            # CkeyLanguage: C
            # CkeyVersion:
            # CkeyLinkerName:
            # CkeyLinkerVersion:
#CC='xcrun  -sdk macosx10.9  clang'
CC='clang'
## workaround clang defect temporarily use line below           SDKROOT='/Developer/SDKs/MacOSX10.6.sdk'
# compute SDK root on the fly
# target 10.7 
            MW_SDK_TEMP="find `xcode-select -print-path` -name MacOSX10.9.sdk"
            MW_SDKROOT=`$MW_SDK_TEMP`
            MACOSX_DEPLOYMENT_TARGET='10.9'
            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="$CLIBS -lstdc++"
            CLIBS="$CLIBS"
            # C++keyName: Clang++
            # C++keyManufacturer: Apple
            # C++keyLanguage: C++
            # C++keyVersion:
            # C++keyLinkerName:
            # C++keyLinkerVersion:
            CXX='clang++'
            CXXFLAGS="-fno-common -fexceptions -arch $ARCHS -isysroot $MW_SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET -std=c++11"
#            CXXLIBS="$MLIBS -lstdc++"
            CXXLIBS="$MLIBS"
            CXXOPTIMFLAGS='-O2 -DNDEBUG'
            CXXDEBUGFLAGS='-g'

Unfortunately, this had no effect on the error. To try and solve this problem @francesco-romano and I would like to gain an insight into the steps taken by simulink when one runs the model. In particular, why is simulink trying to compile WBCLibrary_sfun.c to generate a mex file? I thought all mex files were generated when compiling the WBI toolbox. Maybe @jeljaik can help us on this?

[francesco-romano]

This seems the same problem described here.

But.. reading again the issue, maybe I understood the problem. We are setting the option for C++, but simulink is trying to compile a .c file. @andreadelprete can you try to set CFLAGS="$CFLAGS -fexceptions -std=c11" ?

PS: I can't understand why my matlab works PPS: In Matlab2014 the mex configuration is different. Mathwork has been migrating to XML files instead of the old config one. But.. it is still the default one.

[andreadelprete]

I tried to set CFLAGS as you suggested, but nothing changed!

[jeljaik]

Hello guys,

Andrea, since I don't have Mac OS X myself I will at least try to explain why Matlab is however doing some sort of compilation (I will however check this on @iron76 's laptop). At the beginning of every simulation it does some compiling, but different from the MEX files compilation. If you check the MEX directory in $CODYCO_SUPERBUILD_DIR/build/install/mex you will notice that the libraries we compile are robotState (the main one for most of the blocks), minJerkGenerator, ySynchronizer, yRead and yWrite. There's no WBCLibrary_sfun. The Simulink Engine has a model compiler that converts the Simulink model into an executable besides doing some optimization process before actually running into the simulation cycle. I believe it's there that it's failing. You can find more on this here:

http://www.itu.dk/stud/speciale/segmentering/DittesBinfolder/bin/MATLAB6p5p1/help/toolbox/simulink/ug/how_simulink_works13.html

So, in the directory of any of your models after you run the simulation, this initial compilation process generates also a file xxxx_sfun.mexXXX.

[jeljaik]

I also noticed a backward compatibility problem since I've upgrade to Matlab R2014a and I just realized the library has to be exported for compatibility with earlier versions of Matlab. I'll be back to you guys soon. I'm testing things with @iron76 ... @francesco-romano You might not be experiencing the same issues due to the fact that also you are using my Matlab version.

[jeljaik]

I am not entirely sure if this can be related to your problem but I have saved the Toolbox compatible with earlier versions of Matlab and it is working for @iron76 . Can you try again please and let me know it it had any influence?

I would also like to throw some hints. @iron76 had a similar issue in the past and he solved it by commenting some stuff in the CMakeLists of the WBIToolbox. It might throw some hints: https://github.com/robotology/codyco/commit/8010141d0869e6c25f6254f63e7b048d1f4b2d98#commitcomment-6566181

[francesco-romano]

I add my R2012b mexopts.sh configuration file.

CC='clang'
            SDKROOT='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk'
            MACOSX_DEPLOYMENT_TARGET='10.5'
            ARCHS='x86_64'
            CFLAGS="-fno-common -no-cpp-precomp -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET -Dchar16_t=UINT16_T"
            CFLAGS="$CFLAGS  -fexceptions"
            CLIBS="$MLIBS"
            COPTIMFLAGS='-O2 -DNDEBUG'
            CDEBUGFLAGS='-g'
#
            CLIBS="$CLIBS -lc++" #CLIBS="$CLIBS -lstdc++"
            # C++keyName: GNU C++
            # C++keyManufacturer: GNU
            # C++keyLanguage: C++
            # C++keyVersion:
            # C++keyLinkerName:
            # C++keyLinkerVersion:
            CXX='clang++'
            CXXFLAGS="-fno-common -no-cpp-precomp -fexceptions -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
            CXXLIBS="$MLIBS -lc++" #CXXLIBS="$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="-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"
            LDOPTIMFLAGS='-O'
            LDDEBUGFLAGS='-g'
#
            POSTLINK_CMDS=':'

[andreadelprete]

Hi @jeljaik , sorry I'm late but I couldn't test your solution until today. I updated the codyco superbuild using make update-all but that didn't solve the problem. However, with @francesco-romano we found a VERY DIRTY fix, that is to add the following line in the mexopts.sh: CFLAGS="$CFLAGS -Dchar16_t=uint16_T" Of course, this is not a solution, but only a workaround. Moreover, now when I open the simulink model I get a bunch of warnings (I report here only the firsts, since they're all of the same kind):

Warning: Loading model 'WBCLibrary' generated with a newer  version (8.3) of Simulink 
  In general/private/openmdl at 13
  In general/private/openslx at 9
  In open at 159
  In uiopen at 196 
Warning: WBCLibrary.mdl, line 105: block_diagram does not have a parameter named
'CovEnableCumulative' 
  In general/private/openmdl at 13
  In general/private/openslx at 9
  In open at 159
  In uiopen at 196 
Warning: WBCLibrary.mdl, line 112: block_diagram does not have a parameter named
'CovSFcnEnable' 
  In general/private/openmdl at 13
  In general/private/openslx at 9
  In open at 159
  In uiopen at 196 
...

[iron76]

I had a similar issue and I solved it by specifying a proper SDKROOT and a proper MACOSX_DEPLOYMENT_TARGET. In my case:

SDKROOT='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' MACOSX_DEPLOYMENT_TARGET='10.7'

However, these variables should be configured according to your system configuration. Francesco

---

Francesco Nori Robotics Brain Cognitive Science Department Cognitive Humanoids Lab Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova, Italy http://people.liralab.it/iron/ francesco.nori@iit.itmailto:francesco.nori@iit.it

Phone: (+39) 010 71 781 420 Fax: +39 010 71 70 817

On Jun 23, 2014, at 11:49 AM, Andrea Del Prete wrote:

Hi @jeljaikhttps://github.com/jeljaik , sorry I'm late but I couldn't test your solution until today. I updated the codyco superbuild using make update-all but that didn't solve the problem. However, with @francesco-romanohttps://github.com/francesco-romano we found a VERY DIRTY fix, that is to add the following line in the mexopts.sh: CFLAGS="$CFLAGS -Dchar16_t=uint16_T" Of course, this is not a solution, but only a workaround. Moreover, now when I open the simulink model I get a bunch of warnings (I report here only the firsts, since they're all of the same kind):

Warning: Loading model 'WBCLibrary' generated with a newer version (8.3) of Simulink In general/private/openmdl at 13 In general/private/openslx at 9 In open at 159 In uiopen at 196 Warning: WBCLibrary.mdl, line 105: block_diagram does not have a parameter named 'CovEnableCumulative' In general/private/openmdl at 13 In general/private/openslx at 9 In open at 159 In uiopen at 196 Warning: WBCLibrary.mdl, line 112: block_diagram does not have a parameter named 'CovSFcnEnable' In general/private/openmdl at 13 In general/private/openslx at 9 In open at 159 In uiopen at 196 ...

— Reply to this email directly or view it on GitHubhttps://github.com/robotology-playground/WBI-Toolbox/issues/2#issuecomment-46824801.

[jeljaik]

Closing as solution has been described above and no feedback was ever given.