Unable to compile MEX on linux distro

[HansOlo]

So i am trying to get the mex-files running on my machine. But i get an error in the compilation process:

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../../../../src/shared//utils/Uncopyable.h:19: error: ‘Uncopyable::Uncopyable(const Uncopyable&)’ is private

Am i doing something wrong here? I am using a debian squeeze, which i downgraded to gcc-4.3(.4) and g++-4.3(.4) in combination with MatlabR2011a.

The full output:

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Mex file will be built without multithreading support.
To enable multithreading in mex files, specify -USE_QT as an option to the buildmex command.
Building load_bcidat ...
-> mexopts.sh sourced from directory (DIR = $HOME/.matlab/$REL_VERSION)
   FILE = /root/.matlab/R2011a/mexopts.sh
----------------------------------------------------------------
->    MATLAB                = /usr/local/MATLAB/R2011a
->    CC                    = gcc
->    CC flags:
         CFLAGS             = -ansi -D_GNU_SOURCE  -fexceptions -fPIC -fno-omit-frame-pointer -pthread
         CDEBUGFLAGS        = -g
         COPTIMFLAGS        = -O -DNDEBUG
         CLIBS              = -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
         arguments          =  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32
->    CXX                   = g++
->    CXX flags:
         CXXFLAGS           = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h
         CXXDEBUGFLAGS      = -g
         CXXOPTIMFLAGS      = -O -DNDEBUG
         CXXLIBS            = -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm
         arguments          =  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32
->    FC                    = gfortran
->    FC flags:
         FFLAGS             = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
         FDEBUGFLAGS        = -g
         FOPTIMFLAGS        = -O
         FLIBS              = -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm
         arguments          =  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32
->    LD                    = g++
->    Link flags:
         LDFLAGS            = -pthread -shared -Wl,--version-script,/usr/local/MATLAB/R2011a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -dead_strip
         LDDEBUGFLAGS       = -g
         LDOPTIMFLAGS       = -O
         LDEXTENSION        = .mexa64
         arguments          = 
->    LDCXX                 = 
->    Link flags:
         LDCXXFLAGS         = 
         LDCXXDEBUGFLAGS    = 
         LDCXXOPTIMFLAGS    = 
         LDCXXEXTENSION     = 
         arguments          = 
----------------------------------------------------------------

-> g++ -c  -I../.. -I../../../..//src/extlib/math -I../../../../src/shared/ -I../../../../src/shared//accessors -I../../../../src/shared//bcistream -I../../../../src/shared//config -I../../../../src/shared//fileio -I../../../../src/shared//fileio/dat -I../../../../src/shared//fileio/edf_gdf -I../../../../src/shared//modules -I../../../../src/shared//modules/SignalProcessing -I../../../../src/shared//types -I../../../../src/shared//utils -I../../../../src/shared//utils/Expression -I/usr/local/MATLAB/R2011a/extern/include -I/usr/local/MATLAB/R2011a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32 -O -DNDEBUG  "load_bcidat.cpp"

../../../../src/shared//utils/Uncopyable.h: In copy constructor ‘Lock<BCIError::OutStream>::Lock(const Lock<BCIError::OutStream>&)’:
../../../../src/shared//utils/Lockable.h:35:   instantiated from ‘Lock<T> TemporaryLock(T&) [with T = BCIError::OutStream]’
load_bcidat.cpp:203:   instantiated from here
../../../../src/shared//utils/Uncopyable.h:19: error: ‘Uncopyable::Uncopyable(const Uncopyable&)’ is private
../../../../src/shared//utils/Lockable.h:35: error: within this context
../../../../src/shared//utils/Lockable.h: In function ‘Lock<T> TemporaryLock(T&) [with T = BCIError::OutStream]’:
../../../../src/shared//utils/Lockable.h:79: note: synthesized method ‘Lock<BCIError::OutStream>::Lock(const Lock<BCIError::OutStream>&)’ first required here 

    mex: compile of ' "load_bcidat.cpp"' failed.

??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> buildmex at 274
        mex( args{:} );

Error in ==> buildmex at 217
            buildmex( options_{:}, TARGETS{i} );
 

[mellinger]

Hi,

thank you for reporting this problem. There were quite some issues with compiling BCI2000 under gcc, so mex files were broken for you as well.

I fixed these issues, and verified that mex file compilation works under OS X. Please update to the latest source code version from SVN, and let me know when you still have problems.

Juergen

[HansOlo]

Dear Jürgen,

thanks for your quick reaction. Compiling the MEX now get's a lot further but still doesn't finish without error:

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-> g++ -c  -I../.. -I../../../..//src/extlib/math -I../../../../src/shared/ -I../../../../src/shared//accessors -I../../../../src/shared//bcistream -I../../../../src/shared//config -I../../../../src/shared//fileio -I../../../../src/shared//fileio/dat -I../../../../src/shared//fileio/edf_gdf -I../../../../src/shared//modules -I../../../../src/shared//modules/SignalProcessing -I../../../../src/shared//types -I../../../../src/shared//utils -I../../../../src/shared//utils/Expression -I/usr/local/MATLAB/R2011a/extern/include -I/usr/local/MATLAB/R2011a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32 -O -DNDEBUG  "../../../../src/shared/fileio/edf_gdf/EDFOutputBase.cpp"

../../../../src/shared/fileio/edf_gdf/EDFOutputBase.cpp: In member function ‘virtual void EDFOutputBase::Initialize(const SignalProperties&, const StateVector&)’:
../../../../src/shared/fileio/edf_gdf/EDFOutputBase.cpp:132: error: ‘::strtod’ has not been declared

    mex: compile of ' "../../../../src/shared/fileio/edf_gdf/EDFOutputBase.cpp"' failed.

Shouldn't ::strtod be defined in stdlib.h?

[HansOlo]

Shouldn't ::strtod be defined in stdlib.h?

Added #include "stdlib.h" in EDFOutputBase.cpp, fixes this. Next error, probably again missing include (or bogus installation on my side):

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-> g++ -c  -I../.. -I../../../..//src/extlib/math -I../../../../src/shared/ -I../../../../src/shared//accessors -I../../../../src/shared//bcistream -I../../../../src/shared//config -I../../../../src/shared//fileio -I../../../../src/shared//fileio/dat -I../../../../src/shared//fileio/edf_gdf -I../../../../src/shared//modules -I../../../../src/shared//modules/SignalProcessing -I../../../../src/shared//types -I../../../../src/shared//utils -I../../../../src/shared//utils/Expression -I/usr/local/MATLAB/R2011a/extern/include -I/usr/local/MATLAB/R2011a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32 -O -DNDEBUG  "../../../../src/shared/accessors/Environment.cpp"

../../../../src/shared/accessors/Environment.cpp: In static member function ‘static void EnvironmentBase::EnterConstructionPhase(ParamList*, StateList*, StateVector*)’:
../../../../src/shared/accessors/Environment.cpp:435: error: ‘::atoi’ has not been declared
../../../../src/shared/accessors/Environment.cpp: In static member function ‘static void EnvironmentBase::EnterPreflightPhase(ParamList*, StateList*, StateVector*)’:
../../../../src/shared/accessors/Environment.cpp:461: error: ‘::atoi’ has not been declared
../../../../src/shared/accessors/Environment.cpp:477: error: ‘::atof’ has not been declared
../../../../src/shared/accessors/Environment.cpp:481: error: ‘::atof’ has not been declared
../../../../src/shared/accessors/Environment.cpp:491: error: ‘::atof’ has not been declared
../../../../src/shared/accessors/Environment.cpp:495: error: ‘::atof’ has not been declared

    mex: compile of ' "../../../../src/shared/accessors/Environment.cpp"' failed.

[HansOlo]

probably again missing include

Added include for stdlib.h, fixed this. However something seems to be different here:

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-> g++ -c  -I../.. -I../../../..//src/extlib/math -I../../../../src/shared/ -I../../../../src/shared//accessors -I../../../../src/shared//bcistream -I../../../../src/shared//config -I../../../../src/shared//fileio -I../../../../src/shared//fileio/dat -I../../../../src/shared//fileio/edf_gdf -I../../../../src/shared//modules -I../../../../src/shared//modules/SignalProcessing -I../../../../src/shared//types -I../../../../src/shared//utils -I../../../../src/shared//utils/Expression -I/usr/local/MATLAB/R2011a/extern/include -I/usr/local/MATLAB/R2011a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32 -O -DNDEBUG  "../../../../src/shared/modules/MessageQueue.cpp"


    mex:  ../../../../src/shared/modules/SignalProcessing/ARGroup.cpp  not a normal file or does not exist.

??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> buildmex at 276
        mex( args{:} );

Error in ==> buildmex at 219
            buildmex( options_{:}, TARGETS{i} );

The file exists and is readable:

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# pwd
/home/me/Desktop/bci2000src/src/shared/modules/signalprocessing
# ls -al|grep ARG
-rw-r--r-- 1 me me  1837 15. Aug 17:03 ARGroup.cpp
-rw-r--r-- 1 me me  2512 15. Aug 17:03 ARGroup.h

Might this be a problem withe cases? As in: /SignalProcessing/ and in /signalprocessing

[HansOlo]

Might this be a problem withe cases?

Yep, it was.

Next error, again stdlib.h:

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-> g++ -c  -I../.. -I../../../..//src/extlib/math -I../../../../src/shared/ -I../../../../src/shared//accessors -I../../../../src/shared//bcistream -I../../../../src/shared//config -I../../../../src/shared//fileio -I../../../../src/shared//fileio/dat -I../../../../src/shared//fileio/edf_gdf -I../../../../src/shared//modules -I../../../../src/shared//modules/SignalProcessing -I../../../../src/shared//types -I../../../../src/shared//utils -I../../../../src/shared//utils/Expression -I/usr/local/MATLAB/R2011a/extern/include -I/usr/local/MATLAB/R2011a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -fPIC -include gccprefix.h  -DBCI_TOOL -DBCI_MEX -DNO_STRICT -DNO_PCHINCLUDES -D_USE_MATH_DEFINES -DMX_COMPAT_32 -O -DNDEBUG  "../../../../src/shared/types/GenericVisualization.cpp"

../../../../src/shared/types/GenericVisualization.cpp: In member function ‘std::ostream& VisBase::WriteBinary(std::ostream&) const’:
../../../../src/shared/types/GenericVisualization.cpp:65: error: ‘::atoi’ has not been declared

    mex: compile of ' "../../../../src/shared/types/GenericVisualization.cpp"' failed.

??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> buildmex at 276
        mex( args{:} );

Error in ==> buildmex at 219
            buildmex( options_{:}, TARGETS{i} );

include added, fixed this, next error:

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-> g++ -O -pthread -shared -Wl,--version-script,/usr/local/MATLAB/R2011a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -dead_strip -o  "load_bcidat.mexa64"  load_bcidat.o BCI2000FileReader.o BCI2000OutputFormat.o EDFOutputBase.o EDFOutputFormat.o GDFOutputFormat.o GDF.o Environment.o ParamRef.o MessageHandler.o MessageQueue.o ARGroup.o ARChannel.o Param.o ParamList.o EncodedString.o LabelIndex.o HierarchicalLabel.o Brackets.o State.o StateList.o StateVector.o StateVectorSample.o GenericSignal.o SignalProperties.o SignalType.o PhysicalUnit.o SysCommand.o Status.o GenericVisualization.o BitmapImage.o ArithmeticExpression.o Expression.o ExpressionParser.o ClassName.o OSMutex.o OSThread.o MeasurementUnits.o VersionInfo.o BCIException.o BCIError.o BCIError_mex.o mexutils.o  -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm

OSThread.o: In function `OSThread::Terminate(OSEvent*)':
OSThread.cpp:(.text+0x103): undefined reference to `OSEvent::Set()'
OSThread.o: In function `OSThread::StartThread(void*)':
OSThread.cpp:(.text+0x42e): undefined reference to `OSEvent::Set()'
OSThread.o: In function `bool ExceptionCatcher::Execute<FunctionCall>(FunctionCall&)':
OSThread.cpp:(.text._ZN16ExceptionCatcher7ExecuteI12FunctionCallEEbRT_[bool ExceptionCatcher::Execute<FunctionCall>(FunctionCall&)]+0x1c): undefined reference to `ExceptionCatcher::DoExecute1(ExceptionCatcher::Fn&)'
collect2: ld returned 1 exit status

    mex: link of ' "load_bcidat.mexa64"' failed.

No idea how to fix this.

[mellinger]

So trying under OS X is obviously not enough to make sure mex files can be built on Linux. Thanks for pointing out the missing <cstdlib> includes.

The linker error shows that the Linux linker insists on resolving all referenced symbols, even those that cannot be reached from the mex_function() entry point. On OS X, specifying the -dead_strip linker option, this is not an issue (it appears that the -dead_strip linker option is specific to OS X).

Thank you and best regards,
Juergen

[HansOlo]

Hi again,

so i updated the sources and started the build again. This time it is:

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-> g++ -O -pthread -shared -Wl,--version-script,/usr/local/MATLAB/R2011a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -dead_strip -o  "load_bcidat.mexa64"  load_bcidat.o BCI2000FileReader.o BCI2000OutputFormat.o EDFOutputBase.o EDFOutputFormat.o GDFOutputFormat.o GDF.o Environment.o ParamRef.o MessageHandler.o MessageQueue.o ARGroup.o ARChannel.o Param.o ParamList.o EncodedString.o LabelIndex.o HierarchicalLabel.o Brackets.o State.o StateList.o StateVector.o StateVectorSample.o GenericSignal.o SignalProperties.o SignalType.o PhysicalUnit.o SysCommand.o Status.o GenericVisualization.o BitmapImage.o ArithmeticExpression.o Expression.o ExpressionParser.o ClassName.o OSMutex.o OSThread.o OSEvent.o MeasurementUnits.o VersionInfo.o BCIException.o BCIError.o BCIError_mex.o mexutils.o  -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm

OSThread.o: In function `bool ExceptionCatcher::Execute<FunctionCall>(FunctionCall&)':
OSThread.cpp:(.text._ZN16ExceptionCatcher7ExecuteI12FunctionCallEEbRT_[bool ExceptionCatcher::Execute<FunctionCall>(FunctionCall&)]+0x1c): undefined reference to `ExceptionCatcher::DoExecute1(ExceptionCatcher::Fn&)'
collect2: ld returned 1 exit status

    mex: link of ' "load_bcidat.mexa64"' failed.

??? Error using ==> mex at 208
Unable to complete successfully.

Error in ==> buildmex at 277
        mex( args{:} );

Error in ==> buildmex at 220
            buildmex( options_{:}, TARGETS{i} );

[mellinger]

Hi,

I fixed a number of issues, and made sure that mex files compile under Debian Squeeze with Matlab R2011a.

Let me know how it works for you.

Best regards,
Juergen

[HansOlo]

Hi,

now it compiles successfully (on current 64bit Debian Squeeze). However a warning is given at the end:

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-> g++ -O -pthread -shared -Wl,--version-script,/usr/local/MATLAB/R2011a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -dead_strip -o  "mem.mexa64"  mem.o BCI2000FileReader.o BCI2000OutputFormat.o EDFOutputBase.o EDFOutputFormat.o GDFOutputFormat.o GDF.o Environment.o ParamRef.o MessageHandler.o MessageQueue.o ARGroup.o ARChannel.o Param.o ParamList.o EncodedString.o LabelIndex.o HierarchicalLabel.o Brackets.o State.o StateList.o StateVector.o StateVectorSample.o GenericSignal.o SignalProperties.o SignalType.o PhysicalUnit.o SysCommand.o Status.o GenericVisualization.o BitmapImage.o ArithmeticExpression.o Expression.o ExpressionParser.o ClassName.o OSMutex.o OSThread.o OSEvent.o MeasurementUnits.o VersionInfo.o ExceptionCatcher.o BCIException.o BCIError.o BCIError_mex.o mexutils.o  -Wl,-rpath-link,/usr/local/MATLAB/R2011a/bin/glnxa64 -L/usr/local/MATLAB/R2011a/bin/glnxa64 -lmx -lmex -lmat -lm

Finished building mem
Testing mex files ... Warning: mem: Mismatch between computed spectra (relative error is 1.382997e-07)
Mex files tested OK.

Thanks a lot, Jürgen!

[mellinger]

That warning is ok. Due to (intentionally) incomplete specification of float arithmetic, there are small differences between computation results across compilers, platforms, and even for different optimization settings for the same compiler on the same platform.

Regards,
Juergen