Undefined symbols when linking with R2010a on Mac OSX 10.6
in [Matlab]
|
From: Nicholas Kinar on 9 Apr 2010 11:30 Hello--- I've written some code in C++ which I would like to compile with the Matlab MEX compiler. I am using the current release of Matlab (R2010a, 32-bit), which is running on Mac OS X 10.6.3 (Snow Leopard). I've installed the most current version of the XCode tools (3.2.2, 64-bit), which ships with i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659). The code that I've written in C++ links with the MPFR and GMP libraries, which provide capabilities for handling large numbers using arbitrary-precision arithmetic. I am also using the MPFR C++ wrapper (http://www.holoborodko.com/pavel/?page_id=12). To compile my code, I invoke MEX in the following way: mex -I/usr/local/include mpreal.cpp T_Zeta.cpp -lmpfr -lgmp -v -g However, although I've compiled, checked and installed the MPFR and GMP libraries, the MEX invocation fails in the following manner. Why is MEX complaining about "Undefined symbols"? What would I have to do to ensure that the code will compile? Here is the output of the MEX invocation: mexopts.sh sourced from directory (DIR = $HOME/.matlab/$REL_VERSION) FILE = /Users/nicholaskinar/.matlab/R2010a/mexopts.sh ---------------------------------------------------------------- -> MATLAB = /Applications/MATLAB_R2010aSV.app -> CC = gcc-4.0 -> CC flags: CFLAGS = -fno-common -no-cpp-precomp -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -fexceptions CDEBUGFLAGS = -g COPTIMFLAGS = -O2 -DNDEBUG CLIBS = -L/Applications/MATLAB_R2010aSV.app/bin/maci -lmx -lmex -lmat -lstdc++ arguments = -DMX_COMPAT_32 -> CXX = g++-4.0 -> CXX flags: CXXFLAGS = -fno-common -no-cpp-precomp -fexceptions -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 CXXDEBUGFLAGS = -g CXXOPTIMFLAGS = -O2 -DNDEBUG CXXLIBS = -L/Applications/MATLAB_R2010aSV.app/bin/maci -lmx -lmex -lmat -lstdc++ arguments = -DMX_COMPAT_32 -> FC = gfortran -> FC flags: FFLAGS = -fexceptions -fbackslash FDEBUGFLAGS = -gdwarf-2 FOPTIMFLAGS = -O FLIBS = -L/Applications/MATLAB_R2010aSV.app/bin/maci -lmx -lmex -lmat -L -lgfortran -L -lgfortranbegin arguments = -DMX_COMPAT_32 -> LD = gcc-4.0 -> Link flags: LDFLAGS = -Wl,-twolevel_namespace -undefined error -arch i386 -Wl,-syslibroot,/Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2010aSV.app/extern/lib/maci/mexFunction.map LDDEBUGFLAGS = -g LDOPTIMFLAGS = -O LDEXTENSION = .mexmaci arguments = -lmpfr -lgmp -> LDCXX = -> Link flags: LDCXXFLAGS = LDCXXDEBUGFLAGS = LDCXXOPTIMFLAGS = LDCXXEXTENSION = arguments = -lmpfr -lgmp ---------------------------------------------------------------- -> g++-4.0 -c -I/usr/local/include -I/Applications/MATLAB_R2010aSV.app/extern/include -I/Applications/MATLAB_R2010aSV.app/simulink/include -DMATLAB_MEX_FILE -fno-common -no-cpp-precomp -fexceptions -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -DMX_COMPAT_32 -g "mpreal.cpp" -> g++-4.0 -c -I/usr/local/include -I/Applications/MATLAB_R2010aSV.app/extern/include -I/Applications/MATLAB_R2010aSV.app/simulink/include -DMATLAB_MEX_FILE -fno-common -no-cpp-precomp -fexceptions -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -DMX_COMPAT_32 -g "T_Zeta.cpp" -> gcc-4.0 -g -Wl,-twolevel_namespace -undefined error -arch i386 -Wl,-syslibroot,/Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2010aSV.app/extern/lib/maci/mexFunction.map -o "mpreal.mexmaci" mpreal.o T_Zeta.o -lmpfr -lgmp -L/Applications/MATLAB_R2010aSV.app/bin/maci -lmx -lmex -lmat -lstdc++ Undefined symbols: "_mpfr_mul_d", referenced from: mpfr::mpreal::operator*=(double)in T_Zeta.o "_mpfr_div_d", referenced from: mpfr::mpreal::operator/=(double)in T_Zeta.o ld: symbol(s) not found collect2: ld returned 1 exit status mex: link of ' "mpreal.mexmaci"' failed. ??? Error using ==> mex at 222 Unable to complete successfully.
From: Nicholas Kinar on 9 Apr 2010 15:24 > Undefined symbols: > "_mpfr_mul_d", referenced from: > mpfr::mpreal::operator*=(double)in T_Zeta.o > "_mpfr_div_d", referenced from: > mpfr::mpreal::operator/=(double)in T_Zeta.o > ld: symbol(s) not found > collect2: ld returned 1 exit status > > mex: link of ' "mpreal.mexmaci"' failed. > > ??? Error using ==> mex at 222 > Unable to complete successfully. Perhaps the undefined symbols could be an issue with linking between 32-bit and 64-bit software, as claimed in this thread: http://www.mathworks.co.kr/matlabcentral/newsreader/view_thread/260419 However, how might I force the GMP and MPFR libraries to compile as 32-bit on Snow Leopard? This might be required to be able to compile MEX file on 32-bit Matlab.
From: Nicholas Kinar on 9 Apr 2010 16:00 > > Perhaps the undefined symbols could be an issue with linking between > 32-bit and 64-bit software, as claimed in this thread: > > http://www.mathworks.co.kr/matlabcentral/newsreader/view_thread/260419 > > However, how might I force the GMP and MPFR libraries to compile as > 32-bit on Snow Leopard? This might be required to be able to compile MEX > file on 32-bit Matlab. > I forced the GMP and MPFR libraries to compile as 32-bit by passing the following arguments during the ./configure process. CFLAGS="-arch i386" LDFLAGS="-arch i386" For the GMP library, I also had to pass ABI=32. This created 32-bit libraries. I tried once again running MEX in Matlab, and I found that the error still occurs. mex -I/usr/local/include T_Zeta.cpp mpreal.cpp -lmpfr -lgmp -v -g Undefined symbols: "_mpfr_mul_d", referenced from: mpfr::mpreal::operator*=(double)in T_Zeta.o "_mpfr_div_d", referenced from: mpfr::mpreal::operator/=(double)in T_Zeta.o ld: symbol(s) not found collect2: ld returned 1 exit status mex: link of ' "T_Zeta.mexmaci"' failed. So why am I still getting unresolved symbols during linking of the MEX files?
From: Nicholas Kinar on 9 Apr 2010 16:45 > So why am I still getting unresolved symbols during linking of the MEX > files? So now what I did was run the following at the Matlab command-line: mex -I/usr/local/include T_Zeta.cpp mpreal.cpp /usr/local/lib/libgmp.a /usr/local/lib/libmpfr.a -v -g What I did was replace the "-l" switch with the absolute path to the library. However, now the following linking error results: ld: absolute addressing (perhaps -mdynamic-no-pic) used in ___gmpn_add_n from /Developer/SDKs/MacOSX10.5.sdk/usr/local/lib/libgmp.a(add_n.o) not allowed in slidable image. Use '-read_only_relocs suppress' to enable text relocs collect2: ld returned 1 exit status mex: link of ' "T_Zeta.mexmaci"' failed. What does this mean, and how do I get rid of this error?
From: Nicholas Kinar on 9 Apr 2010 17:37
On 10-04-09 2:45 PM, Nicholas Kinar wrote: >> So why am I still getting unresolved symbols during linking of the MEX >> files? > > So now what I did was run the following at the Matlab command-line: > > mex -I/usr/local/include T_Zeta.cpp mpreal.cpp /usr/local/lib/libgmp.a > /usr/local/lib/libmpfr.a -v -g > > What I did was replace the "-l" switch with the absolute path to the > library. > > However, now the following linking error results: > > ld: absolute addressing (perhaps -mdynamic-no-pic) used in ___gmpn_add_n > from /Developer/SDKs/MacOSX10.5.sdk/usr/local/lib/libgmp.a(add_n.o) not > allowed in slidable image. Use '-read_only_relocs suppress' to enable > text relocs > collect2: ld returned 1 exit status > > mex: link of ' "T_Zeta.mexmaci"' failed. > > > What does this mean, and how do I get rid of this error? > So now what I did was try to link with dynamic libraries: mex -I/usr/local/include T_Zeta.cpp mpreal.cpp /usr/local/lib/libgmp.dylib /usr/local/lib/libmpfr.dylib -v -g Surprisingly, this compiles! However, when I try to run the MEX file, I get the following error, which complains of a library not being loaded: [re, im] = T_Zeta(13.000) ??? Invalid MEX-file '/Volumes/FILES/DEVELOPMENT/reconstruction-algorithms/calculate-T-Zeta/T_Zeta.mexmaci': dlopen(/Volumes/FILES/DEVELOPMENT/reconstruction-algorithms/calculate-T-Zeta/T_Zeta.mexmaci, 1): Library not loaded: /usr/local/lib/libgmp.3.dylib Referenced from: /Volumes/FILES/DEVELOPMENT/reconstruction-algorithms/calculate-T-Zeta/T_Zeta.mexmaci Reason: Incompatible library version: T_Zeta.mexmaci requires version 9.0.0 or later, but libgmp.3.dylib provides version 8.0.0. How do I get rid of this error? What does this error mean? I am fairly certain that both libraries are of the same version. |