My question is about linking errors I get when compiling with external libraries using mex. I'm trying to compile C++ code using the external library fftw3 using Matlab's mex on MacOS using clang++. Here is an example
file: main.cpp
#include "fftw3.h" int main(){ double * test = (double *) fftw_malloc(10*sizeof(double)); }compiling this works
$ clang++ main.cpp -L/usr/local/lib -lfftw3Now I try something similar with mex
file: mex.cpp
#include "math.h" #include "matrix.h" #include "mex.h" #include "fftw3.h" void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) { double * test = (double *) fftw_malloc(10*sizeof(double)); }compiling in MATLAB
>> mex -setup C++; >> mex -L/usr/local/lib -lfftw3 CXXFLAGS='-L/usr/local/lib -lfftw3' mex.cpp Building with 'Xcode Clang++'. Error using mex clang: warning: -lfftw3: 'linker' input unused clang: warning: argument unused during compilation: '-L/usr/local/lib' /path/to/file/mex.cpp:4:10: fatal error: 'fftw3.h' file not found #include "fftw3.h" ^ 1 error generated.using the `-v` flag I get more detailed errors
Verbose mode is on. Neither -compatibleArrayDims nor -largeArrayDims is selected. Using -compatibleArrayDims. In the future, MATLAB will require the use of -largeArrayDims and remove the -compatibleArrayDims option. For more information: http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html. ... Looking for compiler 'Xcode Clang++' ... ... Looking for environment variable 'DEVELOPER_DIR' ...No. ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer' ...Yes. ... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun'). ... Looking for folder '/usr/bin' ...Yes. ... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...No. ... Executing command 'defaults read /Library/Preferences/com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('7.1.1'). ... Executing command ' agreed=7.1.1 if echo $agreed | grep -E '[\.\"]' >/dev/null; then lhs=`expr "$agreed" : '\([0-9]*\)[\.].*'` rhs=`expr "$agreed" : '[0-9]*[\.]\(.*\)$'` if echo $rhs | grep -E '[\."]' >/dev/null; then rhs=`expr "$rhs" : '\([0-9]*\)[\.].*'` fi if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then echo $agreed else exit 1 fi fi' ...Yes ('7.1.1'). ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes. ... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer'). ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No. ... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes. ... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.11'). Found installed compiler 'Xcode Clang++'. Options file details ------------------------------------------------------------------- Compiler location: /Applications/Xcode.app/Contents/Developer Options file: ~/.matlab/R2014b/mex_C++_maci64.xml CMDLINE100 : /usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o CMDLINE200 : /usr/bin/xcrun -sdk macosx10.11 clang++ -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -o mex.mexmaci64 CMDLINE300 : rm -f /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o CXX : /usr/bin/xcrun -sdk macosx10.11 clang++ DEFINES : -DMX_COMPAT_32 -DMATLAB_MEX_FILE MATLABMEX : -DMATLAB_MEX_FILE CXXFLAGS : -L/usr/local/lib -lfftw3 INCLUDE : -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" CXXOPTIMFLAGS : -O2 -DNDEBUG CXXDEBUGFLAGS : -g LDXX : /usr/bin/xcrun -sdk macosx10.11 clang++ LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" LDBUNDLE : -bundle LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" LINKLIBS : -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat LDOPTIMFLAGS : -O LDDEBUGFLAGS : -g OBJEXT : .o LDEXT : .mexmaci64 DEVELOPER_DIR_CHECK : XCODE_DIR : /Applications/Xcode.app/Contents/Developer XCRUN_DIR : /usr/bin XCODE_AGREED_VERSION : 7.1.1 ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk SDKVER : 10.11 MATLABROOT : /Applications/MATLAB_R2014b.app ARCH : maci64 SRC : /path/to/file/mex.cpp OBJ : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o OBJS : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o SRCROOT : /path/to/file/mex DEF : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.def EXP : mex.exp LIB : mex.lib EXE : mex.mexmaci64 ILK : mex.ilk MANIFEST : mex.mexmaci64.manifest TEMPNAME : mex EXEDIR : EXENAME : mex OPTIM : -O2 -DNDEBUG LINKOPTIM : -O ------------------------------------------------------------------- Building with 'Xcode Clang++'. /usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o Error using mex clang: warning: -lfftw3: 'linker' input unused clang: warning: argument unused during compilation: '-L/usr/local/lib' /path/to/file/mex.cpp:4:10: fatal error: 'fftw3.h' file not found #include "fftw3.h" ^ 1 error generated.EDIT:
the paths to the library files are
/usr/local/lib/libfftw3.a /usr/local/lib/libfftw3.la
I did try to symbolically link them to end in .so or .dylib but nothing helps
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