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Thread: Suggestion in library inclusion with rpath

  1. 6th May 2011, 14:22 #1
    jepessen
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    Default Suggestion in library inclusion with rpath

    Hi. I'm trying of use the libmesh library in a project. When I compile a test file by hand, I use a command like this

    Qt Code: 
    1. c++ -o foo foo.C `/mylib/libmesh-config --cxxflags --include --ldflags`
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    when I use the --ldflags option

    Qt Code: 
    1. /mylib/libmesh-config --ldflags
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    I obtain something like this

    Qt Code: 
    1. /mydir/lib/x86_64-unknown-linux-gnu_dbg/libmesh.so 
    2. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/liblaspack.so 
    3. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libparmetis.so 
    4. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libmetis.so 
    5. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libsfcurves.so 
    6. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libgzstream.so -lz 
    7. /mydir/contrib/tecplot/lib/x86_64-unknown-linux-gnu/tecio.a 
    8. /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libgmv.so -Wl,-rpath,/usr/lib
    9.  -L/usr/lib -lvtkIO -lvtkCommon -lvtkFiltering -Wl,-rpath,/usr/lib 
    10.  -L/usr/lib -lglpk 
    11.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libtetgen.so 
    12.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libtriangle.so 
    13.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libexodusii.so 
    14.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libnetcdf.so 
    15.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libnemesis.so 
    16.  /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libHilbert.so -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib 
    17.  -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -lpetsc -lX11 -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib 
    18.  -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -lsuperlu_4.0 -lsuperlu_dist_2.4 -lparmetis -lmetis -lHYPRE -Wl,-rpath,/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -lmpichcxx -lstdc++ -lspooles -lumfpack -lamd -lflapack -lfblas -lnsl -lrt -lm -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -L/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lpthread -lrt -lgcc_s -ldl -lnsl -lrt -Wl,-rpath,/mydir/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -Wl,-rpath,/mydir/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib
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    I add these libraries using this code in the .pro file

    Qt Code: 
    1. ## Adding libraries ##
    2. unix {
    3.     TMPLIBS = $$system(/home/daniele/programs/libmesh-0.7.1/libmesh/contrib/bin/libmesh-config --ldflags)
    4.     LIBS += $$TMPLIBS
    5. }
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    and, if I print the LIBS variable (using message command) I obtain:

    Qt Code: 
    1. Project MESSAGE: LIBS = /mydir/lib/x86_64-unknown-linux-gnu_dbg/libmesh.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/liblaspack.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libparmetis.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libmetis.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libsfcurves.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libgzstream.so -lz /mydir/contrib/tecplot/lib/x86_64-unknown-linux-gnu/tecio.a /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libgmv.so -Wl,-rpath,/usr/lib -L/usr/lib -lvtkIO -lvtkCommon -lvtkFiltering -Wl,-rpath,/usr/lib -L/usr/lib -lglpk /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libtetgen.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libtriangle.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libexodusii.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libnetcdf.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libnemesis.so /mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg/libHilbert.so -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -lpetsc -lX11 -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -lsuperlu_4.0 -lsuperlu_dist_2.4 -lparmetis -lmetis -lHYPRE -Wl,-rpath,/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -lmpichcxx -lstdc++ -lspooles -lumfpack -lamd -lflapack -lfblas -lnsl -lrt -lm -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -L/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -L/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lpthread -lrt -lgcc_s -ldl -lnsl -lrt -Wl,-rpath,/mydir/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib -Wl,-rpath,/mydir/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/mydir/contrib/lib/x86_64-unknown-linux-gnu_dbg -Wl,-rpath,/home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/lib
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    But, in these case, it yet fails to load some library. Without this code, I got a lot of compiler error (about 50), while using this code errors (all of the type "undefined reference") are only 4, but not zero.

    I've seen in the variale something like -rpath with commas around it, and I don't know what's this. I don't know if this is the cause of my error, and I'd like to know how insert all libraries in a correct way.

    Thanks in advance for your reply
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  2. 8th May 2011, 05:03 #2
    ChrisW67
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    Default Re: Suggestion in library inclusion with rpath

    You are doing the correct thing. You are missing a library from the list, or the library no longer exists where the config says it does, but since you don't tell us what the error messages are we cannot even guess what it might be.

    The -rpath setting adds a directory to the runtime library search path (which can have problems after deployment) but should have no effect at build time.
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  3. 9th May 2011, 09:07 #3
    jepessen
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    Default Re: Suggestion in library inclusion with rpath

    Ok, I'll be more explicit...

    I compile manually the main.cpp of the project with this command:

    Qt Code: 
    1. c++ -o test main.cpp `/home/daniele/programs/libmesh-0.7.1/libmesh/contrib/bin/libmesh-config --cxxflags --include --ldflags`
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    I obtain only some warning (unused parameter of the library), but with this command program compiles and the executable file works well.

    The complete .pro file of my project is this one:

    Qt Code: 
    1. #-------------------------------------------------
    2. #
    3. # Project created by QtCreator 2011-05-04T12:27:57
    4. #
    5. #-------------------------------------------------
    6. QT       += core
    7.  
    8. QT       -= gui
    9.  
    10. TARGET = test
    11. CONFIG   += console
    12. CONFIG   -= app_bundle
    13.  
    14. TEMPLATE = app
    15.  
    16.  
    17.  
    18. SOURCES += main.cpp
    19.  
    20. #-------------------------------------------------
    21. # Adding libmesh library
    22. #-------------------------------------------------
    23.  
    24. ## Adding include paths ##
    25. unix {
    26.     TMPPATHS = $$system(/home/daniele/programs/libmesh-0.7.1/libmesh/contrib/bin/libmesh-config --include)
    27.     INCLUDEPATH += $$replace(TMPPATHS, "-I", "")
    28. }
    29.  
    30. # Printing paths
    31. message(INCLUDEPATH = $$INCLUDEPATH)
    32.  
    33. ## Adding libraries ##
    34. unix {
    35.  
    36.     TMPLIBS = $$system(/home/daniele/programs/libmesh-0.7.1/libmesh/contrib/bin/libmesh-config --ldflags)
    37.     LIBS += $$TMPLIBS
    38.  
    39. }
    40.  
    41. # Printing libs
    42. message($$LIBS)
    43.  
    44. ## Adding compiler flags ##
    45. unix {
    46. QMAKE_CXXFLAGS += $$system(/home/daniele/programs/libmesh-0.7.1/libmesh/contrib/bin/libmesh-config --cxxflags)
    47. }
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    The compile output error is this one:

    Qt Code: 
    1. main.o: In function `main':
    2. /home/daniele/Documenti/qt/test/test-build-desktop/../test/main.cpp:38: undefined reference to `libMesh::System::add_variable(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, libMeshEnums::Order, libMeshEnums::FEFamily, std::set<unsigned char, std::less<unsigned char>, std::allocator<unsigned char> > const*)'
    3. main.o: In function `assemble_1D(libMesh::EquationSystems&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
    4. /home/daniele/Documenti/qt/test/test-build-desktop/../test/main.cpp:125: undefined reference to `libMesh::DofMap::dof_indices(libMesh::Elem const*, std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int) const'
    5. /home/daniele/Documenti/qt/test/test-build-desktop/../test/main.cpp:162: undefined reference to `libMesh::DofMap::constrain_element_matrix_and_vector(libMesh::DenseMatrix<double>&, libMesh::DenseVector<double>&, std::vector<unsigned int, std::allocator<unsigned int> >&, bool) const'
    6. main.o: In function `libMesh::MeshOutput<libMesh::MeshBase>::write_equation_systems(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, libMesh::EquationSystems const&)':
    7. /home/daniele/Documenti/qt/test/test-build-desktop/../../../../programs/libmesh-0.7.1/libmesh/include/mesh/mesh_output.h:233: undefined reference to `libMesh::MeshOutput<libMesh::MeshBase>::_build_variable_names_and_solution_vector(libMesh::EquationSystems const&, std::vector<double, std::allocator<double> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)'
    8. main.o:(.rodata._ZTVN7libMesh16StatisticsVectorIfEE[vtable for libMesh::StatisticsVector<float>]+0x70): undefined reference to `libMesh::StatisticsVector<float>::histogram(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int)'
    9. main.o:(.rodata._ZTVN7libMesh16StatisticsVectorIfEE[vtable for libMesh::StatisticsVector<float>]+0x78): undefined reference to `libMesh::StatisticsVector<float>::histogram(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int) const'
    10. main.o:(.rodata._ZTVN7libMesh6FEBaseE[vtable for libMesh::FEBase]+0x68): undefined reference to `libMesh::FEBase::compute_map(std::vector<double, std::allocator<double> > const&, libMesh::Elem const*)'
    11. main.o:(.rodata._ZTVN7libMesh6FEBaseE[vtable for libMesh::FEBase]+0x70): undefined reference to `libMesh::FEBase::compute_affine_map(std::vector<double, std::allocator<double> > const&, libMesh::Elem const*)'
    12. collect2: ld returned 1 exit status
    13. make: Leaving directory `/home/daniele/Documenti/qt/test/test-build-desktop'
    14. make: *** [test] Error 1
    15. The process "/usr/bin/make" exited with code 2.
    16. Error while building project test (target: Desktop)
    17. When executing build step 'Make'
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    If I search the method of the last error, for example (compute_affine_map) I find it in the fe_base.h file, that's in the libmesh-0.7.1/libmesh/src/fe path, that's included in the INCLUDEDPATH variable, as you can see in the .pro message below.

    Qt Code: 
    1. Project MESSAGE: INCLUDEPATH = /home/daniele/programs/libmesh-0.7.1/libmesh/include/base /home/daniele/programs/libmesh-0.7.1/libmesh/include/enums /home/daniele/programs/libmesh-0.7.1/libmesh/include/error_estimation /home/daniele/programs/libmesh-0.7.1/libmesh/include/fe /home/daniele/programs/libmesh-0.7.1/libmesh/include/geom /home/daniele/programs/libmesh-0.7.1/libmesh/include/mesh /home/daniele/programs/libmesh-0.7.1/libmesh/include/numerics /home/daniele/programs/libmesh-0.7.1/libmesh/include/parallel /home/daniele/programs/libmesh-0.7.1/libmesh/include/partitioning /home/daniele/programs/libmesh-0.7.1/libmesh/include/quadrature /home/daniele/programs/libmesh-0.7.1/libmesh/include/solvers /home/daniele/programs/libmesh-0.7.1/libmesh/include/systems /home/daniele/programs/libmesh-0.7.1/libmesh/include/utils /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/boost /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/laspack /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/parmetis/Lib /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/metis/Lib /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/sfcurves /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/gzstream /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/tecplot/include /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/gmv /usr/include/vtk-5.4 /usr/include /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/tetgen /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/triangle /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/exodusii/Lib/include /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/netcdf/Lib /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/nemesis/Lib /home/daniele/programs/libmesh-0.7.1/libmesh/contrib/libHilbert/include /home/daniele/programs/petsc-3.1-p8/include /home/daniele/programs/petsc-3.1-p8/bmake/linux-gnu-dbg /home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/include /home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/include /home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/include /home/daniele/programs/petsc-3.1-p8/linux-gnu-dbg/include
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    Have you any suggestion, please?

    Added after 28 minutes:


    Ok, now it seems to work. It seems that I had to clear and rebuild the project...

    Thank you very much!!!
    Last edited by jepessen; 9th May 2011 at 09:07.
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