Hi,
"omp" stands for OpenMP, so I guess you build OpenMP-enabled code without
providing and setting OpenMP the correct way. Only MITK-Diffusion requires
OpenMP so if you're building plain MITK, I guess you have a corrupted
installation of OpenMP on your macOS that was picked up as optional build
dependency by MITK. You could try to remove it if you do not need it for other
projects. For MITK-Diffusion we recommend to use HomeBrew to install OpenMP.
Best,
Stefan
________________________________
Von: Ngo, Phuc <phuc....@pennmedicine.upenn.edu>
Gesendet: Montag, 9. März 2020 15:55
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Errors while building the MITK superbuild on macOS
I’m trying to build the superbuild on macOS. The version is OSX 10.14. During
the ‘make’ step, it threw this error
Undefined symbols for architecture x86_64:
"___kmpc_end_reduce_nowait", referenced from:
_.omp_outlined._debug__.9 in mitkWeightedPointTransform.cpp.o
"___kmpc_for_static_fini", referenced from:
_.omp_outlined._debug__ in
mitkAnisotropicIterativeClosestPointRegistration.cpp.o
_.omp_outlined._debug__ in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.1 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.9 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.11 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__ in mitkAnisotropicRegistrationCommon.cpp.o
_.omp_outlined._debug__.1 in mitkAnisotropicRegistrationCommon.cpp.o
...
"___kmpc_for_static_init_4", referenced from:
_.omp_outlined._debug__.9 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.11 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.1 in mitkAnisotropicRegistrationCommon.cpp.o
"___kmpc_for_static_init_8", referenced from:
_.omp_outlined._debug__ in
mitkAnisotropicIterativeClosestPointRegistration.cpp.o
_.omp_outlined._debug__ in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.1 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__ in mitkAnisotropicRegistrationCommon.cpp.o
"___kmpc_fork_call", referenced from:
mitk::AnisotropicIterativeClosestPointRegistration::ComputeCorrespondences(vtkPoints*,
vtkPoints*, vtkKdTreePointLocator*, std::__1::vector<itk::Matrix<double, 3u,
3u>, std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > >&,
std::__1::vector<std::__1::pair<unsigned int, double>,
std::__1::allocator<std::__1::pair<unsigned int, double> > >&, double) in
mitkAnisotropicIterativeClosestPointRegistration.cpp.o
mitk::WeightedPointTransform::C_maker(vtkPoints*,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
itk::VariableSizeMatrix<double>&) in mitkWeightedPointTransform.cpp.o
mitk::WeightedPointTransform::E_maker(vtkPoints*, vtkPoints*,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
vnl_vector<double>&) in mitkWeightedPointTransform.cpp.o
ComputeWeightedFRE(vtkPoints*, vtkPoints*,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&, double,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > >&, itk::Matrix<double, 3u,
3u> const&, itk::Vector<double, 3u> const&) in mitkWeightedPointTransform.cpp.o
calculateWeightMatrices(std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > >&, itk::Matrix<double, 3u,
3u> const&) in mitkWeightedPointTransform.cpp.o
mitk::AnisotropicRegistrationCommon::TransformPoints(vtkPoints*,
vtkPoints*, itk::Matrix<double, 3u, 3u> const&, mitk::Vector<double, 3u>
const&) in mitkAnisotropicRegistrationCommon.cpp.o
mitk::AnisotropicRegistrationCommon::PropagateMatrices(std::__1::vector<itk::Matrix<double,
3u, 3u>, std::__1::allocator<itk::Matrix<double, 3u, 3u> > > const&,
std::__1::vector<itk::Matrix<double, 3u, 3u>,
std::__1::allocator<itk::Matrix<double, 3u, 3u> > >&, itk::Matrix<double, 3u,
3u> const&) in mitkAnisotropicRegistrationCommon.cpp.o
...
"___kmpc_global_thread_num", referenced from:
_.omp_outlined._debug__ in
mitkAnisotropicIterativeClosestPointRegistration.cpp.o
_.omp_outlined._debug__ in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.1 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.9 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__.11 in mitkWeightedPointTransform.cpp.o
_.omp_outlined._debug__ in mitkAnisotropicRegistrationCommon.cpp.o
_.omp_outlined._debug__.1 in mitkAnisotropicRegistrationCommon.cpp.o
...
"___kmpc_reduce_nowait", referenced from:
_.omp_outlined._debug__.9 in mitkWeightedPointTransform.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[5]: *** [lib/libMitkAlgorithmsExt.dylib] Error 1
make[4]: *** [Modules/AlgorithmsExt/CMakeFiles/MitkAlgorithmsExt.dir/all] Error
2
I’m not sure how to debug this issue, and looks like no one ran into this
before. Can I get help with this please?
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