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OpenMP support on Mac #2

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djsutherland opened this issue Jul 21, 2017 · 3 comments
Open

OpenMP support on Mac #2

djsutherland opened this issue Jul 21, 2017 · 3 comments

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@djsutherland
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Might be possible with the openmp package, should try it out.
@djsutherland djsutherland mentioned this issue Jul 31, 2017
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@isuruf
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isuruf commented Mar 3, 2020

This failed with,

2020-03-03T21:28:00.0183640Z ld: warning: -pie being ignored. It is only used when linking a main executable
2020-03-03T21:28:00.1340780Z Undefined symbols for architecture x86_64:
2020-03-03T21:28:00.1341620Z   "___kmpc_barrier", referenced from:
2020-03-03T21:28:00.1342070Z       _.omp_outlined. in Distance.cpp.o
2020-03-03T21:28:00.1342530Z       _.omp_outlined..21 in Distance.cpp.o
2020-03-03T21:28:00.1343020Z       _.omp_outlined. in DotFeatures.cpp.o
2020-03-03T21:28:00.1343500Z       _.omp_outlined..10 in DotFeatures.cpp.o
2020-03-03T21:28:00.1354470Z       _.omp_outlined. in DistanceMachine.cpp.o
2020-03-03T21:28:00.1355130Z       _.omp_outlined..6 in DistanceMachine.cpp.o
2020-03-03T21:28:00.1355620Z       _.omp_outlined. in KernelMachine.cpp.o
2020-03-03T21:28:00.1356010Z       ...
2020-03-03T21:28:00.1451070Z   "___kmpc_critical", referenced from:
2020-03-03T21:28:00.1461560Z       _.omp_outlined..162 in Kernel.cpp.o
2020-03-03T21:28:00.1462120Z       _.omp_outlined..164 in Kernel.cpp.o
2020-03-03T21:28:00.1462590Z       _.omp_outlined..166 in Kernel.cpp.o
2020-03-03T21:28:00.1465580Z       _.omp_outlined. in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1466140Z       _.omp_outlined..276 in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1466640Z       _.omp_outlined..306 in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1467100Z       _.omp_outlined..12 in BaggingMachine.cpp.o
2020-03-03T21:28:00.1467480Z       ...
2020-03-03T21:28:00.1563460Z   "___kmpc_end_critical", referenced from:
2020-03-03T21:28:00.1571860Z       _.omp_outlined..162 in Kernel.cpp.o
2020-03-03T21:28:00.1572390Z       _.omp_outlined..164 in Kernel.cpp.o
2020-03-03T21:28:00.1572850Z       _.omp_outlined..166 in Kernel.cpp.o
2020-03-03T21:28:00.1576130Z       _.omp_outlined. in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1576690Z       _.omp_outlined..276 in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1577160Z       _.omp_outlined..306 in tapkee_shogun.cpp.o
2020-03-03T21:28:00.1577660Z       _.omp_outlined..12 in BaggingMachine.cpp.o
2020-03-03T21:28:00.1578030Z       ...
2020-03-03T21:28:00.1676180Z   "___kmpc_end_reduce_nowait", referenced from:
2020-03-03T21:28:00.1676890Z       _.omp_outlined. in KMeans.cpp.o
2020-03-03T21:28:00.1684930Z       _.omp_outlined. in Kernel.cpp.o
2020-03-03T21:28:00.1685530Z       _.omp_outlined..154 in Kernel.cpp.o
2020-03-03T21:28:00.1685980Z       _.omp_outlined..160 in Kernel.cpp.o
2020-03-03T21:28:00.1803070Z   "___kmpc_end_serialized_parallel", referenced from:
2020-03-03T21:28:00.1803910Z       shogun::CKMeans::Lloyd_KMeans(shogun::SGMatrix<double>, int) in KMeans.cpp.o
2020-03-03T21:28:00.1929720Z   "___kmpc_end_single", referenced from:
2020-03-03T21:28:00.1930660Z       _.omp_outlined. in Distance.cpp.o
2020-03-03T21:28:00.1931390Z       _.omp_outlined..21 in Distance.cpp.o
2020-03-03T21:28:00.1932080Z       _.omp_outlined. in DotFeatures.cpp.o
2020-03-03T21:28:00.1932560Z       _.omp_outlined..10 in DotFeatures.cpp.o
2020-03-03T21:28:00.1943090Z       _.omp_outlined. in DistanceMachine.cpp.o
2020-03-03T21:28:00.1943600Z       _.omp_outlined..6 in DistanceMachine.cpp.o
2020-03-03T21:28:00.1944540Z       _.omp_outlined. in KernelMachine.cpp.o
2020-03-03T21:28:00.1944920Z       ...
2020-03-03T21:28:00.2041200Z   "___kmpc_for_static_fini", referenced from:
2020-03-03T21:28:00.2041810Z       _.omp_outlined. in KMeans.cpp.o
2020-03-03T21:28:00.2042300Z       _.omp_outlined. in KMeansBase.cpp.o
2020-03-03T21:28:00.2042810Z       _.omp_outlined..12 in KMeansBase.cpp.o
2020-03-03T21:28:00.2043290Z       _.omp_outlined. in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2043750Z       _.omp_outlined..7 in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2050340Z       _.omp_outlined. in CombinedKernel.cpp.o
2020-03-03T21:28:00.2051060Z       _.omp_outlined..35 in CombinedKernel.cpp.o
2020-03-03T21:28:00.2051470Z       ...
2020-03-03T21:28:00.2143430Z   "___kmpc_for_static_init_4", referenced from:
2020-03-03T21:28:00.2144100Z       _.omp_outlined. in KMeans.cpp.o
2020-03-03T21:28:00.2144670Z       _.omp_outlined. in KMeansBase.cpp.o
2020-03-03T21:28:00.2145070Z       _.omp_outlined..12 in KMeansBase.cpp.o
2020-03-03T21:28:00.2145530Z       _.omp_outlined. in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2145980Z       _.omp_outlined..7 in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2151190Z       _.omp_outlined. in CombinedKernel.cpp.o
2020-03-03T21:28:00.2151720Z       _.omp_outlined..35 in CombinedKernel.cpp.o
2020-03-03T21:28:00.2152290Z       ...
2020-03-03T21:28:00.2245370Z   "___kmpc_for_static_init_8", referenced from:
2020-03-03T21:28:00.2268880Z       _.omp_outlined. in StreamingMMD.cpp.o
2020-03-03T21:28:00.2269700Z       _.omp_outlined..5 in StreamingMMD.cpp.o
2020-03-03T21:28:00.2270220Z       _.omp_outlined. in ComputationManager.cpp.o
2020-03-03T21:28:00.2371230Z   "___kmpc_fork_call", referenced from:
2020-03-03T21:28:00.2371980Z       shogun::CKMeans::Lloyd_KMeans(shogun::SGMatrix<double>, int) in KMeans.cpp.o
2020-03-03T21:28:00.2372590Z       shogun::CKMeansBase::kmeanspp() in KMeansBase.cpp.o
2020-03-03T21:28:00.2373220Z       shogun::SGMatrix<double> shogun::CDistance::get_distance_matrix<double>() in Distance.cpp.o
2020-03-03T21:28:00.2373920Z       shogun::SGMatrix<float> shogun::CDistance::get_distance_matrix<float>() in Distance.cpp.o
2020-03-03T21:28:00.2374570Z       shogun::CEuclideanDistance::precompute_lhs() in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2375160Z       shogun::CEuclideanDistance::precompute_rhs() in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2375840Z       shogun::CDotFeatures::dense_dot_range(double*, int, int, double*, double*, int, double) in DotFeatures.cpp.o
2020-03-03T21:28:00.2376830Z       ...
2020-03-03T21:28:00.2465260Z   "___kmpc_global_thread_num", referenced from:
2020-03-03T21:28:00.2466040Z       shogun::CKMeans::Lloyd_KMeans(shogun::SGMatrix<double>, int) in KMeans.cpp.o
2020-03-03T21:28:00.2466640Z       _.omp_outlined. in KMeans.cpp.o
2020-03-03T21:28:00.2467120Z       _.omp_outlined. in KMeansBase.cpp.o
2020-03-03T21:28:00.2467620Z       _.omp_outlined..12 in KMeansBase.cpp.o
2020-03-03T21:28:00.2468130Z       _.omp_outlined. in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2468640Z       _.omp_outlined..7 in EuclideanDistance.cpp.o
2020-03-03T21:28:00.2474160Z       _.omp_outlined. in CombinedKernel.cpp.o
2020-03-03T21:28:00.2474730Z       ...
2020-03-03T21:28:00.2574200Z   "___kmpc_reduce_nowait", referenced from:
2020-03-03T21:28:00.2575110Z       _.omp_outlined. in KMeans.cpp.o
2020-03-03T21:28:00.2582310Z       _.omp_outlined. in Kernel.cpp.o
2020-03-03T21:28:00.2582910Z       _.omp_outlined..154 in Kernel.cpp.o
2020-03-03T21:28:00.2583410Z       _.omp_outlined..160 in Kernel.cpp.o
2020-03-03T21:28:00.2702980Z   "___kmpc_serialized_parallel", referenced from:
2020-03-03T21:28:00.2703900Z       shogun::CKMeans::Lloyd_KMeans(shogun::SGMatrix<double>, int) in KMeans.cpp.o
2020-03-03T21:28:00.2829920Z   "___kmpc_single", referenced from:
2020-03-03T21:28:00.2830660Z       _.omp_outlined. in Distance.cpp.o
2020-03-03T21:28:00.2831260Z       _.omp_outlined..21 in Distance.cpp.o
2020-03-03T21:28:00.2832280Z       _.omp_outlined. in DotFeatures.cpp.o
2020-03-03T21:28:00.2832750Z       _.omp_outlined..10 in DotFeatures.cpp.o
2020-03-03T21:28:00.2843160Z       _.omp_outlined. in DistanceMachine.cpp.o
2020-03-03T21:28:00.2843740Z       _.omp_outlined..6 in DistanceMachine.cpp.o
2020-03-03T21:28:00.2844240Z       _.omp_outlined. in KernelMachine.cpp.o
2020-03-03T21:28:00.2844660Z       ...
2020-03-03T21:28:00.2943960Z   "_omp_get_max_threads", referenced from:
2020-03-03T21:28:00.2957100Z       tapkee::TapkeeOutput tapkee::embed<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel>, pimpl_distance_callback<shogun::CDistance>, ShogunFeatureVectorCallback>(std::__1::__wrap_iter<int*>, std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel>, pimpl_distance_callback<shogun::CDistance>, ShogunFeatureVectorCallback, tapkee::ParametersSet) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.2966170Z       shogun::CMMD::init() in MMD.cpp.o
2020-03-03T21:28:00.2967190Z       shogun::CStreamingMMD::CStreamingMMD() in StreamingMMD.cpp.o
2020-03-03T21:28:00.3080930Z   "_omp_get_num_threads", referenced from:
2020-03-03T21:28:00.3083050Z       _.omp_outlined. in Distance.cpp.o
2020-03-03T21:28:00.3095150Z       _.omp_outlined..21 in Distance.cpp.o
2020-03-03T21:28:00.3114190Z       _.omp_outlined. in DotFeatures.cpp.o
2020-03-03T21:28:00.3114780Z       _.omp_outlined..10 in DotFeatures.cpp.o
2020-03-03T21:28:00.3115280Z       _.omp_outlined. in DistanceMachine.cpp.o
2020-03-03T21:28:00.3115800Z       _.omp_outlined..6 in DistanceMachine.cpp.o
2020-03-03T21:28:00.3116320Z       _.omp_outlined. in KernelMachine.cpp.o
2020-03-03T21:28:00.3116740Z       ...
2020-03-03T21:28:00.3226580Z   "_omp_get_thread_num", referenced from:
2020-03-03T21:28:00.3227700Z       _.omp_outlined. in Distance.cpp.o
2020-03-03T21:28:00.3228230Z       _.omp_outlined..21 in Distance.cpp.o
2020-03-03T21:28:00.3228730Z       _.omp_outlined. in DotFeatures.cpp.o
2020-03-03T21:28:00.3233140Z       _.omp_outlined..10 in DotFeatures.cpp.o
2020-03-03T21:28:00.3240000Z       _.omp_outlined. in DistanceMachine.cpp.o
2020-03-03T21:28:00.3240770Z       _.omp_outlined..6 in DistanceMachine.cpp.o
2020-03-03T21:28:00.3241280Z       _.omp_outlined. in KernelMachine.cpp.o
2020-03-03T21:28:00.3241790Z       ...
2020-03-03T21:28:00.3346040Z   "_omp_get_wtime", referenced from:
2020-03-03T21:28:00.3360780Z       tapkee::tapkee_internal::ImplementationBase<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel>, pimpl_distance_callback<shogun::CDistance>, ShogunFeatureVectorCallback>::embedUsing(tapkee::DimensionReductionMethod) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3363320Z       Eigen::SparseMatrix<double, 0, int> tapkee::tapkee_internal::linear_weight_matrix<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> >(std::__1::__wrap_iter<int*> const&, std::__1::__wrap_iter<int*> const&, std::__1::vector<std::__1::vector<int, std::__1::allocator<int> >, std::__1::allocator<std::__1::vector<int, std::__1::allocator<int> > > > const&, pimpl_kernel_callback<shogun::CKernel>, double, double) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3366100Z       std::__1::vector<std::__1::vector<int, std::__1::allocator<int> >, std::__1::allocator<std::__1::vector<int, std::__1::allocator<int> > > > tapkee::tapkee_internal::find_neighbors_bruteforce_impl<std::__1::__wrap_iter<int*>, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> > >(std::__1::__wrap_iter<int*> const&, std::__1::__wrap_iter<int*> const&, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> >, int) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3369070Z       std::__1::vector<std::__1::vector<int, std::__1::allocator<int> >, std::__1::allocator<std::__1::vector<int, std::__1::allocator<int> > > > tapkee::tapkee_internal::find_neighbors_vptree_impl<std::__1::__wrap_iter<int*>, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> > >(std::__1::__wrap_iter<int*> const&, std::__1::__wrap_iter<int*> const&, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> >, int) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3372190Z       std::__1::vector<std::__1::vector<int, std::__1::allocator<int> >, std::__1::allocator<std::__1::vector<int, std::__1::allocator<int> > > > tapkee::tapkee_internal::find_neighbors_covertree_impl<std::__1::__wrap_iter<int*>, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> > >(std::__1::__wrap_iter<int*>, std::__1::__wrap_iter<int*>, tapkee::tapkee_internal::KernelDistance<std::__1::__wrap_iter<int*>, pimpl_kernel_callback<shogun::CKernel> >, int) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3374570Z       bool tapkee::tapkee_internal::is_connected<std::__1::__wrap_iter<int*> >(std::__1::__wrap_iter<int*>, std::__1::__wrap_iter<int*>, std::__1::vector<std::__1::vector<int, std::__1::allocator<int> >, std::__1::allocator<std::__1::vector<int, std::__1::allocator<int> > > > const&) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3377460Z       std::__1::pair<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, 1, 0, -1, 1> > tapkee::tapkee_internal::eigendecomposition_impl_arpack<Eigen::SparseMatrix<double, 0, int>, tapkee::tapkee_internal::SparseInverseMatrixOperation>(Eigen::SparseMatrix<double, 0, int> const&, int, unsigned int) in tapkee_shogun.cpp.o
2020-03-03T21:28:00.3378660Z       ...
2020-03-03T21:28:00.3463890Z   "_omp_set_dynamic", referenced from:
2020-03-03T21:28:00.3464580Z       shogun::Parallel::Parallel() in Parallel.cpp.o
2020-03-03T21:28:00.3465100Z       shogun::Parallel::Parallel() in Parallel.cpp.o
2020-03-03T21:28:00.3465660Z       shogun::Parallel::Parallel(shogun::Parallel const&) in Parallel.cpp.o
2020-03-03T21:28:00.3466340Z       shogun::Parallel::Parallel(shogun::Parallel const&) in Parallel.cpp.o
2020-03-03T21:28:00.3596540Z   "_omp_set_num_threads", referenced from:
2020-03-03T21:28:00.3597690Z       shogun::Parallel::Parallel() in Parallel.cpp.o
2020-03-03T21:28:00.3598310Z       shogun::Parallel::Parallel() in Parallel.cpp.o
2020-03-03T21:28:00.3598900Z       shogun::Parallel::Parallel(shogun::Parallel const&) in Parallel.cpp.o
2020-03-03T21:28:00.3599550Z       shogun::Parallel::Parallel(shogun::Parallel const&) in Parallel.cpp.o
2020-03-03T21:28:00.3600180Z       shogun::Parallel::set_num_threads(int) in Parallel.cpp.o
2020-03-03T21:28:00.3824220Z ld: symbol(s) not found for architecture x86_64

@isuruf
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isuruf commented Mar 3, 2020

This might be because -fopenmp is not given in the link line.

@vigsterkr
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mmm yeah, we rely on cmake for setting these things... i guess should look into it before the next release

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@vigsterkr @djsutherland @isuruf