├── .clang-format ├── .github └── workflows │ └── build.yml ├── .gitignore ├── .gitmodules ├── .ipynb_checkpoints ├── Untitled-checkpoint.ipynb └── read_depth-checkpoint.ipynb ├── CMakeLists.txt ├── LICENSE ├── README.md ├── data ├── .ipynb_checkpoints │ ├── Untitled-checkpoint.ipynb │ └── read_depth-checkpoint.ipynb ├── 251370668.pcd ├── 251371071.pcd ├── DSC05572.bin ├── DSC05572.jpg ├── DSC05573.bin ├── DSC05573.jpg ├── Untitled.ipynb ├── depth.png ├── points3D.ply ├── proctime.png ├── read_depth.ipynb ├── relative.txt ├── replica_0.05_pointcloud.gif ├── replica_0.05_traj.png ├── tum_30_elipse.gif └── tum_30_elipse.png ├── docker ├── focal │ └── Dockerfile ├── focal_cuda │ └── Dockerfile ├── kinetic │ └── Dockerfile ├── melodic │ └── Dockerfile ├── melodic_llvm │ └── Dockerfile ├── noetic │ └── Dockerfile └── noetic_llvm │ └── Dockerfile ├── include └── fast_gicp │ ├── cuda │ ├── brute_force_knn.cuh │ ├── compute_derivatives.cuh │ ├── compute_mahalanobis.cuh │ ├── covariance_estimation.cuh │ ├── covariance_regularization.cuh │ ├── fast_vgicp_cuda.cuh │ ├── find_voxel_correspondences.cuh │ ├── gaussian_voxelmap.cuh │ ├── ndt_compute_derivatives.cuh │ ├── ndt_cuda.cuh │ └── vector3_hash.cuh │ ├── gicp │ ├── experimental │ │ ├── fast_gicp_mp.hpp │ │ └── fast_gicp_mp_impl.hpp │ ├── fast_gicp.hpp │ ├── fast_gicp_st.hpp │ ├── fast_vgicp.hpp │ ├── fast_vgicp_cuda.hpp │ ├── fast_vgicp_voxel.hpp │ ├── gicp_settings.hpp │ ├── impl │ │ ├── fast_gicp_impl.hpp │ │ ├── fast_gicp_st_impl.hpp │ │ ├── fast_vgicp_cuda_impl.hpp │ │ ├── fast_vgicp_impl.hpp │ │ └── lsq_registration_impl.hpp │ └── lsq_registration.hpp │ ├── ndt │ ├── impl │ │ └── ndt_cuda_impl.hpp │ ├── ndt_cuda.hpp │ └── ndt_settings.hpp │ └── so3 │ └── so3.hpp ├── package.xml ├── python_tester ├── associations │ ├── fr1_desk.txt │ ├── fr1_desk2.txt │ ├── fr1_room.txt │ ├── fr1_xyz.txt │ ├── fr2_desk.txt │ ├── fr2_xyz.txt │ ├── fr3_nstr_tex_near.txt │ ├── fr3_office.txt │ ├── fr3_office_val.txt │ ├── fr3_str_tex_far.txt │ ├── fr3_str_tex_near.txt │ └── large_loop.txt ├── dataset │ └── Replica.zip ├── download_replica.sh ├── download_tum.sh ├── gicp_odometry2.py ├── ndt_test.py └── using_previous_30.py ├── scripts └── runtest_cuda.sh ├── setup.py ├── src ├── align.cpp ├── fast_gicp │ ├── cuda │ │ ├── brute_force_knn.cu │ │ ├── compute_derivatives.cu │ │ ├── compute_mahalanobis.cu │ │ ├── covariance_estimation.cu │ │ ├── covariance_estimation_rbf.cu │ │ ├── covariance_regularization.cu │ │ ├── fast_vgicp_cuda.cu │ │ ├── find_voxel_correspondences.cu │ │ ├── gaussian_voxelmap.cu │ │ ├── ndt_compute_derivatives.cu │ │ └── ndt_cuda.cu │ ├── gicp │ │ ├── experimental │ │ │ └── fast_gicp_mp.cpp │ │ ├── fast_gicp.cpp │ │ ├── fast_gicp_st.cpp │ │ ├── fast_vgicp.cpp │ │ ├── fast_vgicp_cuda.cpp │ │ └── lsq_registration.cpp │ └── ndt │ │ └── ndt_cuda.cpp ├── kitti.cpp ├── kitti.py ├── python │ └── main.cpp └── test │ └── gicp_test.cpp └── thirdparty ├── Eigen ├── .gitignore ├── .gitlab-ci.yml ├── .gitlab │ ├── issue_templates │ │ ├── Bug Report.md │ │ └── Feature Request.md │ └── merge_request_templates │ │ └── Merge Request Template.md ├── .hgeol ├── CMakeLists.txt ├── COPYING.APACHE ├── COPYING.BSD ├── COPYING.GPL ├── COPYING.LGPL ├── COPYING.MINPACK ├── COPYING.MPL2 ├── COPYING.README ├── CTestConfig.cmake ├── CTestCustom.cmake.in ├── Eigen │ ├── Cholesky │ ├── CholmodSupport │ ├── Core │ ├── Dense │ ├── Eigen │ ├── Eigenvalues │ ├── Geometry │ ├── Householder │ ├── IterativeLinearSolvers │ ├── Jacobi │ ├── KLUSupport │ ├── LU │ ├── MetisSupport │ ├── OrderingMethods │ ├── PaStiXSupport │ ├── PardisoSupport │ ├── QR │ ├── QtAlignedMalloc │ ├── SPQRSupport │ ├── SVD │ ├── Sparse │ ├── SparseCholesky │ ├── SparseCore │ ├── SparseLU │ ├── SparseQR │ ├── StdDeque │ ├── StdList │ ├── StdVector │ ├── SuperLUSupport │ ├── UmfPackSupport │ └── src │ │ ├── Cholesky │ │ ├── LDLT.h │ │ ├── LLT.h │ │ └── LLT_LAPACKE.h │ │ ├── CholmodSupport │ │ └── CholmodSupport.h │ │ ├── Core │ │ ├── ArithmeticSequence.h │ │ ├── Array.h │ │ ├── ArrayBase.h │ │ ├── ArrayWrapper.h │ │ ├── Assign.h │ │ ├── AssignEvaluator.h │ │ ├── Assign_MKL.h │ │ ├── BandMatrix.h │ │ ├── Block.h │ │ ├── BooleanRedux.h │ │ ├── CommaInitializer.h │ │ ├── ConditionEstimator.h │ │ ├── CoreEvaluators.h │ │ ├── CoreIterators.h │ │ ├── CwiseBinaryOp.h │ │ ├── CwiseNullaryOp.h │ │ ├── CwiseTernaryOp.h │ │ ├── CwiseUnaryOp.h │ │ ├── CwiseUnaryView.h │ │ ├── DenseBase.h │ │ ├── DenseCoeffsBase.h │ │ ├── DenseStorage.h │ │ ├── Diagonal.h │ │ ├── DiagonalMatrix.h │ │ ├── DiagonalProduct.h │ │ ├── Dot.h │ │ ├── EigenBase.h │ │ ├── ForceAlignedAccess.h │ │ ├── Fuzzy.h │ │ ├── GeneralProduct.h │ │ ├── GenericPacketMath.h │ │ ├── GlobalFunctions.h │ │ ├── IO.h │ │ ├── IndexedView.h │ │ ├── Inverse.h │ │ ├── Map.h │ │ ├── MapBase.h │ │ ├── MathFunctions.h │ │ ├── MathFunctionsImpl.h │ │ ├── Matrix.h │ │ ├── MatrixBase.h │ │ ├── NestByValue.h │ │ ├── NoAlias.h │ │ ├── NumTraits.h │ │ ├── PartialReduxEvaluator.h │ │ ├── PermutationMatrix.h │ │ ├── PlainObjectBase.h │ │ ├── Product.h │ │ ├── ProductEvaluators.h │ │ ├── Random.h │ │ ├── Redux.h │ │ ├── Ref.h │ │ ├── Replicate.h │ │ ├── Reshaped.h │ │ ├── ReturnByValue.h │ │ ├── Reverse.h │ │ ├── Select.h │ │ ├── SelfAdjointView.h │ │ ├── SelfCwiseBinaryOp.h │ │ ├── Solve.h │ │ ├── SolveTriangular.h │ │ ├── SolverBase.h │ │ ├── StableNorm.h │ │ ├── StlIterators.h │ │ ├── Stride.h │ │ ├── Swap.h │ │ ├── Transpose.h │ │ ├── Transpositions.h │ │ ├── TriangularMatrix.h │ │ ├── VectorBlock.h │ │ ├── VectorwiseOp.h │ │ ├── Visitor.h │ │ ├── arch │ │ │ ├── AVX │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── AVX512 │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── AltiVec │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── MatrixProduct.h │ │ │ │ ├── MatrixProductCommon.h │ │ │ │ ├── MatrixProductMMA.h │ │ │ │ └── PacketMath.h │ │ │ ├── CUDA │ │ │ │ └── Complex.h │ │ │ ├── Default │ │ │ │ ├── BFloat16.h │ │ │ │ ├── ConjHelper.h │ │ │ │ ├── GenericPacketMathFunctions.h │ │ │ │ ├── GenericPacketMathFunctionsFwd.h │ │ │ │ ├── Half.h │ │ │ │ ├── Settings.h │ │ │ │ └── TypeCasting.h │ │ │ ├── GPU │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── HIP │ │ │ │ └── hcc │ │ │ │ │ └── math_constants.h │ │ │ ├── MSA │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ │ ├── NEON │ │ │ │ ├── Complex.h │ │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── SSE │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── SVE │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ └── TypeCasting.h │ │ │ ├── SYCL │ │ │ │ ├── InteropHeaders.h │ │ │ │ ├── MathFunctions.h │ │ │ │ ├── PacketMath.h │ │ │ │ ├── SyclMemoryModel.h │ │ │ │ └── TypeCasting.h │ │ │ └── ZVector │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ ├── functors │ │ │ ├── AssignmentFunctors.h │ │ │ ├── BinaryFunctors.h │ │ │ ├── NullaryFunctors.h │ │ │ ├── StlFunctors.h │ │ │ ├── TernaryFunctors.h │ │ │ └── UnaryFunctors.h │ │ ├── products │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ ├── GeneralMatrixMatrix.h │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ ├── GeneralMatrixMatrixTriangular_BLAS.h │ │ │ ├── GeneralMatrixMatrix_BLAS.h │ │ │ ├── GeneralMatrixVector.h │ │ │ ├── GeneralMatrixVector_BLAS.h │ │ │ ├── Parallelizer.h │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ ├── SelfadjointMatrixMatrix_BLAS.h │ │ │ ├── SelfadjointMatrixVector.h │ │ │ ├── SelfadjointMatrixVector_BLAS.h │ │ │ ├── SelfadjointProduct.h │ │ │ ├── SelfadjointRank2Update.h │ │ │ ├── TriangularMatrixMatrix.h │ │ │ ├── TriangularMatrixMatrix_BLAS.h │ │ │ ├── TriangularMatrixVector.h │ │ │ ├── TriangularMatrixVector_BLAS.h │ │ │ ├── TriangularSolverMatrix.h │ │ │ ├── TriangularSolverMatrix_BLAS.h │ │ │ └── TriangularSolverVector.h │ │ └── util │ │ │ ├── BlasUtil.h │ │ │ ├── ConfigureVectorization.h │ │ │ ├── Constants.h │ │ │ ├── DisableStupidWarnings.h │ │ │ ├── ForwardDeclarations.h │ │ │ ├── IndexedViewHelper.h │ │ │ ├── IntegralConstant.h │ │ │ ├── MKL_support.h │ │ │ ├── Macros.h │ │ │ ├── Memory.h │ │ │ ├── Meta.h │ │ │ ├── NonMPL2.h │ │ │ ├── ReenableStupidWarnings.h │ │ │ ├── ReshapedHelper.h │ │ │ ├── StaticAssert.h │ │ │ ├── SymbolicIndex.h │ │ │ └── XprHelper.h │ │ ├── Eigenvalues │ │ ├── ComplexEigenSolver.h │ │ ├── ComplexSchur.h │ │ ├── ComplexSchur_LAPACKE.h │ │ ├── EigenSolver.h │ │ ├── GeneralizedEigenSolver.h │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ ├── HessenbergDecomposition.h │ │ ├── MatrixBaseEigenvalues.h │ │ ├── RealQZ.h │ │ ├── RealSchur.h │ │ ├── RealSchur_LAPACKE.h │ │ ├── SelfAdjointEigenSolver.h │ │ ├── SelfAdjointEigenSolver_LAPACKE.h │ │ └── Tridiagonalization.h │ │ ├── Geometry │ │ ├── AlignedBox.h │ │ ├── AngleAxis.h │ │ ├── EulerAngles.h │ │ ├── Homogeneous.h │ │ ├── Hyperplane.h │ │ ├── OrthoMethods.h │ │ ├── ParametrizedLine.h │ │ ├── Quaternion.h │ │ ├── Rotation2D.h │ │ ├── RotationBase.h │ │ ├── Scaling.h │ │ ├── Transform.h │ │ ├── Translation.h │ │ ├── Umeyama.h │ │ └── arch │ │ │ └── Geometry_SIMD.h │ │ ├── Householder │ │ ├── BlockHouseholder.h │ │ ├── Householder.h │ │ └── HouseholderSequence.h │ │ ├── IterativeLinearSolvers │ │ ├── BasicPreconditioners.h │ │ ├── BiCGSTAB.h │ │ ├── ConjugateGradient.h │ │ ├── IncompleteCholesky.h │ │ ├── IncompleteLUT.h │ │ ├── IterativeSolverBase.h │ │ ├── LeastSquareConjugateGradient.h │ │ └── SolveWithGuess.h │ │ ├── Jacobi │ │ └── Jacobi.h │ │ ├── KLUSupport │ │ └── KLUSupport.h │ │ ├── LU │ │ ├── Determinant.h │ │ ├── FullPivLU.h │ │ ├── InverseImpl.h │ │ ├── PartialPivLU.h │ │ ├── PartialPivLU_LAPACKE.h │ │ └── arch │ │ │ └── InverseSize4.h │ │ ├── MetisSupport │ │ └── MetisSupport.h │ │ ├── OrderingMethods │ │ ├── Amd.h │ │ ├── Eigen_Colamd.h │ │ └── Ordering.h │ │ ├── PaStiXSupport │ │ └── PaStiXSupport.h │ │ ├── PardisoSupport │ │ └── PardisoSupport.h │ │ ├── QR │ │ ├── ColPivHouseholderQR.h │ │ ├── ColPivHouseholderQR_LAPACKE.h │ │ ├── CompleteOrthogonalDecomposition.h │ │ ├── FullPivHouseholderQR.h │ │ ├── HouseholderQR.h │ │ └── HouseholderQR_LAPACKE.h │ │ ├── SPQRSupport │ │ └── SuiteSparseQRSupport.h │ │ ├── SVD │ │ ├── BDCSVD.h │ │ ├── JacobiSVD.h │ │ ├── JacobiSVD_LAPACKE.h │ │ ├── SVDBase.h │ │ └── UpperBidiagonalization.h │ │ ├── SparseCholesky │ │ ├── SimplicialCholesky.h │ │ └── SimplicialCholesky_impl.h │ │ ├── SparseCore │ │ ├── AmbiVector.h │ │ ├── CompressedStorage.h │ │ ├── ConservativeSparseSparseProduct.h │ │ ├── MappedSparseMatrix.h │ │ ├── SparseAssign.h │ │ ├── SparseBlock.h │ │ ├── SparseColEtree.h │ │ ├── SparseCompressedBase.h │ │ ├── SparseCwiseBinaryOp.h │ │ ├── SparseCwiseUnaryOp.h │ │ ├── SparseDenseProduct.h │ │ ├── SparseDiagonalProduct.h │ │ ├── SparseDot.h │ │ ├── SparseFuzzy.h │ │ ├── SparseMap.h │ │ ├── SparseMatrix.h │ │ ├── SparseMatrixBase.h │ │ ├── SparsePermutation.h │ │ ├── SparseProduct.h │ │ ├── SparseRedux.h │ │ ├── SparseRef.h │ │ ├── SparseSelfAdjointView.h │ │ ├── SparseSolverBase.h │ │ ├── SparseSparseProductWithPruning.h │ │ ├── SparseTranspose.h │ │ ├── SparseTriangularView.h │ │ ├── SparseUtil.h │ │ ├── SparseVector.h │ │ ├── SparseView.h │ │ └── TriangularSolver.h │ │ ├── SparseLU │ │ ├── SparseLU.h │ │ ├── SparseLUImpl.h │ │ ├── SparseLU_Memory.h │ │ ├── SparseLU_Structs.h │ │ ├── SparseLU_SupernodalMatrix.h │ │ ├── SparseLU_Utils.h │ │ ├── SparseLU_column_bmod.h │ │ ├── SparseLU_column_dfs.h │ │ ├── SparseLU_copy_to_ucol.h │ │ ├── SparseLU_gemm_kernel.h │ │ ├── SparseLU_heap_relax_snode.h │ │ ├── SparseLU_kernel_bmod.h │ │ ├── SparseLU_panel_bmod.h │ │ ├── SparseLU_panel_dfs.h │ │ ├── SparseLU_pivotL.h │ │ ├── SparseLU_pruneL.h │ │ └── SparseLU_relax_snode.h │ │ ├── SparseQR │ │ └── SparseQR.h │ │ ├── StlSupport │ │ ├── StdDeque.h │ │ ├── StdList.h │ │ ├── StdVector.h │ │ └── details.h │ │ ├── SuperLUSupport │ │ └── SuperLUSupport.h │ │ ├── UmfPackSupport │ │ └── UmfPackSupport.h │ │ ├── misc │ │ ├── Image.h │ │ ├── Kernel.h │ │ ├── RealSvd2x2.h │ │ ├── blas.h │ │ ├── lapack.h │ │ ├── lapacke.h │ │ └── lapacke_mangling.h │ │ └── plugins │ │ ├── ArrayCwiseBinaryOps.h │ │ ├── ArrayCwiseUnaryOps.h │ │ ├── BlockMethods.h │ │ ├── CommonCwiseBinaryOps.h │ │ ├── CommonCwiseUnaryOps.h │ │ ├── IndexedViewMethods.h │ │ ├── MatrixCwiseBinaryOps.h │ │ ├── MatrixCwiseUnaryOps.h │ │ └── ReshapedMethods.h ├── INSTALL ├── README.md ├── bench │ ├── BenchSparseUtil.h │ ├── BenchTimer.h │ ├── BenchUtil.h │ ├── README.txt │ ├── analyze-blocking-sizes.cpp │ ├── basicbench.cxxlist │ ├── basicbenchmark.cpp │ ├── basicbenchmark.h │ ├── benchBlasGemm.cpp │ ├── benchCholesky.cpp │ ├── benchEigenSolver.cpp │ ├── benchFFT.cpp │ ├── benchGeometry.cpp │ ├── benchVecAdd.cpp │ ├── bench_gemm.cpp │ ├── bench_move_semantics.cpp │ ├── bench_multi_compilers.sh │ ├── bench_norm.cpp │ ├── bench_reverse.cpp │ ├── bench_sum.cpp │ ├── bench_unrolling │ ├── benchmark-blocking-sizes.cpp │ ├── benchmark.cpp │ ├── benchmarkSlice.cpp │ ├── benchmarkX.cpp │ ├── benchmarkXcwise.cpp │ ├── benchmark_suite │ ├── btl │ │ ├── CMakeLists.txt │ │ ├── COPYING │ │ ├── README │ │ ├── actions │ │ │ ├── action_aat_product.hh │ │ │ ├── action_ata_product.hh │ │ │ ├── action_atv_product.hh │ │ │ ├── action_axpby.hh │ │ │ ├── action_axpy.hh │ │ │ ├── action_cholesky.hh │ │ │ ├── action_ger.hh │ │ │ ├── action_hessenberg.hh │ │ │ ├── action_lu_decomp.hh │ │ │ ├── action_lu_solve.hh │ │ │ ├── action_matrix_matrix_product.hh │ │ │ ├── action_matrix_matrix_product_bis.hh │ │ │ ├── action_matrix_vector_product.hh │ │ │ ├── action_partial_lu.hh │ │ │ ├── action_rot.hh │ │ │ ├── action_symv.hh │ │ │ ├── action_syr2.hh │ │ │ ├── action_trisolve.hh │ │ │ ├── action_trisolve_matrix.hh │ │ │ ├── action_trmm.hh │ │ │ └── basic_actions.hh │ │ ├── cmake │ │ │ ├── FindACML.cmake │ │ │ ├── FindATLAS.cmake │ │ │ ├── FindBLAZE.cmake │ │ │ ├── FindBlitz.cmake │ │ │ ├── FindCBLAS.cmake │ │ │ ├── FindGMM.cmake │ │ │ ├── FindMKL.cmake │ │ │ ├── FindMTL4.cmake │ │ │ ├── FindOPENBLAS.cmake │ │ │ ├── FindPackageHandleStandardArgs.cmake │ │ │ ├── FindTvmet.cmake │ │ │ └── MacroOptionalAddSubdirectory.cmake │ │ ├── data │ │ │ ├── CMakeLists.txt │ │ │ ├── action_settings.txt │ │ │ ├── gnuplot_common_settings.hh │ │ │ ├── go_mean │ │ │ ├── mean.cxx │ │ │ ├── mk_gnuplot_script.sh │ │ │ ├── mk_mean_script.sh │ │ │ ├── mk_new_gnuplot.sh │ │ │ ├── perlib_plot_settings.txt │ │ │ ├── regularize.cxx │ │ │ ├── smooth.cxx │ │ │ └── smooth_all.sh │ │ ├── generic_bench │ │ │ ├── bench.hh │ │ │ ├── bench_parameter.hh │ │ │ ├── btl.hh │ │ │ ├── init │ │ │ │ ├── init_function.hh │ │ │ │ ├── init_matrix.hh │ │ │ │ └── init_vector.hh │ │ │ ├── static │ │ │ │ ├── bench_static.hh │ │ │ │ ├── intel_bench_fixed_size.hh │ │ │ │ └── static_size_generator.hh │ │ │ ├── timers │ │ │ │ ├── STL_perf_analyzer.hh │ │ │ │ ├── STL_timer.hh │ │ │ │ ├── mixed_perf_analyzer.hh │ │ │ │ ├── portable_perf_analyzer.hh │ │ │ │ ├── portable_perf_analyzer_old.hh │ │ │ │ ├── portable_timer.hh │ │ │ │ ├── x86_perf_analyzer.hh │ │ │ │ └── x86_timer.hh │ │ │ └── utils │ │ │ │ ├── size_lin_log.hh │ │ │ │ ├── size_log.hh │ │ │ │ ├── utilities.h │ │ │ │ └── xy_file.hh │ │ └── libs │ │ │ ├── BLAS │ │ │ ├── CMakeLists.txt │ │ │ ├── blas.h │ │ │ ├── blas_interface.hh │ │ │ ├── blas_interface_impl.hh │ │ │ ├── c_interface_base.h │ │ │ └── main.cpp │ │ │ ├── STL │ │ │ ├── CMakeLists.txt │ │ │ ├── STL_interface.hh │ │ │ └── main.cpp │ │ │ ├── blaze │ │ │ ├── CMakeLists.txt │ │ │ ├── blaze_interface.hh │ │ │ └── main.cpp │ │ │ ├── blitz │ │ │ ├── CMakeLists.txt │ │ │ ├── blitz_LU_solve_interface.hh │ │ │ ├── blitz_interface.hh │ │ │ ├── btl_blitz.cpp │ │ │ ├── btl_tiny_blitz.cpp │ │ │ └── tiny_blitz_interface.hh │ │ │ ├── eigen2 │ │ │ ├── CMakeLists.txt │ │ │ ├── btl_tiny_eigen2.cpp │ │ │ ├── eigen2_interface.hh │ │ │ ├── main_adv.cpp │ │ │ ├── main_linear.cpp │ │ │ ├── main_matmat.cpp │ │ │ └── main_vecmat.cpp │ │ │ ├── eigen3 │ │ │ ├── CMakeLists.txt │ │ │ ├── btl_tiny_eigen3.cpp │ │ │ ├── eigen3_interface.hh │ │ │ ├── main_adv.cpp │ │ │ ├── main_linear.cpp │ │ │ ├── main_matmat.cpp │ │ │ └── main_vecmat.cpp │ │ │ ├── gmm │ │ │ ├── CMakeLists.txt │ │ │ ├── gmm_LU_solve_interface.hh │ │ │ ├── gmm_interface.hh │ │ │ └── main.cpp │ │ │ ├── mtl4 │ │ │ ├── .kdbgrc.main │ │ │ ├── CMakeLists.txt │ │ │ ├── main.cpp │ │ │ ├── mtl4_LU_solve_interface.hh │ │ │ └── mtl4_interface.hh │ │ │ ├── tensors │ │ │ ├── CMakeLists.txt │ │ │ ├── main_linear.cpp │ │ │ ├── main_matmat.cpp │ │ │ ├── main_vecmat.cpp │ │ │ └── tensor_interface.hh │ │ │ ├── tvmet │ │ │ ├── CMakeLists.txt │ │ │ ├── main.cpp │ │ │ └── tvmet_interface.hh │ │ │ └── ublas │ │ │ ├── CMakeLists.txt │ │ │ ├── main.cpp │ │ │ └── ublas_interface.hh │ ├── check_cache_queries.cpp │ ├── dense_solvers.cpp │ ├── eig33.cpp │ ├── geometry.cpp │ ├── perf_monitoring │ │ ├── changesets.txt │ │ ├── gemm.cpp │ │ ├── gemm_common.h │ │ ├── gemm_settings.txt │ │ ├── gemm_square_settings.txt │ │ ├── gemv.cpp │ │ ├── gemv_common.h │ │ ├── gemv_settings.txt │ │ ├── gemv_square_settings.txt │ │ ├── gemvt.cpp │ │ ├── lazy_gemm.cpp │ │ ├── lazy_gemm_settings.txt │ │ ├── llt.cpp │ │ ├── make_plot.sh │ │ ├── resources │ │ │ ├── chart_footer.html │ │ │ ├── chart_header.html │ │ │ ├── footer.html │ │ │ ├── header.html │ │ │ ├── s1.js │ │ │ └── s2.js │ │ ├── run.sh │ │ ├── runall.sh │ │ ├── trmv_lo.cpp │ │ ├── trmv_lot.cpp │ │ ├── trmv_up.cpp │ │ └── trmv_upt.cpp │ ├── product_threshold.cpp │ ├── quat_slerp.cpp │ ├── quatmul.cpp │ ├── sparse_cholesky.cpp │ ├── sparse_dense_product.cpp │ ├── sparse_lu.cpp │ ├── sparse_product.cpp │ ├── sparse_randomsetter.cpp │ ├── sparse_setter.cpp │ ├── sparse_transpose.cpp │ ├── sparse_trisolver.cpp │ ├── spbench │ │ ├── CMakeLists.txt │ │ ├── sp_solver.cpp │ │ ├── spbench.dtd │ │ ├── spbenchsolver.cpp │ │ ├── spbenchsolver.h │ │ ├── spbenchstyle.h │ │ └── test_sparseLU.cpp │ ├── spmv.cpp │ ├── tensors │ │ ├── README │ │ ├── benchmark.h │ │ ├── benchmark_main.cc │ │ ├── contraction_benchmarks_cpu.cc │ │ ├── eigen_sycl_bench.sh │ │ ├── eigen_sycl_bench_contract.sh │ │ ├── tensor_benchmarks.h │ │ ├── tensor_benchmarks_cpu.cc │ │ ├── tensor_benchmarks_fp16_gpu.cu │ │ ├── tensor_benchmarks_gpu.cu │ │ ├── tensor_benchmarks_sycl.cc │ │ └── tensor_contract_sycl_bench.cc │ └── vdw_new.cpp ├── blas │ ├── BandTriangularSolver.h │ ├── CMakeLists.txt │ ├── GeneralRank1Update.h │ ├── PackedSelfadjointProduct.h │ ├── PackedTriangularMatrixVector.h │ ├── PackedTriangularSolverVector.h │ ├── README.txt │ ├── Rank2Update.h │ ├── common.h │ ├── complex_double.cpp │ ├── complex_single.cpp │ ├── double.cpp │ ├── f2c │ │ ├── chbmv.c │ │ ├── chpmv.c │ │ ├── complexdots.c │ │ ├── ctbmv.c │ │ ├── d_cnjg.c │ │ ├── datatypes.h │ │ ├── drotm.c │ │ ├── drotmg.c │ │ ├── dsbmv.c │ │ ├── dspmv.c │ │ ├── dtbmv.c │ │ ├── lsame.c │ │ ├── r_cnjg.c │ │ ├── srotm.c │ │ ├── srotmg.c │ │ ├── ssbmv.c │ │ ├── sspmv.c │ │ ├── stbmv.c │ │ ├── zhbmv.c │ │ ├── zhpmv.c │ │ └── ztbmv.c │ ├── fortran │ │ └── complexdots.f │ ├── level1_cplx_impl.h │ ├── level1_impl.h │ ├── level1_real_impl.h │ ├── level2_cplx_impl.h │ ├── level2_impl.h │ ├── level2_real_impl.h │ ├── level3_impl.h │ ├── single.cpp │ ├── testing │ │ ├── CMakeLists.txt │ │ ├── cblat1.f │ │ ├── cblat2.dat │ │ ├── cblat2.f │ │ ├── cblat3.dat │ │ ├── cblat3.f │ │ ├── dblat1.f │ │ ├── dblat2.dat │ │ ├── dblat2.f │ │ ├── dblat3.dat │ │ ├── dblat3.f │ │ ├── runblastest.sh │ │ ├── sblat1.f │ │ ├── sblat2.dat │ │ ├── sblat2.f │ │ ├── sblat3.dat │ │ ├── sblat3.f │ │ ├── zblat1.f │ │ ├── zblat2.dat │ │ ├── zblat2.f │ │ ├── zblat3.dat │ │ └── zblat3.f │ └── xerbla.cpp ├── ci │ ├── CTest2JUnit.xsl │ ├── README.md │ ├── build.gitlab-ci.yml │ ├── smoketests.gitlab-ci.yml │ └── test.gitlab-ci.yml ├── cmake │ ├── ComputeCppCompilerChecks.cmake │ ├── ComputeCppIRMap.cmake │ ├── Eigen3Config.cmake.in │ ├── Eigen3ConfigLegacy.cmake.in │ ├── EigenConfigureTesting.cmake │ ├── EigenDetermineOSVersion.cmake │ ├── EigenDetermineVSServicePack.cmake │ ├── EigenSmokeTestList.cmake │ ├── EigenTesting.cmake │ ├── EigenUninstall.cmake │ ├── FindAdolc.cmake │ ├── FindBLAS.cmake │ ├── FindBLASEXT.cmake │ ├── FindCHOLMOD.cmake │ ├── FindComputeCpp.cmake │ ├── FindEigen2.cmake │ ├── FindEigen3.cmake │ ├── FindFFTW.cmake │ ├── FindGLEW.cmake │ ├── FindGMP.cmake │ ├── FindGSL.cmake │ ├── FindGoogleHash.cmake │ ├── FindHWLOC.cmake │ ├── FindKLU.cmake │ ├── FindLAPACK.cmake │ ├── FindMPFR.cmake │ ├── FindMetis.cmake │ ├── FindPTSCOTCH.cmake │ ├── FindPastix.cmake │ ├── FindSPQR.cmake │ ├── FindScotch.cmake │ ├── FindStandardMathLibrary.cmake │ ├── FindSuperLU.cmake │ ├── FindTriSYCL.cmake │ ├── FindUMFPACK.cmake │ ├── RegexUtils.cmake │ └── UseEigen3.cmake ├── debug │ ├── gdb │ │ ├── __init__.py │ │ └── printers.py │ └── msvc │ │ ├── eigen.natvis │ │ └── eigen_autoexp_part.dat ├── demos │ ├── CMakeLists.txt │ ├── mandelbrot │ │ ├── CMakeLists.txt │ │ ├── README │ │ ├── mandelbrot.cpp │ │ └── mandelbrot.h │ ├── mix_eigen_and_c │ │ ├── README │ │ ├── binary_library.cpp │ │ ├── binary_library.h │ │ └── example.c │ └── opengl │ │ ├── CMakeLists.txt │ │ ├── README │ │ ├── camera.cpp │ │ ├── camera.h │ │ ├── gpuhelper.cpp │ │ ├── gpuhelper.h │ │ ├── icosphere.cpp │ │ ├── icosphere.h │ │ ├── quaternion_demo.cpp │ │ ├── quaternion_demo.h │ │ ├── trackball.cpp │ │ └── trackball.h ├── doc │ ├── AsciiQuickReference.txt │ ├── B01_Experimental.dox │ ├── CMakeLists.txt │ ├── ClassHierarchy.dox │ ├── CoeffwiseMathFunctionsTable.dox │ ├── CustomizingEigen_CustomScalar.dox │ ├── CustomizingEigen_InheritingMatrix.dox │ ├── CustomizingEigen_NullaryExpr.dox │ ├── CustomizingEigen_Plugins.dox │ ├── DenseDecompositionBenchmark.dox │ ├── Doxyfile.in │ ├── Eigen_Silly_Professor_64x64.png │ ├── FixedSizeVectorizable.dox │ ├── FunctionsTakingEigenTypes.dox │ ├── HiPerformance.dox │ ├── InplaceDecomposition.dox │ ├── InsideEigenExample.dox │ ├── LeastSquares.dox │ ├── Manual.dox │ ├── MatrixfreeSolverExample.dox │ ├── NewExpressionType.dox │ ├── Overview.dox │ ├── PassingByValue.dox │ ├── Pitfalls.dox │ ├── PreprocessorDirectives.dox │ ├── QuickReference.dox │ ├── QuickStartGuide.dox │ ├── SparseLinearSystems.dox │ ├── SparseQuickReference.dox │ ├── StlContainers.dox │ ├── StorageOrders.dox │ ├── StructHavingEigenMembers.dox │ ├── TemplateKeyword.dox │ ├── TopicAliasing.dox │ ├── TopicAssertions.dox │ ├── TopicCMakeGuide.dox │ ├── TopicEigenExpressionTemplates.dox │ ├── TopicLazyEvaluation.dox │ ├── TopicLinearAlgebraDecompositions.dox │ ├── TopicMultithreading.dox │ ├── TopicResizing.dox │ ├── TopicScalarTypes.dox │ ├── TopicVectorization.dox │ ├── TutorialAdvancedInitialization.dox │ ├── TutorialArrayClass.dox │ ├── TutorialBlockOperations.dox │ ├── TutorialGeometry.dox │ ├── TutorialLinearAlgebra.dox │ ├── TutorialMapClass.dox │ ├── TutorialMatrixArithmetic.dox │ ├── TutorialMatrixClass.dox │ ├── TutorialReductionsVisitorsBroadcasting.dox │ ├── TutorialReshape.dox │ ├── TutorialSTL.dox │ ├── TutorialSlicingIndexing.dox │ ├── TutorialSparse.dox │ ├── TutorialSparse_example_details.dox │ ├── UnalignedArrayAssert.dox │ ├── UsingBlasLapackBackends.dox │ ├── UsingIntelMKL.dox │ ├── UsingNVCC.dox │ ├── WrongStackAlignment.dox │ ├── eigen_navtree_hacks.js │ ├── eigendoxy.css │ ├── eigendoxy_footer.html.in │ ├── eigendoxy_header.html.in │ ├── eigendoxy_layout.xml.in │ ├── eigendoxy_tabs.css │ ├── examples │ │ ├── .krazy │ │ ├── CMakeLists.txt │ │ ├── CustomizingEigen_Inheritance.cpp │ │ ├── Cwise_erf.cpp │ │ ├── Cwise_erfc.cpp │ │ ├── Cwise_lgamma.cpp │ │ ├── DenseBase_middleCols_int.cpp │ │ ├── DenseBase_middleRows_int.cpp │ │ ├── DenseBase_template_int_middleCols.cpp │ │ ├── DenseBase_template_int_middleRows.cpp │ │ ├── QuickStart_example.cpp │ │ ├── QuickStart_example2_dynamic.cpp │ │ ├── QuickStart_example2_fixed.cpp │ │ ├── TemplateKeyword_flexible.cpp │ │ ├── TemplateKeyword_simple.cpp │ │ ├── TutorialInplaceLU.cpp │ │ ├── TutorialLinAlgComputeTwice.cpp │ │ ├── TutorialLinAlgExComputeSolveError.cpp │ │ ├── TutorialLinAlgExSolveColPivHouseholderQR.cpp │ │ ├── TutorialLinAlgExSolveLDLT.cpp │ │ ├── TutorialLinAlgInverseDeterminant.cpp │ │ ├── TutorialLinAlgRankRevealing.cpp │ │ ├── TutorialLinAlgSVDSolve.cpp │ │ ├── TutorialLinAlgSelfAdjointEigenSolver.cpp │ │ ├── TutorialLinAlgSetThreshold.cpp │ │ ├── Tutorial_ArrayClass_accessors.cpp │ │ ├── Tutorial_ArrayClass_addition.cpp │ │ ├── Tutorial_ArrayClass_cwise_other.cpp │ │ ├── Tutorial_ArrayClass_interop.cpp │ │ ├── Tutorial_ArrayClass_interop_matrix.cpp │ │ ├── Tutorial_ArrayClass_mult.cpp │ │ ├── Tutorial_BlockOperations_block_assignment.cpp │ │ ├── Tutorial_BlockOperations_colrow.cpp │ │ ├── Tutorial_BlockOperations_corner.cpp │ │ ├── Tutorial_BlockOperations_print_block.cpp │ │ ├── Tutorial_BlockOperations_vector.cpp │ │ ├── Tutorial_PartialLU_solve.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_broadcast_1nn.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_broadcast_simple.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_broadcast_simple_rowwise.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_colwise.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_maxnorm.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_reductions_bool.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_reductions_norm.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_reductions_operatornorm.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_rowwise.cpp │ │ ├── Tutorial_ReductionsVisitorsBroadcasting_visitors.cpp │ │ ├── Tutorial_simple_example_dynamic_size.cpp │ │ ├── Tutorial_simple_example_fixed_size.cpp │ │ ├── class_Block.cpp │ │ ├── class_CwiseBinaryOp.cpp │ │ ├── class_CwiseUnaryOp.cpp │ │ ├── class_CwiseUnaryOp_ptrfun.cpp │ │ ├── class_FixedBlock.cpp │ │ ├── class_FixedReshaped.cpp │ │ ├── class_FixedVectorBlock.cpp │ │ ├── class_Reshaped.cpp │ │ ├── class_VectorBlock.cpp │ │ ├── function_taking_eigenbase.cpp │ │ ├── function_taking_ref.cpp │ │ ├── make_circulant.cpp │ │ ├── make_circulant.cpp.entry │ │ ├── make_circulant.cpp.evaluator │ │ ├── make_circulant.cpp.expression │ │ ├── make_circulant.cpp.main │ │ ├── make_circulant.cpp.preamble │ │ ├── make_circulant.cpp.traits │ │ ├── make_circulant2.cpp │ │ ├── matrixfree_cg.cpp │ │ ├── nullary_indexing.cpp │ │ ├── tut_arithmetic_add_sub.cpp │ │ ├── tut_arithmetic_dot_cross.cpp │ │ ├── tut_arithmetic_matrix_mul.cpp │ │ ├── tut_arithmetic_redux_basic.cpp │ │ ├── tut_arithmetic_scalar_mul_div.cpp │ │ ├── tut_matrix_coefficient_accessors.cpp │ │ ├── tut_matrix_resize.cpp │ │ └── tut_matrix_resize_fixed_size.cpp │ ├── ftv2node.png │ ├── ftv2pnode.png │ ├── snippets │ │ ├── .krazy │ │ ├── AngleAxis_mimic_euler.cpp │ │ ├── Array_initializer_list_23_cxx11.cpp │ │ ├── Array_initializer_list_vector_cxx11.cpp │ │ ├── Array_variadic_ctor_cxx11.cpp │ │ ├── BiCGSTAB_simple.cpp │ │ ├── BiCGSTAB_step_by_step.cpp │ │ ├── CMakeLists.txt │ │ ├── ColPivHouseholderQR_solve.cpp │ │ ├── ComplexEigenSolver_compute.cpp │ │ ├── ComplexEigenSolver_eigenvalues.cpp │ │ ├── ComplexEigenSolver_eigenvectors.cpp │ │ ├── ComplexSchur_compute.cpp │ │ ├── ComplexSchur_matrixT.cpp │ │ ├── ComplexSchur_matrixU.cpp │ │ ├── Cwise_abs.cpp │ │ ├── Cwise_abs2.cpp │ │ ├── Cwise_acos.cpp │ │ ├── Cwise_arg.cpp │ │ ├── Cwise_array_power_array.cpp │ │ ├── Cwise_asin.cpp │ │ ├── Cwise_atan.cpp │ │ ├── Cwise_boolean_and.cpp │ │ ├── Cwise_boolean_not.cpp │ │ ├── Cwise_boolean_or.cpp │ │ ├── Cwise_boolean_xor.cpp │ │ ├── Cwise_ceil.cpp │ │ ├── Cwise_cos.cpp │ │ ├── Cwise_cosh.cpp │ │ ├── Cwise_cube.cpp │ │ ├── Cwise_equal_equal.cpp │ │ ├── Cwise_exp.cpp │ │ ├── Cwise_floor.cpp │ │ ├── Cwise_greater.cpp │ │ ├── Cwise_greater_equal.cpp │ │ ├── Cwise_inverse.cpp │ │ ├── Cwise_isFinite.cpp │ │ ├── Cwise_isInf.cpp │ │ ├── Cwise_isNaN.cpp │ │ ├── Cwise_less.cpp │ │ ├── Cwise_less_equal.cpp │ │ ├── Cwise_log.cpp │ │ ├── Cwise_log10.cpp │ │ ├── Cwise_max.cpp │ │ ├── Cwise_min.cpp │ │ ├── Cwise_minus.cpp │ │ ├── Cwise_minus_equal.cpp │ │ ├── Cwise_not_equal.cpp │ │ ├── Cwise_plus.cpp │ │ ├── Cwise_plus_equal.cpp │ │ ├── Cwise_pow.cpp │ │ ├── Cwise_product.cpp │ │ ├── Cwise_quotient.cpp │ │ ├── Cwise_rint.cpp │ │ ├── Cwise_round.cpp │ │ ├── Cwise_scalar_power_array.cpp │ │ ├── Cwise_sign.cpp │ │ ├── Cwise_sin.cpp │ │ ├── Cwise_sinh.cpp │ │ ├── Cwise_slash_equal.cpp │ │ ├── Cwise_sqrt.cpp │ │ ├── Cwise_square.cpp │ │ ├── Cwise_tan.cpp │ │ ├── Cwise_tanh.cpp │ │ ├── Cwise_times_equal.cpp │ │ ├── DenseBase_LinSpaced.cpp │ │ ├── DenseBase_LinSpacedInt.cpp │ │ ├── DenseBase_LinSpaced_seq_deprecated.cpp │ │ ├── DenseBase_setLinSpaced.cpp │ │ ├── DirectionWise_hnormalized.cpp │ │ ├── DirectionWise_replicate.cpp │ │ ├── DirectionWise_replicate_int.cpp │ │ ├── EigenSolver_EigenSolver_MatrixType.cpp │ │ ├── EigenSolver_compute.cpp │ │ ├── EigenSolver_eigenvalues.cpp │ │ ├── EigenSolver_eigenvectors.cpp │ │ ├── EigenSolver_pseudoEigenvectors.cpp │ │ ├── FullPivHouseholderQR_solve.cpp │ │ ├── FullPivLU_image.cpp │ │ ├── FullPivLU_kernel.cpp │ │ ├── FullPivLU_solve.cpp │ │ ├── GeneralizedEigenSolver.cpp │ │ ├── HessenbergDecomposition_compute.cpp │ │ ├── HessenbergDecomposition_matrixH.cpp │ │ ├── HessenbergDecomposition_packedMatrix.cpp │ │ ├── HouseholderQR_householderQ.cpp │ │ ├── HouseholderQR_solve.cpp │ │ ├── HouseholderSequence_HouseholderSequence.cpp │ │ ├── IOFormat.cpp │ │ ├── JacobiSVD_basic.cpp │ │ ├── Jacobi_makeGivens.cpp │ │ ├── Jacobi_makeJacobi.cpp │ │ ├── LLT_example.cpp │ │ ├── LLT_solve.cpp │ │ ├── LeastSquaresNormalEquations.cpp │ │ ├── LeastSquaresQR.cpp │ │ ├── Map_general_stride.cpp │ │ ├── Map_inner_stride.cpp │ │ ├── Map_outer_stride.cpp │ │ ├── Map_placement_new.cpp │ │ ├── Map_simple.cpp │ │ ├── MatrixBase_adjoint.cpp │ │ ├── MatrixBase_all.cpp │ │ ├── MatrixBase_applyOnTheLeft.cpp │ │ ├── MatrixBase_applyOnTheRight.cpp │ │ ├── MatrixBase_array.cpp │ │ ├── MatrixBase_array_const.cpp │ │ ├── MatrixBase_asDiagonal.cpp │ │ ├── MatrixBase_block_int_int.cpp │ │ ├── MatrixBase_block_int_int_int_int.cpp │ │ ├── MatrixBase_bottomLeftCorner_int_int.cpp │ │ ├── MatrixBase_bottomRightCorner_int_int.cpp │ │ ├── MatrixBase_bottomRows_int.cpp │ │ ├── MatrixBase_cast.cpp │ │ ├── MatrixBase_col.cpp │ │ ├── MatrixBase_colwise.cpp │ │ ├── MatrixBase_colwise_iterator_cxx11.cpp │ │ ├── MatrixBase_computeInverseAndDetWithCheck.cpp │ │ ├── MatrixBase_computeInverseWithCheck.cpp │ │ ├── MatrixBase_cwiseAbs.cpp │ │ ├── MatrixBase_cwiseAbs2.cpp │ │ ├── MatrixBase_cwiseArg.cpp │ │ ├── MatrixBase_cwiseEqual.cpp │ │ ├── MatrixBase_cwiseInverse.cpp │ │ ├── MatrixBase_cwiseMax.cpp │ │ ├── MatrixBase_cwiseMin.cpp │ │ ├── MatrixBase_cwiseNotEqual.cpp │ │ ├── MatrixBase_cwiseProduct.cpp │ │ ├── MatrixBase_cwiseQuotient.cpp │ │ ├── MatrixBase_cwiseSign.cpp │ │ ├── MatrixBase_cwiseSqrt.cpp │ │ ├── MatrixBase_diagonal.cpp │ │ ├── MatrixBase_diagonal_int.cpp │ │ ├── MatrixBase_diagonal_template_int.cpp │ │ ├── MatrixBase_eigenvalues.cpp │ │ ├── MatrixBase_end_int.cpp │ │ ├── MatrixBase_eval.cpp │ │ ├── MatrixBase_fixedBlock_int_int.cpp │ │ ├── MatrixBase_hnormalized.cpp │ │ ├── MatrixBase_homogeneous.cpp │ │ ├── MatrixBase_identity.cpp │ │ ├── MatrixBase_identity_int_int.cpp │ │ ├── MatrixBase_inverse.cpp │ │ ├── MatrixBase_isDiagonal.cpp │ │ ├── MatrixBase_isIdentity.cpp │ │ ├── MatrixBase_isOnes.cpp │ │ ├── MatrixBase_isOrthogonal.cpp │ │ ├── MatrixBase_isUnitary.cpp │ │ ├── MatrixBase_isZero.cpp │ │ ├── MatrixBase_leftCols_int.cpp │ │ ├── MatrixBase_noalias.cpp │ │ ├── MatrixBase_ones.cpp │ │ ├── MatrixBase_ones_int.cpp │ │ ├── MatrixBase_ones_int_int.cpp │ │ ├── MatrixBase_operatorNorm.cpp │ │ ├── MatrixBase_prod.cpp │ │ ├── MatrixBase_random.cpp │ │ ├── MatrixBase_random_int.cpp │ │ ├── MatrixBase_random_int_int.cpp │ │ ├── MatrixBase_replicate.cpp │ │ ├── MatrixBase_replicate_int_int.cpp │ │ ├── MatrixBase_reshaped_auto.cpp │ │ ├── MatrixBase_reshaped_fixed.cpp │ │ ├── MatrixBase_reshaped_int_int.cpp │ │ ├── MatrixBase_reshaped_to_vector.cpp │ │ ├── MatrixBase_reverse.cpp │ │ ├── MatrixBase_rightCols_int.cpp │ │ ├── MatrixBase_row.cpp │ │ ├── MatrixBase_rowwise.cpp │ │ ├── MatrixBase_segment_int_int.cpp │ │ ├── MatrixBase_select.cpp │ │ ├── MatrixBase_selfadjointView.cpp │ │ ├── MatrixBase_set.cpp │ │ ├── MatrixBase_setIdentity.cpp │ │ ├── MatrixBase_setOnes.cpp │ │ ├── MatrixBase_setRandom.cpp │ │ ├── MatrixBase_setZero.cpp │ │ ├── MatrixBase_start_int.cpp │ │ ├── MatrixBase_template_int_bottomRows.cpp │ │ ├── MatrixBase_template_int_end.cpp │ │ ├── MatrixBase_template_int_int_block_int_int_int_int.cpp │ │ ├── MatrixBase_template_int_int_bottomLeftCorner.cpp │ │ ├── MatrixBase_template_int_int_bottomLeftCorner_int_int.cpp │ │ ├── MatrixBase_template_int_int_bottomRightCorner.cpp │ │ ├── MatrixBase_template_int_int_bottomRightCorner_int_int.cpp │ │ ├── MatrixBase_template_int_int_topLeftCorner.cpp │ │ ├── MatrixBase_template_int_int_topLeftCorner_int_int.cpp │ │ ├── MatrixBase_template_int_int_topRightCorner.cpp │ │ ├── MatrixBase_template_int_int_topRightCorner_int_int.cpp │ │ ├── MatrixBase_template_int_leftCols.cpp │ │ ├── MatrixBase_template_int_rightCols.cpp │ │ ├── MatrixBase_template_int_segment.cpp │ │ ├── MatrixBase_template_int_start.cpp │ │ ├── MatrixBase_template_int_topRows.cpp │ │ ├── MatrixBase_topLeftCorner_int_int.cpp │ │ ├── MatrixBase_topRightCorner_int_int.cpp │ │ ├── MatrixBase_topRows_int.cpp │ │ ├── MatrixBase_transpose.cpp │ │ ├── MatrixBase_triangularView.cpp │ │ ├── MatrixBase_zero.cpp │ │ ├── MatrixBase_zero_int.cpp │ │ ├── MatrixBase_zero_int_int.cpp │ │ ├── Matrix_Map_stride.cpp │ │ ├── Matrix_initializer_list_23_cxx11.cpp │ │ ├── Matrix_initializer_list_vector_cxx11.cpp │ │ ├── Matrix_resize_NoChange_int.cpp │ │ ├── Matrix_resize_int.cpp │ │ ├── Matrix_resize_int_NoChange.cpp │ │ ├── Matrix_resize_int_int.cpp │ │ ├── Matrix_setConstant_int.cpp │ │ ├── Matrix_setConstant_int_int.cpp │ │ ├── Matrix_setIdentity_int_int.cpp │ │ ├── Matrix_setOnes_int.cpp │ │ ├── Matrix_setOnes_int_int.cpp │ │ ├── Matrix_setRandom_int.cpp │ │ ├── Matrix_setRandom_int_int.cpp │ │ ├── Matrix_setZero_int.cpp │ │ ├── Matrix_setZero_int_int.cpp │ │ ├── Matrix_variadic_ctor_cxx11.cpp │ │ ├── PartialPivLU_solve.cpp │ │ ├── PartialRedux_count.cpp │ │ ├── PartialRedux_maxCoeff.cpp │ │ ├── PartialRedux_minCoeff.cpp │ │ ├── PartialRedux_norm.cpp │ │ ├── PartialRedux_prod.cpp │ │ ├── PartialRedux_squaredNorm.cpp │ │ ├── PartialRedux_sum.cpp │ │ ├── RealQZ_compute.cpp │ │ ├── RealSchur_RealSchur_MatrixType.cpp │ │ ├── RealSchur_compute.cpp │ │ ├── SelfAdjointEigenSolver_SelfAdjointEigenSolver.cpp │ │ ├── SelfAdjointEigenSolver_SelfAdjointEigenSolver_MatrixType.cpp │ │ ├── SelfAdjointEigenSolver_SelfAdjointEigenSolver_MatrixType2.cpp │ │ ├── SelfAdjointEigenSolver_compute_MatrixType.cpp │ │ ├── SelfAdjointEigenSolver_compute_MatrixType2.cpp │ │ ├── SelfAdjointEigenSolver_eigenvalues.cpp │ │ ├── SelfAdjointEigenSolver_eigenvectors.cpp │ │ ├── SelfAdjointEigenSolver_operatorInverseSqrt.cpp │ │ ├── SelfAdjointEigenSolver_operatorSqrt.cpp │ │ ├── SelfAdjointView_eigenvalues.cpp │ │ ├── SelfAdjointView_operatorNorm.cpp │ │ ├── Slicing_arrayexpr.cpp │ │ ├── Slicing_custom_padding_cxx11.cpp │ │ ├── Slicing_rawarray_cxx11.cpp │ │ ├── Slicing_stdvector_cxx11.cpp │ │ ├── SparseMatrix_coeffs.cpp │ │ ├── TopicAliasing_block.cpp │ │ ├── TopicAliasing_block_correct.cpp │ │ ├── TopicAliasing_cwise.cpp │ │ ├── TopicAliasing_mult1.cpp │ │ ├── TopicAliasing_mult2.cpp │ │ ├── TopicAliasing_mult3.cpp │ │ ├── TopicAliasing_mult4.cpp │ │ ├── TopicAliasing_mult5.cpp │ │ ├── TopicStorageOrders_example.cpp │ │ ├── Triangular_solve.cpp │ │ ├── Tridiagonalization_Tridiagonalization_MatrixType.cpp │ │ ├── Tridiagonalization_compute.cpp │ │ ├── Tridiagonalization_decomposeInPlace.cpp │ │ ├── Tridiagonalization_diagonal.cpp │ │ ├── Tridiagonalization_householderCoefficients.cpp │ │ ├── Tridiagonalization_packedMatrix.cpp │ │ ├── Tutorial_AdvancedInitialization_Block.cpp │ │ ├── Tutorial_AdvancedInitialization_CommaTemporary.cpp │ │ ├── Tutorial_AdvancedInitialization_Join.cpp │ │ ├── Tutorial_AdvancedInitialization_LinSpaced.cpp │ │ ├── Tutorial_AdvancedInitialization_ThreeWays.cpp │ │ ├── Tutorial_AdvancedInitialization_Zero.cpp │ │ ├── Tutorial_Map_rowmajor.cpp │ │ ├── Tutorial_Map_using.cpp │ │ ├── Tutorial_ReshapeMat2Mat.cpp │ │ ├── Tutorial_ReshapeMat2Vec.cpp │ │ ├── Tutorial_SlicingCol.cpp │ │ ├── Tutorial_SlicingVec.cpp │ │ ├── Tutorial_commainit_01.cpp │ │ ├── Tutorial_commainit_01b.cpp │ │ ├── Tutorial_commainit_02.cpp │ │ ├── Tutorial_range_for_loop_1d_cxx11.cpp │ │ ├── Tutorial_range_for_loop_2d_cxx11.cpp │ │ ├── Tutorial_reshaped_vs_resize_1.cpp │ │ ├── Tutorial_reshaped_vs_resize_2.cpp │ │ ├── Tutorial_solve_matrix_inverse.cpp │ │ ├── Tutorial_solve_multiple_rhs.cpp │ │ ├── Tutorial_solve_reuse_decomposition.cpp │ │ ├── Tutorial_solve_singular.cpp │ │ ├── Tutorial_solve_triangular.cpp │ │ ├── Tutorial_solve_triangular_inplace.cpp │ │ ├── Tutorial_std_sort.cpp │ │ ├── Tutorial_std_sort_rows_cxx11.cpp │ │ ├── VectorwiseOp_homogeneous.cpp │ │ ├── Vectorwise_reverse.cpp │ │ ├── class_FullPivLU.cpp │ │ ├── compile_snippet.cpp.in │ │ ├── tut_arithmetic_redux_minmax.cpp │ │ ├── tut_arithmetic_transpose_aliasing.cpp │ │ ├── tut_arithmetic_transpose_conjugate.cpp │ │ ├── tut_arithmetic_transpose_inplace.cpp │ │ └── tut_matrix_assignment_resizing.cpp │ ├── special_examples │ │ ├── CMakeLists.txt │ │ ├── Tutorial_sparse_example.cpp │ │ ├── Tutorial_sparse_example_details.cpp │ │ └── random_cpp11.cpp │ └── tutorial.cpp ├── eigen3.pc.in ├── failtest │ ├── CMakeLists.txt │ ├── bdcsvd_int.cpp │ ├── block_nonconst_ctor_on_const_xpr_0.cpp │ ├── block_nonconst_ctor_on_const_xpr_1.cpp │ ├── block_nonconst_ctor_on_const_xpr_2.cpp │ ├── block_on_const_type_actually_const_0.cpp │ ├── block_on_const_type_actually_const_1.cpp │ ├── colpivqr_int.cpp │ ├── const_qualified_block_method_retval_0.cpp │ ├── const_qualified_block_method_retval_1.cpp │ ├── const_qualified_diagonal_method_retval.cpp │ ├── const_qualified_transpose_method_retval.cpp │ ├── cwiseunaryview_nonconst_ctor_on_const_xpr.cpp │ ├── cwiseunaryview_on_const_type_actually_const.cpp │ ├── diagonal_nonconst_ctor_on_const_xpr.cpp │ ├── diagonal_on_const_type_actually_const.cpp │ ├── eigensolver_cplx.cpp │ ├── eigensolver_int.cpp │ ├── failtest_sanity_check.cpp │ ├── fullpivlu_int.cpp │ ├── fullpivqr_int.cpp │ ├── initializer_list_1.cpp │ ├── initializer_list_2.cpp │ ├── jacobisvd_int.cpp │ ├── ldlt_int.cpp │ ├── llt_int.cpp │ ├── map_nonconst_ctor_on_const_ptr_0.cpp │ ├── map_nonconst_ctor_on_const_ptr_1.cpp │ ├── map_nonconst_ctor_on_const_ptr_2.cpp │ ├── map_nonconst_ctor_on_const_ptr_3.cpp │ ├── map_nonconst_ctor_on_const_ptr_4.cpp │ ├── map_on_const_type_actually_const_0.cpp │ ├── map_on_const_type_actually_const_1.cpp │ ├── partialpivlu_int.cpp │ ├── qr_int.cpp │ ├── ref_1.cpp │ ├── ref_2.cpp │ ├── ref_3.cpp │ ├── ref_4.cpp │ ├── ref_5.cpp │ ├── selfadjointview_nonconst_ctor_on_const_xpr.cpp │ ├── selfadjointview_on_const_type_actually_const.cpp │ ├── sparse_ref_1.cpp │ ├── sparse_ref_2.cpp │ ├── sparse_ref_3.cpp │ ├── sparse_ref_4.cpp │ ├── sparse_ref_5.cpp │ ├── sparse_storage_mismatch.cpp │ ├── swap_1.cpp │ ├── swap_2.cpp │ ├── ternary_1.cpp │ ├── ternary_2.cpp │ ├── transpose_nonconst_ctor_on_const_xpr.cpp │ ├── transpose_on_const_type_actually_const.cpp │ ├── triangularview_nonconst_ctor_on_const_xpr.cpp │ └── triangularview_on_const_type_actually_const.cpp ├── lapack │ ├── CMakeLists.txt │ ├── cholesky.cpp │ ├── clacgv.f │ ├── cladiv.f │ ├── clarf.f │ ├── clarfb.f │ ├── clarfg.f │ ├── clarft.f │ ├── complex_double.cpp │ ├── complex_single.cpp │ ├── dladiv.f │ ├── dlamch.f │ ├── dlapy2.f │ ├── dlapy3.f │ ├── dlarf.f │ ├── dlarfb.f │ ├── dlarfg.f │ ├── dlarft.f │ ├── double.cpp │ ├── dsecnd_NONE.f │ ├── eigenvalues.cpp │ ├── ilaclc.f │ ├── ilaclr.f │ ├── iladlc.f │ ├── iladlr.f │ ├── ilaslc.f │ ├── ilaslr.f │ ├── ilazlc.f │ ├── ilazlr.f │ ├── lapack_common.h │ ├── lu.cpp │ ├── second_NONE.f │ ├── single.cpp │ ├── sladiv.f │ ├── slamch.f │ ├── slapy2.f │ ├── slapy3.f │ ├── slarf.f │ ├── slarfb.f │ ├── slarfg.f │ ├── slarft.f │ ├── svd.cpp │ ├── zlacgv.f │ ├── zladiv.f │ ├── zlarf.f │ ├── zlarfb.f │ ├── zlarfg.f │ └── zlarft.f ├── scripts │ ├── CMakeLists.txt │ ├── cdashtesting.cmake.in │ ├── check.in │ ├── debug.in │ ├── eigen_gen_credits.cpp │ ├── eigen_gen_docs │ ├── eigen_gen_split_test_help.cmake │ ├── eigen_monitor_perf.sh │ ├── release.in │ └── relicense.py ├── signature_of_eigen3_matrix_library ├── test │ ├── AnnoyingScalar.h │ ├── CMakeLists.txt │ ├── MovableScalar.h │ ├── OffByOneScalar.h │ ├── SafeScalar.h │ ├── adjoint.cpp │ ├── array_cwise.cpp │ ├── array_for_matrix.cpp │ ├── array_of_string.cpp │ ├── array_replicate.cpp │ ├── array_reverse.cpp │ ├── bandmatrix.cpp │ ├── basicstuff.cpp │ ├── bdcsvd.cpp │ ├── bfloat16_float.cpp │ ├── bicgstab.cpp │ ├── blasutil.cpp │ ├── block.cpp │ ├── boostmultiprec.cpp │ ├── bug1213.cpp │ ├── bug1213.h │ ├── bug1213_main.cpp │ ├── cholesky.cpp │ ├── cholmod_support.cpp │ ├── commainitializer.cpp │ ├── conjugate_gradient.cpp │ ├── conservative_resize.cpp │ ├── constructor.cpp │ ├── corners.cpp │ ├── ctorleak.cpp │ ├── denseLM.cpp │ ├── dense_storage.cpp │ ├── determinant.cpp │ ├── diagonal.cpp │ ├── diagonal_matrix_variadic_ctor.cpp │ ├── diagonalmatrices.cpp │ ├── dontalign.cpp │ ├── dynalloc.cpp │ ├── eigen2support.cpp │ ├── eigensolver_complex.cpp │ ├── eigensolver_generalized_real.cpp │ ├── eigensolver_generic.cpp │ ├── eigensolver_selfadjoint.cpp │ ├── evaluator_common.h │ ├── evaluators.cpp │ ├── exceptions.cpp │ ├── fastmath.cpp │ ├── first_aligned.cpp │ ├── geo_alignedbox.cpp │ ├── geo_eulerangles.cpp │ ├── geo_homogeneous.cpp │ ├── geo_hyperplane.cpp │ ├── geo_orthomethods.cpp │ ├── geo_parametrizedline.cpp │ ├── geo_quaternion.cpp │ ├── geo_transformations.cpp │ ├── gpu_basic.cu │ ├── gpu_common.h │ ├── half_float.cpp │ ├── hessenberg.cpp │ ├── householder.cpp │ ├── incomplete_cholesky.cpp │ ├── indexed_view.cpp │ ├── initializer_list_construction.cpp │ ├── inplace_decomposition.cpp │ ├── integer_types.cpp │ ├── inverse.cpp │ ├── io.cpp │ ├── is_same_dense.cpp │ ├── jacobi.cpp │ ├── jacobisvd.cpp │ ├── klu_support.cpp │ ├── linearstructure.cpp │ ├── lscg.cpp │ ├── lu.cpp │ ├── main.h │ ├── mapped_matrix.cpp │ ├── mapstaticmethods.cpp │ ├── mapstride.cpp │ ├── meta.cpp │ ├── metis_support.cpp │ ├── miscmatrices.cpp │ ├── mixingtypes.cpp │ ├── mpl2only.cpp │ ├── nestbyvalue.cpp │ ├── nesting_ops.cpp │ ├── nomalloc.cpp │ ├── nullary.cpp │ ├── num_dimensions.cpp │ ├── numext.cpp │ ├── packetmath.cpp │ ├── packetmath_test_shared.h │ ├── pardiso_support.cpp │ ├── pastix_support.cpp │ ├── permutationmatrices.cpp │ ├── prec_inverse_4x4.cpp │ ├── product.h │ ├── product_extra.cpp │ ├── product_large.cpp │ ├── product_mmtr.cpp │ ├── product_notemporary.cpp │ ├── product_selfadjoint.cpp │ ├── product_small.cpp │ ├── product_symm.cpp │ ├── product_syrk.cpp │ ├── product_trmm.cpp │ ├── product_trmv.cpp │ ├── product_trsolve.cpp │ ├── qr.cpp │ ├── qr_colpivoting.cpp │ ├── qr_fullpivoting.cpp │ ├── qtvector.cpp │ ├── rand.cpp │ ├── random_without_cast_overflow.h │ ├── real_qz.cpp │ ├── redux.cpp │ ├── ref.cpp │ ├── reshape.cpp │ ├── resize.cpp │ ├── rvalue_types.cpp │ ├── schur_complex.cpp │ ├── schur_real.cpp │ ├── selfadjoint.cpp │ ├── simplicial_cholesky.cpp │ ├── sizeof.cpp │ ├── sizeoverflow.cpp │ ├── smallvectors.cpp │ ├── solverbase.h │ ├── sparse.h │ ├── sparseLM.cpp │ ├── sparse_basic.cpp │ ├── sparse_block.cpp │ ├── sparse_permutations.cpp │ ├── sparse_product.cpp │ ├── sparse_ref.cpp │ ├── sparse_solver.h │ ├── sparse_solvers.cpp │ ├── sparse_vector.cpp │ ├── sparselu.cpp │ ├── sparseqr.cpp │ ├── special_numbers.cpp │ ├── split_test_helper.h │ ├── spqr_support.cpp │ ├── stable_norm.cpp │ ├── stddeque.cpp │ ├── stddeque_overload.cpp │ ├── stdlist.cpp │ ├── stdlist_overload.cpp │ ├── stdvector.cpp │ ├── stdvector_overload.cpp │ ├── stl_iterators.cpp │ ├── superlu_support.cpp │ ├── svd_common.h │ ├── svd_fill.h │ ├── swap.cpp │ ├── symbolic_index.cpp │ ├── triangular.cpp │ ├── type_alias.cpp │ ├── umeyama.cpp │ ├── umfpack_support.cpp │ ├── unalignedassert.cpp │ ├── unalignedcount.cpp │ ├── upperbidiagonalization.cpp │ ├── vectorization_logic.cpp │ ├── vectorwiseop.cpp │ ├── visitor.cpp │ └── zerosized.cpp └── unsupported │ ├── CMakeLists.txt │ ├── Eigen │ ├── AdolcForward │ ├── AlignedVector3 │ ├── ArpackSupport │ ├── AutoDiff │ ├── BVH │ ├── CMakeLists.txt │ ├── CXX11 │ │ ├── CMakeLists.txt │ │ ├── Tensor │ │ ├── TensorSymmetry │ │ ├── ThreadPool │ │ └── src │ │ │ ├── Tensor │ │ │ ├── README.md │ │ │ ├── Tensor.h │ │ │ ├── TensorArgMax.h │ │ │ ├── TensorAssign.h │ │ │ ├── TensorBase.h │ │ │ ├── TensorBlock.h │ │ │ ├── TensorBroadcasting.h │ │ │ ├── TensorChipping.h │ │ │ ├── TensorConcatenation.h │ │ │ ├── TensorContraction.h │ │ │ ├── TensorContractionBlocking.h │ │ │ ├── TensorContractionCuda.h │ │ │ ├── TensorContractionGpu.h │ │ │ ├── TensorContractionMapper.h │ │ │ ├── TensorContractionSycl.h │ │ │ ├── TensorContractionThreadPool.h │ │ │ ├── TensorConversion.h │ │ │ ├── TensorConvolution.h │ │ │ ├── TensorConvolutionSycl.h │ │ │ ├── TensorCostModel.h │ │ │ ├── TensorCustomOp.h │ │ │ ├── TensorDevice.h │ │ │ ├── TensorDeviceCuda.h │ │ │ ├── TensorDeviceDefault.h │ │ │ ├── TensorDeviceGpu.h │ │ │ ├── TensorDeviceSycl.h │ │ │ ├── TensorDeviceThreadPool.h │ │ │ ├── TensorDimensionList.h │ │ │ ├── TensorDimensions.h │ │ │ ├── TensorEvalTo.h │ │ │ ├── TensorEvaluator.h │ │ │ ├── TensorExecutor.h │ │ │ ├── TensorExpr.h │ │ │ ├── TensorFFT.h │ │ │ ├── TensorFixedSize.h │ │ │ ├── TensorForcedEval.h │ │ │ ├── TensorForwardDeclarations.h │ │ │ ├── TensorFunctors.h │ │ │ ├── TensorGenerator.h │ │ │ ├── TensorGlobalFunctions.h │ │ │ ├── TensorGpuHipCudaDefines.h │ │ │ ├── TensorGpuHipCudaUndefines.h │ │ │ ├── TensorIO.h │ │ │ ├── TensorImagePatch.h │ │ │ ├── TensorIndexList.h │ │ │ ├── TensorInflation.h │ │ │ ├── TensorInitializer.h │ │ │ ├── TensorIntDiv.h │ │ │ ├── TensorLayoutSwap.h │ │ │ ├── TensorMacros.h │ │ │ ├── TensorMap.h │ │ │ ├── TensorMeta.h │ │ │ ├── TensorMorphing.h │ │ │ ├── TensorPadding.h │ │ │ ├── TensorPatch.h │ │ │ ├── TensorRandom.h │ │ │ ├── TensorReduction.h │ │ │ ├── TensorReductionCuda.h │ │ │ ├── TensorReductionGpu.h │ │ │ ├── TensorReductionSycl.h │ │ │ ├── TensorRef.h │ │ │ ├── TensorReverse.h │ │ │ ├── TensorScan.h │ │ │ ├── TensorScanSycl.h │ │ │ ├── TensorShuffling.h │ │ │ ├── TensorStorage.h │ │ │ ├── TensorStriding.h │ │ │ ├── TensorTrace.h │ │ │ ├── TensorTraits.h │ │ │ ├── TensorUInt128.h │ │ │ └── TensorVolumePatch.h │ │ │ ├── TensorSymmetry │ │ │ ├── DynamicSymmetry.h │ │ │ ├── StaticSymmetry.h │ │ │ ├── Symmetry.h │ │ │ └── util │ │ │ │ └── TemplateGroupTheory.h │ │ │ ├── ThreadPool │ │ │ ├── Barrier.h │ │ │ ├── EventCount.h │ │ │ ├── NonBlockingThreadPool.h │ │ │ ├── RunQueue.h │ │ │ ├── ThreadCancel.h │ │ │ ├── ThreadEnvironment.h │ │ │ ├── ThreadLocal.h │ │ │ ├── ThreadPoolInterface.h │ │ │ └── ThreadYield.h │ │ │ └── util │ │ │ ├── CXX11Meta.h │ │ │ ├── CXX11Workarounds.h │ │ │ ├── EmulateArray.h │ │ │ └── MaxSizeVector.h │ ├── EulerAngles │ ├── FFT │ ├── IterativeSolvers │ ├── KroneckerProduct │ ├── LevenbergMarquardt │ ├── MPRealSupport │ ├── MatrixFunctions │ ├── MoreVectorization │ ├── NonLinearOptimization │ ├── NumericalDiff │ ├── OpenGLSupport │ ├── Polynomials │ ├── Skyline │ ├── SparseExtra │ ├── SpecialFunctions │ ├── Splines │ └── src │ │ ├── AutoDiff │ │ ├── AutoDiffJacobian.h │ │ ├── AutoDiffScalar.h │ │ └── AutoDiffVector.h │ │ ├── BVH │ │ ├── BVAlgorithms.h │ │ └── KdBVH.h │ │ ├── Eigenvalues │ │ └── ArpackSelfAdjointEigenSolver.h │ │ ├── EulerAngles │ │ ├── CMakeLists.txt │ │ ├── EulerAngles.h │ │ └── EulerSystem.h │ │ ├── FFT │ │ ├── ei_fftw_impl.h │ │ └── ei_kissfft_impl.h │ │ ├── IterativeSolvers │ │ ├── ConstrainedConjGrad.h │ │ ├── DGMRES.h │ │ ├── GMRES.h │ │ ├── IDRS.h │ │ ├── IncompleteLU.h │ │ ├── IterationController.h │ │ ├── MINRES.h │ │ └── Scaling.h │ │ ├── KroneckerProduct │ │ └── KroneckerTensorProduct.h │ │ ├── LevenbergMarquardt │ │ ├── CopyrightMINPACK.txt │ │ ├── LMcovar.h │ │ ├── LMonestep.h │ │ ├── LMpar.h │ │ ├── LMqrsolv.h │ │ └── LevenbergMarquardt.h │ │ ├── MatrixFunctions │ │ ├── MatrixExponential.h │ │ ├── MatrixFunction.h │ │ ├── MatrixLogarithm.h │ │ ├── MatrixPower.h │ │ ├── MatrixSquareRoot.h │ │ └── StemFunction.h │ │ ├── MoreVectorization │ │ └── MathFunctions.h │ │ ├── NonLinearOptimization │ │ ├── HybridNonLinearSolver.h │ │ ├── LevenbergMarquardt.h │ │ ├── chkder.h │ │ ├── covar.h │ │ ├── dogleg.h │ │ ├── fdjac1.h │ │ ├── lmpar.h │ │ ├── qrsolv.h │ │ ├── r1mpyq.h │ │ ├── r1updt.h │ │ └── rwupdt.h │ │ ├── NumericalDiff │ │ └── NumericalDiff.h │ │ ├── Polynomials │ │ ├── Companion.h │ │ ├── PolynomialSolver.h │ │ └── PolynomialUtils.h │ │ ├── Skyline │ │ ├── SkylineInplaceLU.h │ │ ├── SkylineMatrix.h │ │ ├── SkylineMatrixBase.h │ │ ├── SkylineProduct.h │ │ ├── SkylineStorage.h │ │ └── SkylineUtil.h │ │ ├── SparseExtra │ │ ├── BlockOfDynamicSparseMatrix.h │ │ ├── BlockSparseMatrix.h │ │ ├── DynamicSparseMatrix.h │ │ ├── MarketIO.h │ │ ├── MatrixMarketIterator.h │ │ └── RandomSetter.h │ │ ├── SpecialFunctions │ │ ├── BesselFunctionsArrayAPI.h │ │ ├── BesselFunctionsBFloat16.h │ │ ├── BesselFunctionsFunctors.h │ │ ├── BesselFunctionsHalf.h │ │ ├── BesselFunctionsImpl.h │ │ ├── BesselFunctionsPacketMath.h │ │ ├── HipVectorCompatibility.h │ │ ├── SpecialFunctionsArrayAPI.h │ │ ├── SpecialFunctionsBFloat16.h │ │ ├── SpecialFunctionsFunctors.h │ │ ├── SpecialFunctionsHalf.h │ │ ├── SpecialFunctionsImpl.h │ │ ├── SpecialFunctionsPacketMath.h │ │ └── arch │ │ │ ├── AVX │ │ │ ├── BesselFunctions.h │ │ │ └── SpecialFunctions.h │ │ │ ├── AVX512 │ │ │ ├── BesselFunctions.h │ │ │ └── SpecialFunctions.h │ │ │ ├── GPU │ │ │ └── SpecialFunctions.h │ │ │ └── NEON │ │ │ ├── BesselFunctions.h │ │ │ └── SpecialFunctions.h │ │ └── Splines │ │ ├── Spline.h │ │ ├── SplineFitting.h │ │ └── SplineFwd.h │ ├── README.txt │ ├── bench │ └── bench_svd.cpp │ ├── doc │ ├── CMakeLists.txt │ ├── Overview.dox │ ├── SYCL.dox │ ├── eigendoxy_layout.xml.in │ ├── examples │ │ ├── BVH_Example.cpp │ │ ├── CMakeLists.txt │ │ ├── EulerAngles.cpp │ │ ├── FFT.cpp │ │ ├── MatrixExponential.cpp │ │ ├── MatrixFunction.cpp │ │ ├── MatrixLogarithm.cpp │ │ ├── MatrixPower.cpp │ │ ├── MatrixPower_optimal.cpp │ │ ├── MatrixSine.cpp │ │ ├── MatrixSinh.cpp │ │ ├── MatrixSquareRoot.cpp │ │ ├── PolynomialSolver1.cpp │ │ ├── PolynomialUtils1.cpp │ │ └── SYCL │ │ │ ├── CMakeLists.txt │ │ │ └── CwiseMul.cpp │ └── snippets │ │ └── CMakeLists.txt │ └── test │ ├── BVH.cpp │ ├── CMakeLists.txt │ ├── EulerAngles.cpp │ ├── FFT.cpp │ ├── FFTW.cpp │ ├── NonLinearOptimization.cpp │ ├── NumericalDiff.cpp │ ├── alignedvector3.cpp │ ├── autodiff.cpp │ ├── autodiff_scalar.cpp │ ├── bessel_functions.cpp │ ├── cxx11_eventcount.cpp │ ├── cxx11_maxsizevector.cpp │ ├── cxx11_meta.cpp │ ├── cxx11_non_blocking_thread_pool.cpp │ ├── cxx11_runqueue.cpp │ ├── cxx11_tensor_argmax.cpp │ ├── cxx11_tensor_argmax_gpu.cu │ ├── cxx11_tensor_argmax_sycl.cpp │ ├── cxx11_tensor_assign.cpp │ ├── cxx11_tensor_block_access.cpp │ ├── cxx11_tensor_block_eval.cpp │ ├── cxx11_tensor_block_io.cpp │ ├── cxx11_tensor_broadcast_sycl.cpp │ ├── cxx11_tensor_broadcasting.cpp │ ├── cxx11_tensor_builtins_sycl.cpp │ ├── cxx11_tensor_cast_float16_gpu.cu │ ├── cxx11_tensor_casts.cpp │ ├── cxx11_tensor_chipping.cpp │ ├── cxx11_tensor_chipping_sycl.cpp │ ├── cxx11_tensor_comparisons.cpp │ ├── cxx11_tensor_complex_cwise_ops_gpu.cu │ ├── cxx11_tensor_complex_gpu.cu │ ├── cxx11_tensor_concatenation.cpp │ ├── cxx11_tensor_concatenation_sycl.cpp │ ├── cxx11_tensor_const.cpp │ ├── cxx11_tensor_contract_gpu.cu │ ├── cxx11_tensor_contract_sycl.cpp │ ├── cxx11_tensor_contraction.cpp │ ├── cxx11_tensor_convolution.cpp │ ├── cxx11_tensor_convolution_sycl.cpp │ ├── cxx11_tensor_custom_index.cpp │ ├── cxx11_tensor_custom_op.cpp │ ├── cxx11_tensor_custom_op_sycl.cpp │ ├── cxx11_tensor_device.cu │ ├── cxx11_tensor_device_sycl.cpp │ ├── cxx11_tensor_dimension.cpp │ ├── cxx11_tensor_empty.cpp │ ├── cxx11_tensor_executor.cpp │ ├── cxx11_tensor_expr.cpp │ ├── cxx11_tensor_fft.cpp │ ├── cxx11_tensor_fixed_size.cpp │ ├── cxx11_tensor_forced_eval.cpp │ ├── cxx11_tensor_forced_eval_sycl.cpp │ ├── cxx11_tensor_generator.cpp │ ├── cxx11_tensor_generator_sycl.cpp │ ├── cxx11_tensor_gpu.cu │ ├── cxx11_tensor_ifft.cpp │ ├── cxx11_tensor_image_op_sycl.cpp │ ├── cxx11_tensor_image_patch.cpp │ ├── cxx11_tensor_image_patch_sycl.cpp │ ├── cxx11_tensor_index_list.cpp │ ├── cxx11_tensor_inflation.cpp │ ├── cxx11_tensor_inflation_sycl.cpp │ ├── cxx11_tensor_intdiv.cpp │ ├── cxx11_tensor_io.cpp │ ├── cxx11_tensor_layout_swap.cpp │ ├── cxx11_tensor_layout_swap_sycl.cpp │ ├── cxx11_tensor_lvalue.cpp │ ├── cxx11_tensor_map.cpp │ ├── cxx11_tensor_math.cpp │ ├── cxx11_tensor_math_sycl.cpp │ ├── cxx11_tensor_mixed_indices.cpp │ ├── cxx11_tensor_morphing.cpp │ ├── cxx11_tensor_morphing_sycl.cpp │ ├── cxx11_tensor_move.cpp │ ├── cxx11_tensor_notification.cpp │ ├── cxx11_tensor_of_complex.cpp │ ├── cxx11_tensor_of_const_values.cpp │ ├── cxx11_tensor_of_float16_gpu.cu │ ├── cxx11_tensor_of_strings.cpp │ ├── cxx11_tensor_padding.cpp │ ├── cxx11_tensor_padding_sycl.cpp │ ├── cxx11_tensor_patch.cpp │ ├── cxx11_tensor_patch_sycl.cpp │ ├── cxx11_tensor_random.cpp │ ├── cxx11_tensor_random_gpu.cu │ ├── cxx11_tensor_random_sycl.cpp │ ├── cxx11_tensor_reduction.cpp │ ├── cxx11_tensor_reduction_gpu.cu │ ├── cxx11_tensor_reduction_sycl.cpp │ ├── cxx11_tensor_ref.cpp │ ├── cxx11_tensor_reverse.cpp │ ├── cxx11_tensor_reverse_sycl.cpp │ ├── cxx11_tensor_roundings.cpp │ ├── cxx11_tensor_scan.cpp │ ├── cxx11_tensor_scan_gpu.cu │ ├── cxx11_tensor_scan_sycl.cpp │ ├── cxx11_tensor_shuffling.cpp │ ├── cxx11_tensor_shuffling_sycl.cpp │ ├── cxx11_tensor_simple.cpp │ ├── cxx11_tensor_striding.cpp │ ├── cxx11_tensor_striding_sycl.cpp │ ├── cxx11_tensor_sugar.cpp │ ├── cxx11_tensor_sycl.cpp │ ├── cxx11_tensor_symmetry.cpp │ ├── cxx11_tensor_thread_local.cpp │ ├── cxx11_tensor_thread_pool.cpp │ ├── cxx11_tensor_trace.cpp │ ├── cxx11_tensor_uint128.cpp │ ├── cxx11_tensor_volume_patch.cpp │ ├── cxx11_tensor_volume_patch_sycl.cpp │ ├── dgmres.cpp │ ├── forward_adolc.cpp │ ├── gmres.cpp │ ├── idrs.cpp │ ├── kronecker_product.cpp │ ├── levenberg_marquardt.cpp │ ├── matrix_exponential.cpp │ ├── matrix_function.cpp │ ├── matrix_functions.h │ ├── matrix_power.cpp │ ├── matrix_square_root.cpp │ ├── minres.cpp │ ├── mpreal │ └── mpreal.h │ ├── mpreal_support.cpp │ ├── openglsupport.cpp │ ├── polynomialsolver.cpp │ ├── polynomialutils.cpp │ ├── sparse_extra.cpp │ ├── special_functions.cpp │ ├── special_packetmath.cpp │ └── splines.cpp ├── Sophus ├── .clang-format ├── .gitignore ├── .travis.yml ├── CMakeLists.txt ├── LICENSE.txt ├── README.rst ├── SophusConfig.cmake.in ├── appveyor.yml ├── cmake_modules │ └── FindEigen3.cmake ├── doxyfile ├── doxyrest-config.lua ├── examples │ ├── CMakeLists.txt │ └── HelloSO3.cpp ├── make_docs.sh ├── package.xml ├── py │ ├── cpp_gencode │ │ ├── Se2_Dx_exp_x.cpp │ │ ├── Se2_Dx_this_mul_exp_x_at_0.cpp │ │ ├── Se3_Dx_exp_x.cpp │ │ ├── Se3_Dx_this_mul_exp_x_at_0.cpp │ │ ├── So2_Dx_exp_x.cpp │ │ ├── So2_Dx_this_mul_exp_x_at_0.cpp │ │ ├── So3_Dx_exp_x.cpp │ │ └── So3_Dx_this_mul_exp_x_at_0.cpp │ ├── run_tests.sh │ └── sophus │ │ ├── __init__.py │ │ ├── complex.py │ │ ├── cse_codegen.py │ │ ├── dual_quaternion.py │ │ ├── matrix.py │ │ ├── quaternion.py │ │ ├── se2.py │ │ ├── se3.py │ │ ├── so2.py │ │ ├── so3.py │ │ └── so3_codegen.py ├── rst-dir │ ├── conf.py │ ├── page_index.rst │ └── pysophus.rst ├── run_format.sh ├── scripts │ ├── install_docs_deps.sh │ ├── install_linux_deps.sh │ ├── install_osx_deps.sh │ └── run_cpp_tests.sh ├── sophus │ ├── average.hpp │ ├── common.hpp │ ├── example_ensure_handler.cpp │ ├── formatstring.hpp │ ├── geometry.hpp │ ├── interpolate.hpp │ ├── interpolate_details.hpp │ ├── num_diff.hpp │ ├── rotation_matrix.hpp │ ├── rxso2.hpp │ ├── rxso3.hpp │ ├── se2.hpp │ ├── se3.hpp │ ├── sim2.hpp │ ├── sim3.hpp │ ├── sim_details.hpp │ ├── so2.hpp │ ├── so3.hpp │ ├── test_macros.hpp │ ├── types.hpp │ └── velocities.hpp └── test │ ├── CMakeLists.txt │ ├── ceres │ ├── CMakeLists.txt │ ├── local_parameterization_se3.hpp │ └── test_ceres_se3.cpp │ └── core │ ├── CMakeLists.txt │ ├── test_common.cpp │ ├── test_geometry.cpp │ ├── test_rxso2.cpp │ ├── test_rxso3.cpp │ ├── test_se2.cpp │ ├── test_se3.cpp │ ├── test_sim2.cpp │ ├── test_sim3.cpp │ ├── test_so2.cpp │ ├── test_so3.cpp │ ├── test_velocities.cpp │ └── tests.hpp ├── nvbio ├── BOOST.license ├── CMakeLists.txt ├── LICENSE ├── README.md ├── cmake-local │ ├── gcc.cmake │ └── nvbio.cmake ├── contrib │ ├── bamtools │ │ ├── BGZF.cpp │ │ ├── BGZF.h │ │ ├── BamAux.h │ │ ├── BamReader.cpp │ │ ├── BamReader.h │ │ ├── BamWriter.cpp │ │ ├── BamWriter.h │ │ └── CMakeLists.txt │ ├── crc │ │ ├── CMakeLists.txt │ │ ├── crc.cpp │ │ └── crc.h │ ├── cub │ │ ├── block │ │ │ ├── block_discontinuity.cuh │ │ │ ├── block_exchange.cuh │ │ │ ├── block_histo_256.cuh │ │ │ ├── block_histogram.cuh │ │ │ ├── block_load.cuh │ │ │ ├── block_radix_rank.cuh │ │ │ ├── block_radix_sort.cuh │ │ │ ├── block_raking_layout.cuh │ │ │ ├── block_reduce.cuh │ │ │ ├── block_scan.cuh │ │ │ ├── block_shift.cuh │ │ │ ├── block_store.cuh │ │ │ └── specializations │ │ │ │ ├── block_histogram_atomic.cuh │ │ │ │ ├── block_histogram_sort.cuh │ │ │ │ ├── block_reduce_raking.cuh │ │ │ │ ├── block_reduce_raking_commutative_only.cuh │ │ │ │ ├── block_reduce_warp_reductions.cuh │ │ │ │ ├── block_scan_raking.cuh │ │ │ │ └── block_scan_warp_scans.cuh │ │ ├── cub.cuh │ │ ├── device │ │ │ ├── block │ │ │ │ ├── block_histo_tiles.cuh │ │ │ │ ├── block_partition_tiles.cuh │ │ │ │ ├── block_radix_sort_downsweep_tiles.cuh │ │ │ │ ├── block_radix_sort_upsweep_tiles.cuh │ │ │ │ ├── block_reduce_by_key_tiles.cuh │ │ │ │ ├── block_reduce_tiles.cuh │ │ │ │ ├── block_scan_tiles.cuh │ │ │ │ ├── scan_tiles_types.cuh │ │ │ │ └── specializations │ │ │ │ │ ├── block_histo_tiles_gatomic.cuh │ │ │ │ │ ├── block_histo_tiles_satomic.cuh │ │ │ │ │ └── block_histo_tiles_sort.cuh │ │ │ ├── block_region │ │ │ │ ├── block_region_histo.cuh │ │ │ │ ├── block_region_radix_sort_downsweep.cuh │ │ │ │ ├── block_region_radix_sort_upsweep.cuh │ │ │ │ ├── block_region_reduce.cuh │ │ │ │ ├── block_region_reduce_by_key.cuh │ │ │ │ ├── block_region_scan.cuh │ │ │ │ ├── block_region_select.cuh │ │ │ │ ├── device_scan_types.cuh │ │ │ │ └── specializations │ │ │ │ │ ├── block_region_histo_gatomic.cuh │ │ │ │ │ ├── block_region_histo_satomic.cuh │ │ │ │ │ └── block_region_histo_sort.cuh │ │ │ ├── device_histo_256.cuh │ │ │ ├── device_histogram.cuh │ │ │ ├── device_partition.cuh │ │ │ ├── device_radix_sort.cuh │ │ │ ├── device_reduce.cuh │ │ │ ├── device_reduce_by_key.cuh │ │ │ ├── device_reorder.cuh │ │ │ ├── device_scan.cuh │ │ │ ├── device_select.cuh │ │ │ ├── dispatch │ │ │ │ ├── device_histogram_dispatch.cuh │ │ │ │ ├── device_radix_sort_dispatch.cuh │ │ │ │ ├── device_reduce_by_key_dispatch.cuh │ │ │ │ ├── device_reduce_dispatch.cuh │ │ │ │ ├── device_scan_dispatch.cuh │ │ │ │ └── device_select_dispatch.cuh │ │ │ ├── persistent_block │ │ │ │ ├── persistent_block_histo_256.cuh │ │ │ │ ├── persistent_block_reduce.cuh │ │ │ │ └── persistent_block_scan.cuh │ │ │ └── region │ │ │ │ ├── block_histo_region.cuh │ │ │ │ ├── block_radix_sort_downsweep_region.cuh │ │ │ │ ├── block_radix_sort_upsweep_region.cuh │ │ │ │ ├── block_reduce_by_key_region.cuh │ │ │ │ ├── block_reduce_region.cuh │ │ │ │ ├── block_scan_region.cuh │ │ │ │ ├── block_select_region.cuh │ │ │ │ ├── device_scan_types.cuh │ │ │ │ └── specializations │ │ │ │ ├── block_histo_region_gatomic.cuh │ │ │ │ ├── block_histo_region_satomic.cuh │ │ │ │ └── block_histo_region_sort.cuh │ │ ├── grid │ │ │ ├── grid_barrier.cuh │ │ │ ├── grid_even_share.cuh │ │ │ ├── grid_mapping.cuh │ │ │ ├── grid_multi_buffer.cuh │ │ │ └── grid_queue.cuh │ │ ├── host │ │ │ └── spinlock.cuh │ │ ├── iterator │ │ │ ├── arg_index_input_iterator.cuh │ │ │ ├── cache_modified_input_iterator.cuh │ │ │ ├── cache_modified_output_iterator.cuh │ │ │ ├── constant_input_iterator.cuh │ │ │ ├── counting_input_iterator.cuh │ │ │ ├── tex_obj_input_iterator.cuh │ │ │ ├── tex_ref_input_iterator.cuh │ │ │ └── transform_input_iterator.cuh │ │ ├── thread │ │ │ ├── thread_load.cuh │ │ │ ├── thread_operators.cuh │ │ │ ├── thread_reduce.cuh │ │ │ ├── thread_scan.cuh │ │ │ └── thread_store.cuh │ │ ├── util_allocator.cuh │ │ ├── util_arch.cuh │ │ ├── util_debug.cuh │ │ ├── util_device.cuh │ │ ├── util_iterator.cuh │ │ ├── util_macro.cuh │ │ ├── util_namespace.cuh │ │ ├── util_ptx.cuh │ │ ├── util_type.cuh │ │ ├── util_vector.cuh │ │ └── warp │ │ │ ├── specializations │ │ │ ├── warp_reduce_shfl.cuh │ │ │ ├── warp_reduce_smem.cuh │ │ │ ├── warp_scan_shfl.cuh │ │ │ └── warp_scan_smem.cuh │ │ │ ├── warp_reduce.cuh │ │ │ └── warp_scan.cuh │ ├── htslib │ │ ├── .cproject │ │ ├── .project │ │ ├── .travis.yml │ │ ├── CMakeLists.txt │ │ ├── Makefile │ │ ├── README.md │ │ ├── README.nvbio │ │ ├── bgzf.c │ │ ├── bgzip.c │ │ ├── config.h │ │ ├── cram │ │ │ ├── cram.h │ │ │ ├── cram_codecs.c │ │ │ ├── cram_codecs.h │ │ │ ├── cram_decode.c │ │ │ ├── cram_decode.h │ │ │ ├── cram_encode.c │ │ │ ├── cram_encode.h │ │ │ ├── cram_index.c │ │ │ ├── cram_index.h │ │ │ ├── cram_io.c │ │ │ ├── cram_io.h │ │ │ ├── cram_samtools.c │ │ │ ├── cram_samtools.h │ │ │ ├── cram_stats.c │ │ │ ├── cram_stats.h │ │ │ ├── cram_structs.h │ │ │ ├── files.c │ │ │ ├── mFILE.c │ │ │ ├── mFILE.h │ │ │ ├── md5.c │ │ │ ├── md5.h │ │ │ ├── misc.h │ │ │ ├── open_trace_file.c │ │ │ ├── open_trace_file.h │ │ │ ├── os.h │ │ │ ├── pooled_alloc.c │ │ │ ├── pooled_alloc.h │ │ │ ├── sam_header.c │ │ │ ├── sam_header.h │ │ │ ├── string_alloc.c │ │ │ ├── string_alloc.h │ │ │ ├── thread_pool.c │ │ │ ├── thread_pool.h │ │ │ ├── vlen.c │ │ │ ├── vlen.h │ │ │ ├── zfio.c │ │ │ └── zfio.h │ │ ├── faidx.5 │ │ ├── faidx.c │ │ ├── hfile.c │ │ ├── hfile_internal.h │ │ ├── hfile_net.c │ │ ├── hts.c │ │ ├── htslib.mk │ │ ├── htslib │ │ │ ├── bgzf.h │ │ │ ├── faidx.h │ │ │ ├── hfile.h │ │ │ ├── hts.h │ │ │ ├── hts_defs.h │ │ │ ├── kfunc.h │ │ │ ├── khash.h │ │ │ ├── khash_str2int.h │ │ │ ├── klist.h │ │ │ ├── knetfile.h │ │ │ ├── kseq.h │ │ │ ├── ksort.h │ │ │ ├── kstdint.h │ │ │ ├── kstring.h │ │ │ ├── sam.h │ │ │ ├── synced_bcf_reader.h │ │ │ ├── tbx.h │ │ │ ├── vcf.h │ │ │ ├── vcf_sweep.h │ │ │ └── vcfutils.h │ │ ├── htslib_vars.mk │ │ ├── kfunc.c │ │ ├── knetfile.c │ │ ├── kstring.c │ │ ├── sam.5 │ │ ├── sam.c │ │ ├── synced_bcf_reader.c │ │ ├── tabix.1 │ │ ├── tabix.c │ │ ├── tbx.c │ │ ├── vcf.5 │ │ ├── vcf.c │ │ ├── vcf_sweep.c │ │ ├── vcfutils.c │ │ └── version.h │ ├── libbwtsw-bin │ │ ├── README │ │ ├── bwtsw.idb │ │ ├── bwtsw.lib │ │ ├── bwtsw.pdb │ │ └── libbwtsw-linux-amd64-release.a │ ├── libdivsufsort-lite │ │ ├── AUTHORS │ │ ├── COPYING │ │ ├── README │ │ ├── VERSION │ │ ├── divsufsort.c │ │ ├── divsufsort.h │ │ └── suftest.c │ ├── libdivsufsortxx │ │ └── divsufsortxx.h │ ├── lz4 │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── liblz4.pc.in │ │ ├── lz4.c │ │ ├── lz4.h │ │ ├── lz4frame.c │ │ ├── lz4frame.h │ │ ├── lz4frame_static.h │ │ ├── lz4hc.c │ │ ├── lz4hc.h │ │ ├── xxhash.c │ │ └── xxhash.h │ ├── moderngpu │ │ ├── CMakeLists.txt │ │ ├── README.md │ │ ├── include │ │ │ ├── device │ │ │ │ ├── ctaloadbalance.cuh │ │ │ │ ├── ctamerge.cuh │ │ │ │ ├── ctascan.cuh │ │ │ │ ├── ctasearch.cuh │ │ │ │ ├── ctasegreduce.cuh │ │ │ │ ├── ctasegscan.cuh │ │ │ │ ├── ctasegsort.cuh │ │ │ │ ├── ctasortedsearch.cuh │ │ │ │ ├── devicetypes.cuh │ │ │ │ ├── deviceutil.cuh │ │ │ │ ├── intrinsics.cuh │ │ │ │ ├── launchbox.cuh │ │ │ │ ├── loadstore.cuh │ │ │ │ ├── serialsets.cuh │ │ │ │ └── sortnetwork.cuh │ │ │ ├── kernels │ │ │ │ ├── bulkinsert.cuh │ │ │ │ ├── bulkremove.cuh │ │ │ │ ├── csrtools.cuh │ │ │ │ ├── cubradixsort.cuh │ │ │ │ ├── intervalmove.cuh │ │ │ │ ├── join.cuh │ │ │ │ ├── loadbalance.cuh │ │ │ │ ├── localitysort.cuh │ │ │ │ ├── merge.cuh │ │ │ │ ├── mergesort.cuh │ │ │ │ ├── reduce.cuh │ │ │ │ ├── reducebykey.cuh │ │ │ │ ├── scan.cuh │ │ │ │ ├── search.cuh │ │ │ │ ├── segmentedsort.cuh │ │ │ │ ├── segreduce.cuh │ │ │ │ ├── segreducecsr.cuh │ │ │ │ ├── sets.cuh │ │ │ │ ├── sortedsearch.cuh │ │ │ │ └── spmvcsr.cuh │ │ │ ├── mgpudevice.cuh │ │ │ ├── mgpuenums.h │ │ │ ├── mgpuhost.cuh │ │ │ ├── mmio.h │ │ │ ├── moderngpu.cuh │ │ │ ├── sparsematrix.h │ │ │ └── util │ │ │ │ ├── format.h │ │ │ │ ├── mgpualloc.h │ │ │ │ ├── mgpucontext.h │ │ │ │ ├── static.h │ │ │ │ └── util.h │ │ └── src │ │ │ ├── mgpucontext.cu │ │ │ ├── mgpuutil.cpp │ │ │ ├── mmio.cpp │ │ │ └── sparsematrix.cpp │ ├── priority-deque │ │ ├── README.md │ │ ├── interval_heap.hpp │ │ ├── main.cpp │ │ ├── priority_deque.hpp │ │ └── priority_deque_verify.hpp │ ├── sais.h │ ├── zlib-1.2.7 │ │ ├── CMakeLists.txt │ │ ├── ChangeLog │ │ ├── FAQ │ │ ├── INDEX │ │ ├── Makefile │ │ ├── Makefile.in │ │ ├── README │ │ ├── adler32.c │ │ ├── compress.c │ │ ├── configure │ │ ├── configure.log │ │ ├── crc32.c │ │ ├── crc32.h │ │ ├── deflate.c │ │ ├── deflate.h │ │ ├── gzclose.c │ │ ├── gzguts.h │ │ ├── gzlib.c │ │ ├── gzread.c │ │ ├── gzwrite.c │ │ ├── infback.c │ │ ├── inffast.c │ │ ├── inffast.h │ │ ├── inffixed.h │ │ ├── inflate.c │ │ ├── inflate.h │ │ ├── inftrees.c │ │ ├── inftrees.h │ │ ├── make_vms.com │ │ ├── treebuild.xml │ │ ├── trees.c │ │ ├── trees.h │ │ ├── uncompr.c │ │ ├── zconf.h.cmakein │ │ ├── zconf.h.in │ │ ├── zlib.3 │ │ ├── zlib.3.pdf │ │ ├── zlib.h │ │ ├── zlib.map │ │ ├── zlib.pc │ │ ├── zlib.pc.cmakein │ │ ├── zlib.pc.in │ │ ├── zlib2ansi │ │ ├── zutil.c │ │ └── zutil.h │ └── zlib │ │ ├── lib │ │ └── libz.a │ │ ├── zconf.h │ │ └── zlib.h ├── doxy │ ├── Doxyfile.bk │ ├── Doxyfile.in │ ├── DoxygenLayout.xml │ ├── extra_stylesheet.css │ ├── header.html │ └── images │ │ ├── benchmark-bwt.png │ │ ├── benchmark-fm-index-speedup.png │ │ ├── benchmark-fm-index.png │ │ ├── benchmark-nvbowtie-speedup.png │ │ ├── benchmark-qgram-counting.png │ │ ├── benchmark-qgram-indexing.png │ │ ├── benchmark-sw.png │ │ ├── browse-icon.png │ │ ├── cuda.png │ │ ├── cuda_small.png │ │ ├── download-icon.png │ │ ├── groups-icon.png │ │ ├── nvBowtie-ROC-pe-100-large-indels.png │ │ ├── nvBowtie-ROC-pe-100-zoom.png │ │ ├── nvBowtie-ROC-pe-100.png │ │ ├── nvBowtie-ROC-pe-250.png │ │ ├── nvBowtie-ROC-se-100.png │ │ ├── nvBowtie-pe-100-ROC-zoom.png │ │ ├── nvbio-logo.xcf │ │ ├── nvidia.png │ │ ├── nvidia_cubes.jpg │ │ ├── nvidia_cubes.png │ │ ├── spiral.jpg │ │ ├── tree.png │ │ └── tree.ppt ├── examples │ ├── fmmap │ │ ├── CMakeLists.txt │ │ ├── fmmap.cu │ │ └── util.h │ ├── hello_world │ │ └── hello_world.cu │ ├── hello_world2 │ │ └── hello_world2.cu │ ├── mem │ │ ├── CMakeLists.txt │ │ └── mem.cu │ ├── proteinsw │ │ ├── CMakeLists.txt │ │ ├── proteinsw.cu │ │ └── proteinsw_qp.cu │ ├── qmap │ │ ├── CMakeLists.txt │ │ ├── alignment.h │ │ ├── qmap.cu │ │ └── util.h │ ├── seeding │ │ ├── CMakeLists.txt │ │ └── seeding.cu │ └── waveletfm │ │ ├── CMakeLists.txt │ │ └── waveletfm.cu ├── nvBWT │ ├── CMakeLists.txt │ ├── filelist.cpp │ ├── filelist.h │ ├── nvBWT.cu │ └── nvBWT.dox ├── nvBowtie │ ├── CMakeLists.txt │ ├── bowtie2 │ │ ├── CMakeLists.txt │ │ ├── cuda │ │ │ ├── CMakeLists.txt │ │ │ ├── aligner.h │ │ │ ├── aligner_all.h │ │ │ ├── aligner_all_ed.cu │ │ │ ├── aligner_all_sw.cu │ │ │ ├── aligner_best_approx.h │ │ │ ├── aligner_best_approx_ed.cu │ │ │ ├── aligner_best_approx_paired.h │ │ │ ├── aligner_best_approx_paired_ed.cu │ │ │ ├── aligner_best_approx_paired_sw.cu │ │ │ ├── aligner_best_approx_sw.cu │ │ │ ├── aligner_best_exact.h │ │ │ ├── aligner_init.cu │ │ │ ├── aligner_inst.h │ │ │ ├── aligner_sort.cu │ │ │ ├── alignment_utils.h │ │ │ ├── checksums.cu │ │ │ ├── checksums.h │ │ │ ├── compute_thread.cu │ │ │ ├── compute_thread.h │ │ │ ├── defs.h │ │ │ ├── fmindex_def.h │ │ │ ├── func.h │ │ │ ├── input_thread.cpp │ │ │ ├── input_thread.h │ │ │ ├── locate.h │ │ │ ├── locate_inl.h │ │ │ ├── mapping.cu │ │ │ ├── mapping.h │ │ │ ├── mapping_impl.h │ │ │ ├── mapping_inl.h │ │ │ ├── mapq.cpp │ │ │ ├── mapq.h │ │ │ ├── params.cpp │ │ │ ├── params.h │ │ │ ├── persist.cu │ │ │ ├── persist.h │ │ │ ├── pipeline_states.h │ │ │ ├── reads_def.h │ │ │ ├── reduce.cu │ │ │ ├── reduce.h │ │ │ ├── reduce_impl.h │ │ │ ├── reduce_inl.h │ │ │ ├── score.cu │ │ │ ├── score.h │ │ │ ├── score_all.cu │ │ │ ├── score_all_impl.h │ │ │ ├── score_all_inl.h │ │ │ ├── score_best.cu │ │ │ ├── score_best_impl.h │ │ │ ├── score_best_inl.h │ │ │ ├── score_gapped.cu │ │ │ ├── score_opposite_impl.h │ │ │ ├── score_opposite_inl.h │ │ │ ├── score_paired.cu │ │ │ ├── score_paired_impl.h │ │ │ ├── score_paired_inl.h │ │ │ ├── score_ungapped.cu │ │ │ ├── scoring.h │ │ │ ├── scoring_inl.h │ │ │ ├── scoring_queues.h │ │ │ ├── scoring_queues_inl.h │ │ │ ├── scoring_queues_test.cu │ │ │ ├── seed_hit.h │ │ │ ├── seed_hit_deque_array.cu │ │ │ ├── seed_hit_deque_array.h │ │ │ ├── seed_hit_deque_array_inl.h │ │ │ ├── seed_hit_deque_array_test.cu │ │ │ ├── select.cu │ │ │ ├── select.h │ │ │ ├── select_impl.h │ │ │ ├── select_inl.h │ │ │ ├── stats.cpp │ │ │ ├── stats.h │ │ │ ├── string_utils.h │ │ │ ├── traceback.cu │ │ │ ├── traceback.h │ │ │ ├── traceback_impl.h │ │ │ ├── traceback_inl.h │ │ │ └── utils.h │ │ ├── quality_coeffs.cpp │ │ └── quality_coeffs.h │ ├── nvBowtie.cpp │ └── nvBowtie.dox ├── nvExtractReads │ ├── CMakeLists.txt │ └── nvExtractReads.cu ├── nvFM-server │ ├── CMakeLists.txt │ ├── nvFM-server.cpp │ └── nvFM-server.dox ├── nvLighter │ ├── CMakeLists.txt │ ├── bloom_filters.h │ ├── bloom_filters_inl.h │ ├── error_correct.cu │ ├── error_correct.h │ ├── input_thread.cu │ ├── input_thread.h │ ├── nvLighter.cu │ ├── nvLighter.dox │ ├── output_thread.cu │ ├── output_thread.h │ ├── sample_kmers.cu │ ├── sample_kmers.h │ └── utils.h ├── nvMicroAssembly │ ├── CMakeLists.txt │ ├── assembly.h │ ├── assembly_graph.h │ ├── assembly_graph_inl.h │ ├── assembly_types.h │ ├── bam_io.cu │ ├── bam_io.h │ ├── haplotype_caller.cu │ ├── haplotype_caller.h │ ├── kmers.h │ ├── kmers_inl.h │ └── regions.h ├── nvSSA │ ├── CMakeLists.txt │ ├── nvSSA.cpp │ └── nvSSA.dox ├── nvSetBWT │ ├── CMakeLists.txt │ ├── input_thread.h │ ├── nvSetBWT.cu │ └── nvSetBWT.dox ├── nvbio-aln-diff │ ├── CMakeLists.txt │ ├── alignment.cpp │ ├── alignment.h │ ├── alignment_bam.cpp │ ├── alignment_dbg.cpp │ ├── filter.h │ ├── html.h │ ├── nvbio-aln-diff.cpp │ ├── pe_analyzer.cpp │ ├── pe_analyzer.h │ ├── se_analyzer.cpp │ ├── se_analyzer.h │ ├── stats.h │ └── utils.h ├── nvbio-test │ ├── CMakeLists.txt │ ├── alignment_test.cu │ ├── alignment_test_utils.h │ ├── alloc_test.cu │ ├── bloom_filter_test.cu │ ├── bwt_test.cpp │ ├── cache_test.cpp │ ├── condtion_test.cu │ ├── fasta_test.cpp │ ├── fastq_test.cpp │ ├── fmindex_test.cu │ ├── nvbio-test.cpp │ ├── packedstream_test.cpp │ ├── qgram_test.cu │ ├── rank_test.cu │ ├── sequence_test.cu │ ├── string_set_test.cu │ ├── sum_tree_test.cpp │ ├── syncblocks_test.cu │ ├── utils.h │ ├── wavelet_test.cu │ └── work_queue_test.cu ├── nvbio │ ├── CMakeLists.txt │ ├── alignment │ │ ├── alignment.h │ │ ├── alignment_base.h │ │ ├── alignment_base_inl.h │ │ ├── alignment_inl.h │ │ ├── banded_inl.h │ │ ├── batched.h │ │ ├── batched_banded_inl.h │ │ ├── batched_inl.h │ │ ├── batched_stream.h │ │ ├── ed │ │ │ ├── ed_banded_inl.h │ │ │ ├── ed_inl.h │ │ │ ├── ed_utils.h │ │ │ └── ed_warp_inl.h │ │ ├── gotoh │ │ │ ├── gotoh_banded_inl.h │ │ │ ├── gotoh_inl.h │ │ │ └── gotoh_warp_inl.h │ │ ├── hamming │ │ │ └── hamming_inl.h │ │ ├── myers │ │ │ └── myers_banded_inl.h │ │ ├── sink.h │ │ ├── sink_inl.h │ │ ├── sw │ │ │ ├── sw_banded_inl.h │ │ │ ├── sw_inl.h │ │ │ └── sw_warp_inl.h │ │ ├── utils.h │ │ ├── utils_inl.h │ │ └── warp_utils.h │ ├── basic.dox │ ├── basic │ │ ├── CMakeLists.txt │ │ ├── algorithms.h │ │ ├── atomics.cpp │ │ ├── atomics.h │ │ ├── bloom_filter.h │ │ ├── bloom_filter_inl.h │ │ ├── bnt.cpp │ │ ├── bnt.h │ │ ├── cache.h │ │ ├── cache_inl.h │ │ ├── cached_iterator.h │ │ ├── cached_iterator_inl.h │ │ ├── cast_iterator.h │ │ ├── console.cpp │ │ ├── console.h │ │ ├── cuda │ │ │ ├── CMakeLists.txt │ │ │ ├── arch.h │ │ │ ├── arch_inl.h │ │ │ ├── atomics.h │ │ │ ├── condition.h │ │ │ ├── host_device_buffer.h │ │ │ ├── ldg.h │ │ │ ├── pingpong_queues.h │ │ │ ├── primitives.h │ │ │ ├── primitives_inl.h │ │ │ ├── scan.h │ │ │ ├── scan_test.cu │ │ │ ├── simd_functions.h │ │ │ ├── sort.cu │ │ │ ├── sort.h │ │ │ ├── syncblocks.h │ │ │ ├── syncblocks_inl.h │ │ │ ├── tex.h │ │ │ ├── timer.h │ │ │ ├── work_queue.h │ │ │ ├── work_queue_inl.h │ │ │ ├── work_queue_multipass.h │ │ │ ├── work_queue_multipass_inl.h │ │ │ ├── work_queue_ordered.h │ │ │ ├── work_queue_ordered_inl.h │ │ │ ├── work_queue_persistent.h │ │ │ └── work_queue_persistent_inl.h │ │ ├── deinterleaved_iterator.h │ │ ├── dna.h │ │ ├── exceptions.cpp │ │ ├── exceptions.h │ │ ├── html.cpp │ │ ├── html.h │ │ ├── index_transform_iterator.h │ │ ├── interval_heap.h │ │ ├── iterator.h │ │ ├── iterator_reference.h │ │ ├── merge_sort.h │ │ ├── mmap.cpp │ │ ├── mmap.h │ │ ├── numbers.h │ │ ├── omp.h │ │ ├── options.h │ │ ├── packed_vector.h │ │ ├── packed_vector_inl.h │ │ ├── packedstream.h │ │ ├── packedstream_inl.h │ │ ├── packedstream_loader.h │ │ ├── packedstream_loader_inl.h │ │ ├── pipeline.h │ │ ├── pipeline_context.h │ │ ├── pipeline_inl.h │ │ ├── pod.h │ │ ├── popcount.h │ │ ├── popcount_inl.h │ │ ├── primitives.h │ │ ├── primitives_inl.h │ │ ├── priority_deque.h │ │ ├── priority_queue.h │ │ ├── priority_queue_inline.h │ │ ├── profiling.h │ │ ├── shared_pointer.h │ │ ├── simd.h │ │ ├── simd_inl.h │ │ ├── static_vector.h │ │ ├── static_vector_inl.h │ │ ├── strided_iterator.h │ │ ├── sum_tree.h │ │ ├── sum_tree_inl.h │ │ ├── system.cpp │ │ ├── system.h │ │ ├── threads.cpp │ │ ├── threads.h │ │ ├── thrust_view.h │ │ ├── timer.cpp │ │ ├── timer.h │ │ ├── transform_iterator.h │ │ ├── types.h │ │ ├── vector.h │ │ ├── vector_array.h │ │ ├── vector_loads.h │ │ ├── vector_view.h │ │ └── version.h │ ├── fasta │ │ ├── CMakeLists.txt │ │ ├── fasta.h │ │ └── fasta_inl.h │ ├── fastq │ │ ├── CMakeLists.txt │ │ ├── fastq.cpp │ │ ├── fastq.h │ │ └── fastq_inl.h │ ├── fmindex │ │ ├── CMakeLists.txt │ │ ├── backtrack.h │ │ ├── bidir.h │ │ ├── bidir_inl.h │ │ ├── bwt.h │ │ ├── filter.h │ │ ├── filter_inl.h │ │ ├── fmindex.h │ │ ├── fmindex_device.h │ │ ├── fmindex_inl.h │ │ ├── mem.h │ │ ├── mem_inl.h │ │ ├── paged_text.cpp │ │ ├── paged_text.h │ │ ├── paged_text_inl.h │ │ ├── rank_dictionary.h │ │ ├── rank_dictionary_inl.h │ │ ├── ssa.h │ │ └── ssa_inl.h │ ├── io.dox │ ├── io │ │ ├── CMakeLists.txt │ │ ├── alignments.h │ │ ├── alignments_inl.h │ │ ├── bam_format.h │ │ ├── bufferedtextfile.h │ │ ├── fmindex │ │ │ ├── CMakeLists.txt │ │ │ ├── fmindex.h │ │ │ └── fmindex_impl.cu │ │ ├── output │ │ │ ├── CMakeLists.txt │ │ │ ├── output_bam.cpp │ │ │ ├── output_bam.h │ │ │ ├── output_batch.cpp │ │ │ ├── output_batch.h │ │ │ ├── output_databuffer.cpp │ │ │ ├── output_databuffer.h │ │ │ ├── output_debug.cpp │ │ │ ├── output_debug.h │ │ │ ├── output_file.cpp │ │ │ ├── output_file.h │ │ │ ├── output_gzip.cpp │ │ │ ├── output_gzip.h │ │ │ ├── output_priv.cpp │ │ │ ├── output_priv.h │ │ │ ├── output_sam.cpp │ │ │ ├── output_sam.h │ │ │ ├── output_stats.cpp │ │ │ ├── output_stats.h │ │ │ ├── output_types.h │ │ │ └── output_utils.h │ │ ├── output_stream.cpp │ │ ├── output_stream.h │ │ ├── reads │ │ │ ├── CMakeLists.txt │ │ │ ├── bam.cpp │ │ │ ├── bam.h │ │ │ ├── reads.cpp │ │ │ ├── reads.h │ │ │ ├── reads_fastq.cpp │ │ │ ├── reads_fastq.h │ │ │ ├── reads_priv.h │ │ │ ├── reads_txt.cpp │ │ │ ├── reads_txt.h │ │ │ ├── sam.cpp │ │ │ └── sam.h │ │ ├── sequence │ │ │ ├── CMakeLists.txt │ │ │ ├── sequence.h │ │ │ ├── sequence_access.h │ │ │ ├── sequence_bam.cpp │ │ │ ├── sequence_bam.h │ │ │ ├── sequence_encoder.cpp │ │ │ ├── sequence_encoder.h │ │ │ ├── sequence_fasta.cpp │ │ │ ├── sequence_fasta.h │ │ │ ├── sequence_fastq.cpp │ │ │ ├── sequence_fastq.h │ │ │ ├── sequence_mmap.cpp │ │ │ ├── sequence_mmap.h │ │ │ ├── sequence_pac.cpp │ │ │ ├── sequence_pac.h │ │ │ ├── sequence_priv.cpp │ │ │ ├── sequence_priv.h │ │ │ ├── sequence_sam.cpp │ │ │ ├── sequence_sam.h │ │ │ ├── sequence_traits.h │ │ │ ├── sequence_txt.cpp │ │ │ └── sequence_txt.h │ │ ├── utils.h │ │ ├── vcf.cpp │ │ └── vcf.h │ ├── mainpage.dox │ ├── nvbio.dox │ ├── qgram │ │ ├── filter.h │ │ ├── filter_inl.h │ │ ├── qgram.h │ │ ├── qgram_inl.h │ │ ├── qgroup.h │ │ └── qgroup_inl.h │ ├── strings │ │ ├── CMakeLists.txt │ │ ├── alphabet.h │ │ ├── alphabet_inl.h │ │ ├── infix.h │ │ ├── prefetcher.h │ │ ├── prefix.h │ │ ├── seeds.h │ │ ├── seeds_inl.h │ │ ├── string.h │ │ ├── string_iterator.h │ │ ├── string_iterator_inl.h │ │ ├── string_set.h │ │ ├── string_set_inl.h │ │ ├── string_set_transform.h │ │ ├── string_traits.h │ │ ├── suffix.h │ │ ├── vectorized_string.h │ │ ├── wavelet_tree.h │ │ └── wavelet_tree_inl.h │ ├── sufsort │ │ ├── CMakeLists.txt │ │ ├── blockwise_sufsort.h │ │ ├── bwte.h │ │ ├── bwte_inl.h │ │ ├── compression_sort.h │ │ ├── dcs.h │ │ ├── dcs_inl.h │ │ ├── file_bwt.cu │ │ ├── file_bwt.h │ │ ├── file_bwt_bgz.cu │ │ ├── file_bwt_bgz.h │ │ ├── file_bwt_lz4.cu │ │ ├── file_bwt_lz4.h │ │ ├── prefix_doubling_sufsort.h │ │ ├── sufsort.h │ │ ├── sufsort_bucketing.h │ │ ├── sufsort_inl.h │ │ ├── sufsort_priv.cu │ │ ├── sufsort_priv.h │ │ └── sufsort_utils.h │ └── trie │ │ ├── CMakeLists.txt │ │ ├── sorted_dictionary.h │ │ ├── sorted_dictionary_inl.h │ │ ├── suffix_trie.h │ │ └── suffix_trie_inl.h ├── nvmem │ ├── CMakeLists.txt │ ├── align.cu │ ├── align.h │ ├── build-chains.cu │ ├── build-chains.h │ ├── filter-chains.cu │ ├── filter-chains.h │ ├── mem-search.cu │ ├── mem-search.h │ ├── nvmem.cu │ ├── options.cpp │ ├── options.h │ ├── pipeline.h │ ├── util.cu │ └── util.h ├── prototypes │ ├── bamsort │ │ ├── CMakeLists.txt │ │ ├── bam_io.cu │ │ ├── bam_io.h │ │ ├── bam_sort.cu │ │ ├── bam_sort.h │ │ └── bamsort_types.h │ └── psa │ │ ├── README.md │ │ ├── bin │ │ └── .gitignore │ │ ├── build │ │ └── .gitignore │ │ ├── data │ │ ├── 1K-1000nt.prof │ │ ├── 1K-100nt.prof │ │ ├── 1K-200nt.prof │ │ ├── 1K-400nt.prof │ │ ├── 1K-600nt.prof │ │ └── 1K-800nt.prof │ │ ├── docs │ │ ├── analysis.txt │ │ └── profile.txt │ │ ├── include │ │ ├── psa_alignments.h │ │ ├── psa_commons.h │ │ ├── psa_errors.h │ │ ├── psa_pairwise.h │ │ ├── psa_pairwise_gpu.h │ │ ├── psa_profile.h │ │ ├── psa_regions.h │ │ ├── psa_sequences.h │ │ ├── psa_time.h │ │ └── simd_functions.h │ │ ├── makefile │ │ ├── src │ │ ├── gotoh │ │ │ ├── misc │ │ │ │ ├── psa_swfarrar_gpu.c │ │ │ │ ├── psa_swfarrar_gpu.cu │ │ │ │ ├── psa_swgotoh_registers_16b_gpu.cu │ │ │ │ ├── psa_swgotoh_registers_32b_gpu.cu │ │ │ │ ├── psa_swgotoh_registers_tilling_2D_gpu.cu │ │ │ │ ├── psa_swwozniak_gpu.c │ │ │ │ └── psa_swwozniak_gpu.cu │ │ │ ├── psa_swgotoh_2b_gpu.c │ │ │ ├── psa_swgotoh_2b_integer_gpu.cu │ │ │ ├── psa_swgotoh_2b_mixed_gpu.cu │ │ │ ├── psa_swgotoh_2b_mixedsim_gpu.cu │ │ │ ├── psa_swgotoh_2b_video_gpu.cu │ │ │ ├── psa_swgotoh_cpu.c │ │ │ ├── psa_swgotoh_ref_2b_gpu.c │ │ │ └── psa_swgotoh_ref_2b_integer_gpu.cu │ │ ├── psa_alignments.c │ │ ├── psa_errors.c │ │ ├── psa_profile.c │ │ ├── psa_regions.c │ │ ├── psa_sequences.c │ │ └── psa_time.c │ │ └── tools │ │ ├── benchmark.c │ │ ├── checksum.c │ │ └── genRegions.c ├── sufsort-test │ ├── CMakeLists.txt │ └── sufsort_test.cu └── sw-benchmark │ ├── CMakeLists.txt │ └── sw-benchmark.cu └── pybind11 ├── .appveyor.yml ├── .clang-format ├── .clang-tidy ├── .cmake-format.yaml ├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug-report.md │ ├── config.yml │ ├── feature-request.md │ └── question.md ├── dependabot.yml ├── labeler.yml ├── labeler_merged.yml ├── pull_request_template.md └── workflows │ ├── ci.yml │ ├── configure.yml │ ├── format.yml │ ├── labeler.yml │ └── pip.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CMakeLists.txt ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Doxyfile ├── _static │ └── theme_overrides.css ├── advanced │ ├── cast │ │ ├── chrono.rst │ │ ├── custom.rst │ │ ├── eigen.rst │ │ ├── functional.rst │ │ ├── index.rst │ │ ├── overview.rst │ │ ├── stl.rst │ │ └── strings.rst │ ├── classes.rst │ ├── embedding.rst │ ├── exceptions.rst │ ├── functions.rst │ ├── misc.rst │ ├── pycpp │ │ ├── index.rst │ │ ├── numpy.rst │ │ ├── object.rst │ │ └── utilities.rst │ └── smart_ptrs.rst ├── basics.rst ├── benchmark.py ├── benchmark.rst ├── changelog.rst ├── classes.rst ├── cmake │ └── index.rst ├── compiling.rst ├── conf.py ├── faq.rst ├── index.rst ├── installing.rst ├── limitations.rst ├── pybind11-logo.png ├── pybind11_vs_boost_python1.png ├── pybind11_vs_boost_python1.svg ├── pybind11_vs_boost_python2.png ├── pybind11_vs_boost_python2.svg ├── reference.rst ├── release.rst ├── requirements.txt └── upgrade.rst ├── include └── pybind11 │ ├── attr.h │ ├── buffer_info.h │ ├── cast.h │ ├── chrono.h │ ├── common.h │ ├── complex.h │ ├── detail │ ├── class.h │ ├── common.h │ ├── descr.h │ ├── init.h │ ├── internals.h │ ├── type_caster_base.h │ └── typeid.h │ ├── eigen.h │ ├── embed.h │ ├── eval.h │ ├── functional.h │ ├── gil.h │ ├── iostream.h │ ├── numpy.h │ ├── operators.h │ ├── options.h │ ├── pybind11.h │ ├── pytypes.h │ ├── stl.h │ └── stl_bind.h ├── pybind11 ├── __init__.py ├── __main__.py ├── _version.py ├── _version.pyi ├── commands.py ├── py.typed ├── setup_helpers.py └── setup_helpers.pyi ├── pyproject.toml ├── setup.cfg ├── setup.py ├── tests ├── CMakeLists.txt ├── conftest.py ├── constructor_stats.h ├── cross_module_gil_utils.cpp ├── env.py ├── extra_python_package │ ├── pytest.ini │ └── test_files.py ├── extra_setuptools │ ├── pytest.ini │ └── test_setuphelper.py ├── local_bindings.h ├── object.h ├── pybind11_cross_module_tests.cpp ├── pybind11_tests.cpp ├── pybind11_tests.h ├── pytest.ini ├── requirements.txt ├── test_async.cpp ├── test_async.py ├── test_buffers.cpp ├── test_buffers.py ├── test_builtin_casters.cpp ├── test_builtin_casters.py ├── test_call_policies.cpp ├── test_call_policies.py ├── test_callbacks.cpp ├── test_callbacks.py ├── test_chrono.cpp ├── test_chrono.py ├── test_class.cpp ├── test_class.py ├── test_cmake_build │ ├── CMakeLists.txt │ ├── embed.cpp │ ├── installed_embed │ │ └── CMakeLists.txt │ ├── installed_function │ │ └── CMakeLists.txt │ ├── installed_target │ │ └── CMakeLists.txt │ ├── main.cpp │ ├── subdirectory_embed │ │ └── CMakeLists.txt │ ├── subdirectory_function │ │ └── CMakeLists.txt │ ├── subdirectory_target │ │ └── CMakeLists.txt │ └── test.py ├── test_constants_and_functions.cpp ├── test_constants_and_functions.py ├── test_copy_move.cpp ├── test_copy_move.py ├── test_custom_type_casters.cpp ├── test_custom_type_casters.py ├── test_docstring_options.cpp ├── test_docstring_options.py ├── test_eigen.cpp ├── test_eigen.py ├── test_embed │ ├── CMakeLists.txt │ ├── catch.cpp │ ├── external_module.cpp │ ├── test_interpreter.cpp │ └── test_interpreter.py ├── test_enum.cpp ├── test_enum.py ├── test_eval.cpp ├── test_eval.py ├── test_eval_call.py ├── test_exceptions.cpp ├── test_exceptions.py ├── test_factory_constructors.cpp ├── test_factory_constructors.py ├── test_gil_scoped.cpp ├── test_gil_scoped.py ├── test_iostream.cpp ├── test_iostream.py ├── test_kwargs_and_defaults.cpp ├── test_kwargs_and_defaults.py ├── test_local_bindings.cpp ├── test_local_bindings.py ├── test_methods_and_attributes.cpp ├── test_methods_and_attributes.py ├── test_modules.cpp ├── test_modules.py ├── test_multiple_inheritance.cpp ├── test_multiple_inheritance.py ├── test_numpy_array.cpp ├── test_numpy_array.py ├── test_numpy_dtypes.cpp ├── test_numpy_dtypes.py ├── test_numpy_vectorize.cpp ├── test_numpy_vectorize.py ├── test_opaque_types.cpp ├── test_opaque_types.py ├── test_operator_overloading.cpp ├── test_operator_overloading.py ├── test_pickling.cpp ├── test_pickling.py ├── test_pytypes.cpp ├── test_pytypes.py ├── test_sequences_and_iterators.cpp ├── test_sequences_and_iterators.py ├── test_smart_ptr.cpp ├── test_smart_ptr.py ├── test_stl.cpp ├── test_stl.py ├── test_stl_binders.cpp ├── test_stl_binders.py ├── test_tagbased_polymorphic.cpp ├── test_tagbased_polymorphic.py ├── test_union.cpp ├── test_union.py ├── test_virtual_functions.cpp ├── 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