sequenzo 0.1.18__cp311-cp311-win_amd64.whl → 0.1.20__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_BLOCK_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_BLOCK_H
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-
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- namespace Eigen {
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- namespace internal {
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-
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- // -------------------------------------------------------------------------- //
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- // Forward declarations for templates defined below.
16
- template <typename Scalar, typename IndexType, int NumDims, int Layout>
17
- class TensorBlockIO;
18
-
19
- // -------------------------------------------------------------------------- //
20
- // Helper function to compute strides for densely stored buffer of given
21
- // dimensions.
22
-
23
- // TODO(ezhulenev): We compute strides 1000 times in different evaluators, use
24
- // this function instead everywhere.
25
- template <int Layout, typename IndexType, int NumDims>
26
- EIGEN_ALWAYS_INLINE DSizes<IndexType, NumDims> strides(
27
- const DSizes<IndexType, NumDims>& dimensions) {
28
- DSizes<IndexType, NumDims> strides;
29
- if (NumDims == 0) return strides;
30
-
31
- // TODO(ezhulenev): Use templates to unroll this loop (similar to
32
- // h_array_reduce in CXX11meta.h)? Benchmark it.
33
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
34
- strides[0] = 1;
35
- for (int i = 1; i < NumDims; ++i) {
36
- strides[i] = strides[i - 1] * dimensions[i - 1];
37
- }
38
- } else {
39
- strides[NumDims - 1] = 1;
40
- for (int i = NumDims - 2; i >= 0; --i) {
41
- strides[i] = strides[i + 1] * dimensions[i + 1];
42
- }
43
- }
44
-
45
- return strides;
46
- }
47
-
48
- template <int Layout, typename IndexType, size_t NumDims>
49
- EIGEN_ALWAYS_INLINE DSizes<IndexType, NumDims> strides(
50
- const Eigen::array<IndexType, NumDims>& dimensions) {
51
- return strides<Layout>(DSizes<IndexType, NumDims>(dimensions));
52
- }
53
-
54
- template <int Layout, std::ptrdiff_t... Indices>
55
- EIGEN_STRONG_INLINE DSizes<std::ptrdiff_t, sizeof...(Indices)> strides(
56
- const Sizes<Indices...>& sizes) {
57
- return strides<Layout>(DSizes<std::ptrdiff_t, sizeof...(Indices)>(sizes));
58
- }
59
-
60
- // -------------------------------------------------------------------------- //
61
-
62
- // Tensor block shape type defines what are the shape preference for the blocks
63
- // extracted from the larger tensor.
64
- //
65
- // Example: blocks of 100 elements from the large 100x100 tensor:
66
- // - tensor: 100x100
67
- // - target_block_size: 100
68
- //
69
- // TensorBlockShapeType:
70
- // - kUniformAllDims: 100 blocks of size 10x10
71
- // - kSkewedInnerDims: 100 blocks of size 100x1 (or 1x100 depending on a column
72
- // or row major layout)
73
- enum class TensorBlockShapeType { kUniformAllDims, kSkewedInnerDims };
74
-
75
- struct TensorBlockResourceRequirements {
76
- TensorBlockShapeType shape_type; // target block shape
77
- size_t size; // target block size
78
- TensorOpCost cost_per_coeff; // cost of computing a single block element
79
-
80
- #ifdef EIGEN_HIPCC
81
- // For HIPCC, we need to explicitly declare as a "device fun", the constructor
82
- // which is implicitly invoked in the "merge" / "any" routines. else HIPCC
83
- // errors out complaining about the lack of a matching constructor
84
- EIGEN_DEVICE_FUNC
85
- TensorBlockResourceRequirements(TensorBlockShapeType shape_type_, size_t size_,
86
- TensorOpCost cost_)
87
- : shape_type(shape_type_), size(size_), cost_per_coeff(cost_)
88
- {}
89
- #endif
90
-
91
- template <typename Scalar>
92
- EIGEN_DEVICE_FUNC static TensorBlockResourceRequirements withShapeAndSize(
93
- TensorBlockShapeType shape_type, size_t size_in_bytes,
94
- TensorOpCost cost) {
95
- const size_t size = numext::maxi(size_t(1), size_in_bytes / sizeof(Scalar));
96
- return {shape_type, size, cost};
97
- }
98
-
99
- template <typename Scalar>
100
- EIGEN_DEVICE_FUNC static TensorBlockResourceRequirements withShapeAndSize(
101
- TensorBlockShapeType shape_type, size_t size_in_bytes) {
102
- // This default cost per coefficient is valid for most materialized tensor
103
- // block evaluation implementations, because they typically just read
104
- // coefficients from the underlying tensor storage, and write to the tensor
105
- // block buffer (scratch or destination memory, reads and writes have linear
106
- // access pattern). We ignore the fixed cost of block evaluation, because in
107
- // practice it should negligible.
108
- //
109
- // Lazy block evaluation adds the cost of calling a functor for each
110
- // coefficient.
111
- //
112
- // All non-trivial block evaluation implementations must provide their own
113
- // cost approximation (e.g. shuffling inner dimension has a much higher cost
114
- // because it reads memory randomly, although the total number of moved
115
- // bytes is the same).
116
- return withShapeAndSize<Scalar>(shape_type, size_in_bytes,
117
- {/*bytes_loaded=*/sizeof(Scalar),
118
- /*bytes_stored=*/sizeof(Scalar),
119
- /*compute_cycles=*/0});
120
- }
121
-
122
- template <typename Scalar>
123
- EIGEN_DEVICE_FUNC static TensorBlockResourceRequirements skewed(
124
- size_t size_in_bytes) {
125
- return withShapeAndSize<Scalar>(TensorBlockShapeType::kSkewedInnerDims,
126
- size_in_bytes);
127
- }
128
-
129
- template <typename Scalar>
130
- EIGEN_DEVICE_FUNC static TensorBlockResourceRequirements uniform(
131
- size_t size_in_bytes) {
132
- return withShapeAndSize<Scalar>(TensorBlockShapeType::kUniformAllDims,
133
- size_in_bytes);
134
- }
135
-
136
- EIGEN_DEVICE_FUNC
137
- static EIGEN_STRONG_INLINE TensorBlockResourceRequirements
138
- merge(const TensorBlockResourceRequirements& lhs,
139
- const TensorBlockResourceRequirements& rhs) {
140
- return {merge(lhs.shape_type, rhs.shape_type), // shape_type
141
- merge(lhs.size, rhs.size), // size
142
- merge(lhs.cost_per_coeff, rhs.cost_per_coeff)}; // cost_per_coeff
143
- }
144
-
145
- EIGEN_DEVICE_FUNC TensorBlockResourceRequirements& addCostPerCoeff(
146
- TensorOpCost cost) {
147
- cost_per_coeff += cost;
148
- return *this;
149
- }
150
-
151
- // This is a resource requirement that should be returned from expressions
152
- // that do not have any block evaluation preference (e.g. default tensor
153
- // expression with raw buffer access).
154
- EIGEN_DEVICE_FUNC
155
- static EIGEN_STRONG_INLINE TensorBlockResourceRequirements any() {
156
- return {TensorBlockShapeType::kUniformAllDims, 1, {0, 0, 0}};
157
- }
158
-
159
- private:
160
- using Requirements = TensorBlockResourceRequirements;
161
-
162
- EIGEN_DEVICE_FUNC
163
- static EIGEN_STRONG_INLINE size_t merge(size_t lhs_size, size_t rhs_size) {
164
- return numext::maxi(lhs_size, rhs_size);
165
- }
166
-
167
- EIGEN_DEVICE_FUNC
168
- static EIGEN_STRONG_INLINE TensorBlockShapeType
169
- merge(TensorBlockShapeType lhs, TensorBlockShapeType rhs) {
170
- return (lhs == TensorBlockShapeType::kSkewedInnerDims ||
171
- rhs == TensorBlockShapeType::kSkewedInnerDims)
172
- ? TensorBlockShapeType::kSkewedInnerDims
173
- : TensorBlockShapeType::kUniformAllDims;
174
- }
175
-
176
- EIGEN_DEVICE_FUNC
177
- static EIGEN_STRONG_INLINE TensorOpCost merge(TensorOpCost lhs_cost,
178
- TensorOpCost rhs_cost) {
179
- return lhs_cost + rhs_cost;
180
- }
181
- };
182
-
183
- // -------------------------------------------------------------------------- //
184
- // TensorBlockDescriptor specifies a block offset within a tensor and the block
185
- // sizes along each of the tensor dimensions.
186
-
187
- template <int NumDims, typename IndexType = Eigen::Index>
188
- class TensorBlockDescriptor {
189
- public:
190
- typedef DSizes<IndexType, NumDims> Dimensions;
191
-
192
- // If we evaluate a Tensor assignment, and expression on the left, already has
193
- // a memory buffer, then we might do performance optimization, and evaluate
194
- // the root expression directly into the final output memory. Some time it's
195
- // possible to reuse it for materializing subexpressions inside an expression
196
- // tree, to to avoid dynamic memory allocation.
197
- //
198
- // The pointer type of the underlying storage is erased, because passing
199
- // Scalar type through all the expression evaluation layers is way too many
200
- // templates. In practice destination buffer type should always match the
201
- // evaluated expression scalar type.
202
- class DestinationBuffer {
203
- public:
204
- enum DestinationBufferKind : int {
205
- // The above explicit specification of "int" as the enum basetype is
206
- // needed to get around a HIPCC link error ("the field type is not
207
- // amp-compatible")
208
- // which is issued for class members with the enum type.
209
- // TODO(rocm):
210
- // remove the "int" basetype once HIPCC has been fixed to not error out
211
- // in the above scenario.
212
-
213
- // Destination buffer is not defined (`m_data` == nullptr).
214
- kEmpty,
215
-
216
- // Tensor block defined by an owning tensor block descriptor can fit
217
- // contiguously into the destination buffer. In this case it's safe to
218
- // materialize tensor block in the destination buffer, wrap it in a
219
- // TensorMap, and use to build Eigen expression on top of it.
220
- kContiguous,
221
-
222
- // Destination buffer strides do not match strides of the contiguously
223
- // stored block, and it's impossible to define a TensorMap over this
224
- // buffer. However if we are evaluating a root of an expression tree, we
225
- // still can materialize an output into this destination, because we can
226
- // guarantee that no one will ever access it through block API.
227
- //
228
- // In theory it is possible to build valid TensorStriding<TensorMap>
229
- // expression on top of this destination buffer, however it has
230
- // inefficient coeff/packet access, and defeats the purpose of fast block
231
- // evaluation API.
232
- kStrided
233
- };
234
-
235
- template <typename Scalar>
236
- Scalar* data() const {
237
- eigen_assert(m_data_type_size == sizeof(Scalar));
238
- return static_cast<Scalar*>(m_data);
239
- }
240
-
241
- const Dimensions& strides() const { return m_strides; }
242
- const DestinationBufferKind& kind() const { return m_kind; }
243
-
244
- private:
245
- friend class TensorBlockDescriptor;
246
-
247
- DestinationBuffer() : m_data(NULL), m_data_type_size(0), m_kind(kEmpty) {}
248
-
249
- template <typename Scalar>
250
- DestinationBuffer(Scalar* data, const Dimensions& strides,
251
- DestinationBufferKind kind)
252
- : m_data(static_cast<void*>(data)),
253
- m_data_type_size(sizeof(Scalar)),
254
- m_strides(strides),
255
- m_kind(kind) {}
256
-
257
- template <int Layout, typename Scalar>
258
- static DestinationBuffer make(const TensorBlockDescriptor& desc,
259
- Scalar* data, const Dimensions& strides) {
260
- return DestinationBuffer(data, strides, kind<Layout>(desc, strides));
261
- }
262
-
263
- template <int Layout>
264
- static DestinationBufferKind kind(const TensorBlockDescriptor& desc,
265
- const Dimensions& strides) {
266
- const Dimensions& desc_dims = desc.dimensions();
267
- const Dimensions& desc_strides = internal::strides<Layout>(desc_dims);
268
- for (int i = 0; i < NumDims; ++i) {
269
- if (desc_dims[i] == 1) continue;
270
- if (desc_strides[i] != strides[i]) return kStrided;
271
- }
272
- return kContiguous;
273
- }
274
-
275
- // Storage pointer is type erased, to reduce template bloat, but we still
276
- // keep the size of the underlying element type for error checking.
277
- void* m_data;
278
- size_t m_data_type_size;
279
-
280
- // Destination buffer dimensions always match the dimensions of a tensor
281
- // block descriptor it belongs to, however strides might be different.
282
- Dimensions m_strides;
283
-
284
- DestinationBufferKind m_kind;
285
- };
286
-
287
- TensorBlockDescriptor(const IndexType offset, const Dimensions& dimensions,
288
- const DestinationBuffer& destination)
289
- : m_offset(offset),
290
- m_dimensions(dimensions),
291
- m_destination(destination) {}
292
-
293
- TensorBlockDescriptor(const IndexType offset, const Dimensions& dimensions)
294
- : m_offset(offset),
295
- m_dimensions(dimensions),
296
- m_destination(DestinationBuffer()) {}
297
-
298
- IndexType offset() const { return m_offset; }
299
- const Dimensions& dimensions() const { return m_dimensions; }
300
- IndexType dimension(int index) const { return m_dimensions[index]; }
301
- IndexType size() const { return array_prod<IndexType>(m_dimensions); }
302
-
303
- const DestinationBuffer& destination() const { return m_destination; }
304
-
305
- template <int Layout, typename Scalar>
306
- void AddDestinationBuffer(Scalar* dst_base, const Dimensions& dst_strides) {
307
- eigen_assert(dst_base != NULL);
308
- m_destination =
309
- DestinationBuffer::template make<Layout>(*this, dst_base, dst_strides);
310
- }
311
-
312
- template <int Layout, typename Scalar, typename DstStridesIndexType>
313
- void AddDestinationBuffer(
314
- Scalar* dst_base,
315
- const DSizes<DstStridesIndexType, NumDims>& dst_strides) {
316
- // DSizes constructor will do index type promotion if it's safe.
317
- AddDestinationBuffer<Layout>(dst_base, Dimensions(dst_strides));
318
- }
319
-
320
- TensorBlockDescriptor& DropDestinationBuffer() {
321
- m_destination.m_data = NULL;
322
- m_destination.m_kind = DestinationBuffer::kEmpty;
323
- return *this;
324
- }
325
-
326
- bool HasDestinationBuffer() const {
327
- return m_destination.kind() != DestinationBuffer::kEmpty;
328
- }
329
-
330
- // Returns a copy of `*this` with updated offset.
331
- TensorBlockDescriptor WithOffset(IndexType offset) const {
332
- return TensorBlockDescriptor(offset, m_dimensions, m_destination);
333
- }
334
-
335
- private:
336
- // Offset and dimensions are immutable after construction. Block descriptor
337
- // can only be mutated by adding or dropping destination.
338
- const IndexType m_offset;
339
- const Dimensions m_dimensions;
340
- DestinationBuffer m_destination;
341
- };
342
-
343
- // -------------------------------------------------------------------------- //
344
- // TensorBlockMapper is responsible for iterating over the blocks of a tensor.
345
-
346
- template <int NumDims, int Layout, typename IndexType = Eigen::Index>
347
- class TensorBlockMapper {
348
- typedef TensorBlockDescriptor<NumDims, IndexType> BlockDescriptor;
349
-
350
- public:
351
- typedef DSizes<IndexType, NumDims> Dimensions;
352
-
353
- TensorBlockMapper() = default;
354
- TensorBlockMapper(const DSizes<IndexType, NumDims>& dimensions,
355
- const TensorBlockResourceRequirements& requirements)
356
- : m_tensor_dimensions(dimensions), m_requirements(requirements) {
357
- // Compute block dimensions and the total number of blocks.
358
- InitializeBlockDimensions();
359
- }
360
-
361
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE IndexType blockCount() const {
362
- return m_total_block_count;
363
- }
364
-
365
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE IndexType blockTotalSize() const {
366
- return m_block_dimensions.TotalSize();
367
- }
368
-
369
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const DSizes<IndexType, NumDims>&
370
- blockDimensions() const {
371
- return m_block_dimensions;
372
- }
373
-
374
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE BlockDescriptor
375
- blockDescriptor(IndexType block_index) const {
376
- static const bool isColMajor = Layout == static_cast<int>(ColMajor);
377
-
378
- IndexType offset = 0;
379
- DSizes<IndexType, NumDims> dimensions;
380
-
381
- if (NumDims == 0) return BlockDescriptor(offset, dimensions);
382
-
383
- // Iterate outer -> inner dimensions.
384
- for (int i = NumDims - 1; i >= 0; --i) {
385
- const int dim = isColMajor ? i : NumDims - i - 1;
386
-
387
- const IndexType idx = block_index / m_block_strides[dim];
388
- block_index -= idx * m_block_strides[dim];
389
-
390
- const IndexType coord = idx * m_block_dimensions[dim];
391
- dimensions[dim] = numext::mini(m_tensor_dimensions[dim] - coord,
392
- m_block_dimensions[dim]);
393
- offset += coord * m_tensor_strides[dim];
394
- }
395
-
396
- return {offset, dimensions};
397
- }
398
-
399
- private:
400
- void InitializeBlockDimensions() {
401
- // Requested block shape and size.
402
- const TensorBlockShapeType shape_type = m_requirements.shape_type;
403
- IndexType target_block_size =
404
- numext::maxi<IndexType>(1, static_cast<IndexType>(m_requirements.size));
405
-
406
- IndexType tensor_size = m_tensor_dimensions.TotalSize();
407
-
408
- // Corner case: one of the dimensions is zero. Logic below is too complex
409
- // to handle this case on a general basis, just use unit block size.
410
- // Note: we must not yield blocks with zero dimensions (recipe for
411
- // overflows/underflows, divisions by zero and NaNs later).
412
- if (tensor_size == 0) {
413
- for (int i = 0; i < NumDims; ++i) {
414
- m_block_dimensions[i] = 1;
415
- }
416
- m_total_block_count = 0;
417
- return;
418
- }
419
-
420
- // If tensor fits into a target block size, evaluate it as a single block.
421
- if (tensor_size <= target_block_size) {
422
- m_block_dimensions = m_tensor_dimensions;
423
- m_total_block_count = 1;
424
- // The only valid block index is `0`, and in this case we do not need
425
- // to compute real strides for tensor or blocks (see blockDescriptor).
426
- for (int i = 0; i < NumDims; ++i) {
427
- m_tensor_strides[i] = 0;
428
- m_block_strides[i] = 1;
429
- }
430
- return;
431
- }
432
-
433
- static const bool isColMajor = Layout == static_cast<int>(ColMajor);
434
-
435
- // Block shape skewed towards inner dimension.
436
- if (shape_type == TensorBlockShapeType::kSkewedInnerDims) {
437
- IndexType coeff_to_allocate = target_block_size;
438
-
439
- for (int i = 0; i < NumDims; ++i) {
440
- const int dim = isColMajor ? i : NumDims - i - 1;
441
- m_block_dimensions[dim] =
442
- numext::mini(coeff_to_allocate, m_tensor_dimensions[dim]);
443
- coeff_to_allocate = divup(
444
- coeff_to_allocate,
445
- numext::maxi(static_cast<IndexType>(1), m_block_dimensions[dim]));
446
- }
447
- eigen_assert(coeff_to_allocate == 1);
448
-
449
- } else if (shape_type == TensorBlockShapeType::kUniformAllDims) {
450
- // Tensor will not fit within 'target_block_size' budget: calculate tensor
451
- // block dimension sizes based on "square" dimension size target.
452
- const IndexType dim_size_target = convert_index<IndexType>(
453
- std::pow(static_cast<float>(target_block_size),
454
- 1.0f / static_cast<float>(m_block_dimensions.rank())));
455
-
456
- for (int i = 0; i < NumDims; ++i) {
457
- // TODO(andydavis) Adjust the inner most 'block_dim_size' to make it
458
- // a multiple of the packet size. Note that reducing
459
- // 'block_dim_size' in this manner can increase the number of
460
- // blocks, and so will amplify any per-block overhead.
461
- m_block_dimensions[i] =
462
- numext::mini(dim_size_target, m_tensor_dimensions[i]);
463
- }
464
-
465
- // Add any un-allocated coefficients to inner dimension(s).
466
- IndexType total_size = m_block_dimensions.TotalSize();
467
- for (int i = 0; i < NumDims; ++i) {
468
- const int dim = isColMajor ? i : NumDims - i - 1;
469
-
470
- if (m_block_dimensions[dim] < m_tensor_dimensions[dim]) {
471
- const IndexType total_size_other_dims =
472
- total_size / m_block_dimensions[dim];
473
- const IndexType alloc_avail =
474
- divup<IndexType>(target_block_size, total_size_other_dims);
475
- if (alloc_avail == m_block_dimensions[dim]) {
476
- // Insufficient excess coefficients to allocate.
477
- break;
478
- }
479
- m_block_dimensions[dim] =
480
- numext::mini(m_tensor_dimensions[dim], alloc_avail);
481
- total_size = total_size_other_dims * m_block_dimensions[dim];
482
- }
483
- }
484
-
485
- } else {
486
- eigen_assert(false); // unknown block shape
487
- }
488
-
489
- eigen_assert(m_block_dimensions.TotalSize() >=
490
- numext::mini<IndexType>(target_block_size,
491
- m_tensor_dimensions.TotalSize()));
492
-
493
- // Calculate block counts by dimension and total block count.
494
- DSizes<IndexType, NumDims> block_count;
495
- for (int i = 0; i < NumDims; ++i) {
496
- block_count[i] = divup(m_tensor_dimensions[i], m_block_dimensions[i]);
497
- }
498
- m_total_block_count = array_prod(block_count);
499
-
500
- // Calculate block strides (used for enumerating blocks).
501
- m_tensor_strides = strides<Layout>(m_tensor_dimensions);
502
- m_block_strides = strides<Layout>(block_count);
503
- }
504
-
505
- DSizes<IndexType, NumDims> m_tensor_dimensions;
506
- TensorBlockResourceRequirements m_requirements;
507
-
508
- DSizes<IndexType, NumDims> m_block_dimensions;
509
- IndexType m_total_block_count;
510
-
511
- DSizes<IndexType, NumDims> m_tensor_strides;
512
- DSizes<IndexType, NumDims> m_block_strides;
513
- };
514
-
515
- // -------------------------------------------------------------------------- //
516
- // TensorBlockScratchAllocator is responsible for allocating temporary buffers
517
- // for block evaluation (output or input block materialization). Given that
518
- // Eigen expression traversal order is deterministic, all temporary allocations
519
- // are happening in the same order, and usually have exactly the same size.
520
- // Scratch allocator keeps a trace of all dynamic allocations, and after the
521
- // first block evaluation is completed, we should be able to reuse all the
522
- // temporary buffers for the next block evaluation.
523
-
524
- template <typename Device>
525
- class TensorBlockScratchAllocator {
526
- public:
527
- explicit TensorBlockScratchAllocator(const Device& device)
528
- : m_device(device), m_allocation_index(0) {}
529
-
530
- ~TensorBlockScratchAllocator() {
531
- for (size_t i = 0; i < m_allocations.size(); ++i) {
532
- m_device.deallocate(m_allocations[i].ptr);
533
- }
534
- }
535
-
536
- void* allocate(size_t size) {
537
- // TODO(ezhulenev): Remove when replaced with inlined vector.
538
- if (m_allocations.capacity() == 0) m_allocations.reserve(8);
539
-
540
- // Check if we already have an existing allocation att current index.
541
- const int num_allocations = static_cast<int>(m_allocations.size());
542
- const bool has_allocation = m_allocation_index < num_allocations;
543
-
544
- // Allocation index can't be larger than the number of allocations.
545
- eigen_assert(m_allocation_index <= num_allocations);
546
-
547
- // If we have existing allocation, and its size is larger or equal to
548
- // requested size, we do nothing.
549
-
550
- // If current allocation can't fit requested size, we deallocate it, and
551
- // replace with a larger allocation.
552
- if (has_allocation && m_allocations[m_allocation_index].size < size) {
553
- m_device.deallocate(m_allocations[m_allocation_index].ptr);
554
- m_allocations[m_allocation_index].ptr = m_device.allocate(size);
555
- m_allocations[m_allocation_index].size = size;
556
- }
557
-
558
- // Make a new allocation if we don't have and existing one.
559
- if (!has_allocation) {
560
- Allocation allocation;
561
- allocation.ptr = m_device.allocate(size);
562
- allocation.size = size;
563
- m_allocations.push_back(allocation);
564
- }
565
-
566
- eigen_assert(m_allocations[m_allocation_index].ptr != NULL);
567
- eigen_assert(m_allocations[m_allocation_index].size >= size);
568
-
569
- return m_allocations[m_allocation_index++].ptr;
570
- }
571
-
572
- void reset() { m_allocation_index = 0; }
573
-
574
- private:
575
- struct Allocation {
576
- void* ptr;
577
- size_t size;
578
- };
579
-
580
- const Device& m_device;
581
- int m_allocation_index;
582
- // TODO(ezhulenev): This should be an inlined vector.
583
- std::vector<Allocation> m_allocations;
584
- };
585
-
586
- // -------------------------------------------------------------------------- //
587
- // TensorBlockKind represents all possible block kinds, that can be produced by
588
- // TensorEvaluator::evalBlock function.
589
- enum TensorBlockKind {
590
- // Tensor block that is a lazy expression that must be assigned to a
591
- // destination using TensorBlockAssign.
592
- kExpr,
593
-
594
- // Tensor block that is a view into a memory buffer owned by an underlying
595
- // Tensor expression (e.g. it can be a view into a Tensor buffer).
596
- kView,
597
-
598
- // Tensor block that was materialized in a scratch memory buffer, allocated
599
- // with TensorBlockScratchAllocator. This block must be copied to a
600
- // destination, similar to a block of `kExpr` type.
601
- kMaterializedInScratch,
602
-
603
- // Tensor block that was materialized directly into the final output memory
604
- // buffer. For example if the left side of an assignment is a Tensor, we can
605
- // directly materialize the block in the destination memory.
606
- //
607
- // If strides in the output buffer do not match tensor block strides, the
608
- // Tensor expression will be invalid, and should not be used by
609
- // TensorBlockAssign or for constructing another block expression.
610
- kMaterializedInOutput
611
- };
612
-
613
- // -------------------------------------------------------------------------- //
614
- // TensorBlockNotImplemented should be used to defined TensorBlock typedef in
615
- // TensorEvaluators that do not support block evaluation.
616
-
617
- class TensorBlockNotImplemented {
618
- public:
619
- typedef void XprType;
620
- };
621
-
622
- // -------------------------------------------------------------------------- //
623
- // XprScalar extracts Scalar type from the Eigen expressions (if expression type
624
- // is not void). It's required to be able to define lazy block expression for
625
- // argument types, that do not support block evaluation.
626
-
627
- template <typename XprType>
628
- struct XprScalar {
629
- typedef typename XprType::Scalar type;
630
- };
631
- template <>
632
- struct XprScalar<void> {
633
- typedef void type;
634
- };
635
-
636
- // -------------------------------------------------------------------------- //
637
- // TensorMaterializedBlock is a fully evaluated block of the original tensor,
638
- // and XprType is just a TensorMap over the data. This block type is typically
639
- // used to materialize blocks of tensor expressions, that can't be efficiently
640
- // represented as lazy Tensor expressions with fast coeff/packet operations,
641
- // e.g. we materialize all broadcasts into evaluated blocks.
642
- //
643
- // TensorMaterializedBlock does not own its memory buffer, it's either a memory
644
- // buffer that backs the original expression (e.g. block is just a view into a
645
- // Tensor), or a memory buffer allocated with scratch allocator, and in this
646
- // case the scratch allocator will deallocate it at the end of block based
647
- // expression execution.
648
- //
649
- // If the block was evaluated directly into the output buffer, and strides in
650
- // the output buffer do not match block strides, the TensorMap expression will
651
- // be invalid, and should never be used in block assignment or any other tensor
652
- // expression.
653
-
654
- template <typename Scalar, int NumDims, int Layout,
655
- typename IndexType = Eigen::Index>
656
- class TensorMaterializedBlock {
657
- public:
658
- typedef DSizes<IndexType, NumDims> Dimensions;
659
- typedef TensorMap<const Tensor<Scalar, NumDims, Layout> > XprType;
660
-
661
- TensorMaterializedBlock(TensorBlockKind kind, const Scalar* data,
662
- const Dimensions& dimensions, bool valid_expr = true)
663
- : m_kind(kind),
664
- m_data(data),
665
- m_dimensions(dimensions),
666
- m_expr(m_data, m_dimensions),
667
- m_valid_expr(valid_expr) {
668
- eigen_assert(m_kind == internal::TensorBlockKind::kView ||
669
- m_kind == internal::TensorBlockKind::kMaterializedInScratch ||
670
- m_kind == internal::TensorBlockKind::kMaterializedInOutput);
671
- }
672
-
673
- TensorBlockKind kind() const { return m_kind; }
674
- // NOTE(ezhulenev): Returning XprType by value like in other block types
675
- // causes asan failures. The theory is that XprType::Nested doesn't work
676
- // properly for TensorMap.
677
- const XprType& expr() const {
678
- eigen_assert(m_valid_expr);
679
- return m_expr;
680
- }
681
- const Scalar* data() const { return m_data; }
682
- void cleanup() {}
683
-
684
- typedef internal::TensorBlockDescriptor<NumDims, IndexType> TensorBlockDesc;
685
-
686
- // TensorMaterializedBlock can be backed by different types of storage:
687
- //
688
- // (1) Contiguous block of memory allocated with scratch allocator.
689
- // (2) Contiguous block of memory reused from tensor block descriptor
690
- // destination buffer.
691
- // (3) Strided block of memory reused from tensor block descriptor
692
- // destination buffer.
693
- //
694
- class Storage {
695
- public:
696
- Scalar* data() const { return m_data; }
697
- const Dimensions& dimensions() const { return m_dimensions; }
698
- const Dimensions& strides() const { return m_strides; }
699
-
700
- TensorMaterializedBlock AsTensorMaterializedBlock() const {
701
- return TensorMaterializedBlock(
702
- m_materialized_in_output
703
- ? internal::TensorBlockKind::kMaterializedInOutput
704
- : internal::TensorBlockKind::kMaterializedInScratch,
705
- m_data, m_dimensions, !m_strided_storage);
706
- }
707
-
708
- private:
709
- friend class TensorMaterializedBlock;
710
-
711
- Storage(Scalar* data, const Dimensions& dimensions,
712
- const Dimensions& strides, bool materialized_in_output,
713
- bool strided_storage)
714
- : m_data(data),
715
- m_dimensions(dimensions),
716
- m_strides(strides),
717
- m_materialized_in_output(materialized_in_output),
718
- m_strided_storage(strided_storage) {}
719
-
720
- Scalar* m_data;
721
- Dimensions m_dimensions;
722
- Dimensions m_strides;
723
- bool m_materialized_in_output;
724
- bool m_strided_storage;
725
- };
726
-
727
- // Creates a storage for materialized block either from the block descriptor
728
- // destination buffer, or allocates a new buffer with scratch allocator.
729
- template <typename TensorBlockScratch>
730
- EIGEN_STRONG_INLINE static Storage prepareStorage(
731
- TensorBlockDesc& desc, TensorBlockScratch& scratch,
732
- bool allow_strided_storage = false) {
733
- // Try to reuse destination as an output block buffer.
734
- typedef typename TensorBlockDesc::DestinationBuffer DestinationBuffer;
735
-
736
- if (desc.destination().kind() == DestinationBuffer::kContiguous) {
737
- Scalar* buffer = desc.destination().template data<Scalar>();
738
- desc.DropDestinationBuffer();
739
- return Storage(buffer, desc.dimensions(),
740
- internal::strides<Layout>(desc.dimensions()),
741
- /*materialized_in_output=*/true,
742
- /*strided_storage=*/false);
743
-
744
- } else if (desc.destination().kind() == DestinationBuffer::kStrided &&
745
- allow_strided_storage) {
746
- Scalar* buffer = desc.destination().template data<Scalar>();
747
- desc.DropDestinationBuffer();
748
- return Storage(buffer, desc.dimensions(), desc.destination().strides(),
749
- /*materialized_in_output=*/true, /*strided_storage=*/true);
750
-
751
- } else {
752
- void* mem = scratch.allocate(desc.size() * sizeof(Scalar));
753
- return Storage(static_cast<Scalar*>(mem), desc.dimensions(),
754
- internal::strides<Layout>(desc.dimensions()),
755
- /*materialized_in_output=*/false,
756
- /*strided_storage=*/false);
757
- }
758
- }
759
-
760
- // Creates a materialized block for the given descriptor from a memory buffer.
761
- template <typename DataDimensions, typename TensorBlockScratch>
762
- EIGEN_STRONG_INLINE static TensorMaterializedBlock materialize(
763
- const Scalar* data, const DataDimensions& data_dims,
764
- TensorBlockDesc& desc, TensorBlockScratch& scratch) {
765
- eigen_assert(array_size<DataDimensions>::value == desc.dimensions().size());
766
-
767
- // If a tensor block dimensions covers a contiguous block of the underlying
768
- // memory, we can skip block buffer memory allocation, and construct a block
769
- // from existing `data` memory buffer.
770
- //
771
- // Example: (RowMajor layout)
772
- // data_dims: [11, 12, 13, 14]
773
- // desc.dimensions(): [1, 1, 3, 14]
774
- //
775
- // In this case we can construct a TensorBlock starting at
776
- // `data + desc.offset()`, with a `desc.dimensions()` block sizes.
777
- static const bool is_col_major = Layout == ColMajor;
778
-
779
- // Find out how many inner dimensions have a matching size.
780
- int num_matching_inner_dims = 0;
781
- for (int i = 0; i < NumDims; ++i) {
782
- int dim = is_col_major ? i : NumDims - i - 1;
783
- if (data_dims[dim] != desc.dimensions()[dim]) break;
784
- ++num_matching_inner_dims;
785
- }
786
-
787
- // All the outer dimensions must be of size `1`, except a single dimension
788
- // before the matching inner dimension (`3` in the example above).
789
- bool can_use_direct_access = true;
790
- for (int i = num_matching_inner_dims + 1; i < NumDims; ++i) {
791
- int dim = is_col_major ? i : NumDims - i - 1;
792
- if (desc.dimension(dim) != 1) {
793
- can_use_direct_access = false;
794
- break;
795
- }
796
- }
797
-
798
- if (can_use_direct_access) {
799
- const Scalar* block_start = data + desc.offset();
800
- return TensorMaterializedBlock(internal::TensorBlockKind::kView,
801
- block_start, desc.dimensions());
802
-
803
- } else {
804
- // Reuse destination buffer or allocate new buffer with scratch allocator.
805
- const Storage storage = prepareStorage(desc, scratch);
806
-
807
- typedef internal::TensorBlockIO<Scalar, IndexType, NumDims, Layout>
808
- TensorBlockIO;
809
- typedef typename TensorBlockIO::Dst TensorBlockIODst;
810
- typedef typename TensorBlockIO::Src TensorBlockIOSrc;
811
-
812
- TensorBlockIOSrc src(internal::strides<Layout>(Dimensions(data_dims)),
813
- data, desc.offset());
814
- TensorBlockIODst dst(storage.dimensions(), storage.strides(),
815
- storage.data());
816
-
817
- TensorBlockIO::Copy(dst, src);
818
- return storage.AsTensorMaterializedBlock();
819
- }
820
- }
821
-
822
- private:
823
- TensorBlockKind m_kind;
824
- const Scalar* m_data;
825
- Dimensions m_dimensions;
826
- XprType m_expr;
827
- bool m_valid_expr;
828
- };
829
-
830
- // -------------------------------------------------------------------------- //
831
- // TensorCwiseUnaryBlock is a lazy tensor expression block that applies UnaryOp
832
- // functor to the blocks produced by the underlying Tensor expression.
833
-
834
- template <typename UnaryOp, typename ArgTensorBlock>
835
- class TensorCwiseUnaryBlock {
836
- static const bool NoArgBlockAccess =
837
- internal::is_void<typename ArgTensorBlock::XprType>::value;
838
-
839
- public:
840
- typedef typename conditional<
841
- NoArgBlockAccess, void,
842
- TensorCwiseUnaryOp<UnaryOp, const typename ArgTensorBlock::XprType> >::
843
- type XprType;
844
-
845
- typedef typename XprScalar<XprType>::type Scalar;
846
-
847
- TensorCwiseUnaryBlock(const ArgTensorBlock& arg_block, const UnaryOp& functor)
848
- : m_arg_block(arg_block), m_functor(functor) {}
849
-
850
- TensorBlockKind kind() const { return internal::TensorBlockKind::kExpr; }
851
-
852
- XprType expr() const { return XprType(m_arg_block.expr(), m_functor); }
853
- const Scalar* data() const { return NULL; }
854
- void cleanup() { m_arg_block.cleanup(); }
855
-
856
- private:
857
- ArgTensorBlock m_arg_block;
858
- UnaryOp m_functor;
859
- };
860
-
861
- // -------------------------------------------------------------------------- //
862
- // TensorCwiseUnaryBlock is a lazy tensor expression block that applies BinaryOp
863
- // functor to the blocks produced by the underlying Tensor expression.
864
-
865
- template <typename BinaryOp, typename LhsTensorBlock, typename RhsTensorBlock>
866
- class TensorCwiseBinaryBlock {
867
- static const bool NoArgBlockAccess =
868
- internal::is_void<typename LhsTensorBlock::XprType>::value ||
869
- internal::is_void<typename RhsTensorBlock::XprType>::value;
870
-
871
- public:
872
- typedef typename conditional<
873
- NoArgBlockAccess, void,
874
- TensorCwiseBinaryOp<BinaryOp, const typename LhsTensorBlock::XprType,
875
- const typename RhsTensorBlock::XprType> >::type
876
- XprType;
877
-
878
- typedef typename XprScalar<XprType>::type Scalar;
879
-
880
- TensorCwiseBinaryBlock(const LhsTensorBlock& left_block,
881
- const RhsTensorBlock& right_block,
882
- const BinaryOp& functor)
883
- : m_left_block(left_block),
884
- m_right_block(right_block),
885
- m_functor(functor) {}
886
-
887
- TensorBlockKind kind() const { return internal::TensorBlockKind::kExpr; }
888
-
889
- XprType expr() const {
890
- return XprType(m_left_block.expr(), m_right_block.expr(), m_functor);
891
- }
892
-
893
- const Scalar* data() const { return NULL; }
894
-
895
- void cleanup() {
896
- m_left_block.cleanup();
897
- m_right_block.cleanup();
898
- }
899
-
900
- private:
901
- LhsTensorBlock m_left_block;
902
- RhsTensorBlock m_right_block;
903
- BinaryOp m_functor;
904
- };
905
-
906
- // -------------------------------------------------------------------------- //
907
- // TensorUnaryExprBlock is a lazy tensor expression block that can construct
908
- // an arbitrary tensor expression from a block of the underlying type (this is a
909
- // generalization of the TensorCwiseUnaryBlock for arbitrary expressions).
910
-
911
- template <typename BlockFactory, typename ArgTensorBlock>
912
- class TensorUnaryExprBlock {
913
- typedef typename ArgTensorBlock::XprType ArgXprType;
914
- static const bool NoArgBlockAccess = internal::is_void<ArgXprType>::value;
915
-
916
- public:
917
- typedef typename conditional<
918
- NoArgBlockAccess, void,
919
- typename BlockFactory::template XprType<ArgXprType>::type>::type XprType;
920
-
921
- typedef typename XprScalar<XprType>::type Scalar;
922
-
923
- TensorUnaryExprBlock(const ArgTensorBlock& arg_block,
924
- const BlockFactory& factory)
925
- : m_arg_block(arg_block), m_factory(factory) {}
926
-
927
- TensorBlockKind kind() const { return internal::TensorBlockKind::kExpr; }
928
- XprType expr() const { return m_factory.expr(m_arg_block.expr()); }
929
- const Scalar* data() const { return NULL; }
930
- void cleanup() { m_arg_block.cleanup(); }
931
-
932
- private:
933
- ArgTensorBlock m_arg_block;
934
- BlockFactory m_factory;
935
- };
936
-
937
- // -------------------------------------------------------------------------- //
938
- // TensorTernaryExprBlock is a lazy tensor expression block that can construct
939
- // an arbitrary tensor expression from three blocks of the underlying type.
940
-
941
- template <typename BlockFactory, typename Arg1TensorBlock,
942
- typename Arg2TensorBlock, typename Arg3TensorBlock>
943
- class TensorTernaryExprBlock {
944
- typedef typename Arg1TensorBlock::XprType Arg1XprType;
945
- typedef typename Arg2TensorBlock::XprType Arg2XprType;
946
- typedef typename Arg3TensorBlock::XprType Arg3XprType;
947
-
948
- static const bool NoArgBlockAccess = internal::is_void<Arg1XprType>::value ||
949
- internal::is_void<Arg2XprType>::value ||
950
- internal::is_void<Arg3XprType>::value;
951
-
952
- public:
953
- typedef typename conditional<
954
- NoArgBlockAccess, void,
955
- typename BlockFactory::template XprType<Arg1XprType, Arg2XprType,
956
- Arg3XprType>::type>::type XprType;
957
-
958
- typedef typename XprScalar<XprType>::type Scalar;
959
-
960
- TensorTernaryExprBlock(const Arg1TensorBlock& arg1_block,
961
- const Arg2TensorBlock& arg2_block,
962
- const Arg3TensorBlock& arg3_block,
963
- const BlockFactory& factory)
964
- : m_arg1_block(arg1_block),
965
- m_arg2_block(arg2_block),
966
- m_arg3_block(arg3_block),
967
- m_factory(factory) {}
968
-
969
- TensorBlockKind kind() const { return internal::TensorBlockKind::kExpr; }
970
- XprType expr() const {
971
- return m_factory.expr(m_arg1_block.expr(), m_arg2_block.expr(),
972
- m_arg3_block.expr());
973
- }
974
- const Scalar* data() const { return NULL; }
975
- void cleanup() {
976
- m_arg1_block.cleanup();
977
- m_arg2_block.cleanup();
978
- m_arg3_block.cleanup();
979
- }
980
-
981
- private:
982
- Arg1TensorBlock m_arg1_block;
983
- Arg2TensorBlock m_arg2_block;
984
- Arg3TensorBlock m_arg3_block;
985
- BlockFactory m_factory;
986
- };
987
-
988
- // -------------------------------------------------------------------------- //
989
- // StridedLinearBufferCopy provides a method to copy data between two linear
990
- // buffers with different strides, with optimized paths for scatter/gather.
991
-
992
- template <typename Scalar, typename IndexType>
993
- class StridedLinearBufferCopy {
994
- typedef typename packet_traits<Scalar>::type Packet;
995
- enum {
996
- Vectorizable = packet_traits<Scalar>::Vectorizable,
997
- PacketSize = packet_traits<Scalar>::size
998
- };
999
-
1000
- public:
1001
- // Specifying linear copy kind statically gives ~30% speedup for small sizes.
1002
- enum class Kind {
1003
- Linear = 0, // src_stride == 1 && dst_stride == 1
1004
- Scatter = 1, // src_stride == 1 && dst_stride != 1
1005
- FillLinear = 2, // src_stride == 0 && dst_stride == 1
1006
- FillScatter = 3, // src_stride == 0 && dst_stride != 1
1007
- Gather = 4, // dst_stride == 1
1008
- Random = 5 // everything else
1009
- };
1010
-
1011
- struct Dst {
1012
- Dst(IndexType o, IndexType s, Scalar* d) : offset(o), stride(s), data(d) {}
1013
-
1014
- IndexType offset;
1015
- IndexType stride;
1016
- Scalar* data;
1017
- };
1018
-
1019
- struct Src {
1020
- Src(IndexType o, IndexType s, const Scalar* d)
1021
- : offset(o), stride(s), data(d) {}
1022
-
1023
- IndexType offset;
1024
- IndexType stride;
1025
- const Scalar* data;
1026
- };
1027
-
1028
- template <typename StridedLinearBufferCopy::Kind kind>
1029
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(const Dst& dst,
1030
- const Src& src,
1031
- const size_t count) {
1032
- Run<kind>(count, dst.offset, dst.stride, dst.data, src.offset, src.stride,
1033
- src.data);
1034
- }
1035
-
1036
- private:
1037
- template <typename StridedLinearBufferCopy::Kind kind>
1038
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(
1039
- const IndexType count, const IndexType dst_offset,
1040
- const IndexType dst_stride, Scalar* EIGEN_RESTRICT dst_data,
1041
- const IndexType src_offset, const IndexType src_stride,
1042
- const Scalar* EIGEN_RESTRICT src_data) {
1043
- const Scalar* src = &src_data[src_offset];
1044
- Scalar* dst = &dst_data[dst_offset];
1045
-
1046
- if (!Vectorizable) {
1047
- for (Index i = 0; i < count; ++i) {
1048
- dst[i * dst_stride] = src[i * src_stride];
1049
- }
1050
- return;
1051
- }
1052
-
1053
- const IndexType vectorized_size = count - PacketSize;
1054
- IndexType i = 0;
1055
-
1056
- if (kind == StridedLinearBufferCopy::Kind::Linear) {
1057
- // ******************************************************************** //
1058
- // Linear copy from `src` to `dst`.
1059
- const IndexType unrolled_size = count - 4 * PacketSize;
1060
- eigen_assert(src_stride == 1 && dst_stride == 1);
1061
- for (; i <= unrolled_size; i += 4 * PacketSize) {
1062
- for (int j = 0; j < 4; ++j) {
1063
- Packet p = ploadu<Packet>(src + i + j * PacketSize);
1064
- pstoreu<Scalar, Packet>(dst + i + j * PacketSize, p);
1065
- }
1066
- }
1067
- for (; i <= vectorized_size; i += PacketSize) {
1068
- Packet p = ploadu<Packet>(src + i);
1069
- pstoreu<Scalar, Packet>(dst + i, p);
1070
- }
1071
- for (; i < count; ++i) {
1072
- dst[i] = src[i];
1073
- }
1074
- // ******************************************************************** //
1075
- } else if (kind == StridedLinearBufferCopy::Kind::Scatter) {
1076
- // Scatter from `src` to `dst`.
1077
- eigen_assert(src_stride == 1 && dst_stride != 1);
1078
- for (; i <= vectorized_size; i += PacketSize) {
1079
- Packet p = ploadu<Packet>(src + i);
1080
- pscatter<Scalar, Packet>(dst + i * dst_stride, p, dst_stride);
1081
- }
1082
- for (; i < count; ++i) {
1083
- dst[i * dst_stride] = src[i];
1084
- }
1085
- // ******************************************************************** //
1086
- } else if (kind == StridedLinearBufferCopy::Kind::FillLinear) {
1087
- // Fill `dst` with value at `*src`.
1088
- eigen_assert(src_stride == 0 && dst_stride == 1);
1089
- const IndexType unrolled_size = count - 4 * PacketSize;
1090
- Packet p = pload1<Packet>(src);
1091
- for (; i <= unrolled_size; i += 4 * PacketSize) {
1092
- for (int j = 0; j < 4; ++j) {
1093
- pstoreu<Scalar, Packet>(dst + i + j * PacketSize, p);
1094
- }
1095
- }
1096
- for (; i <= vectorized_size; i += PacketSize) {
1097
- pstoreu<Scalar, Packet>(dst + i, p);
1098
- }
1099
- for (; i < count; ++i) {
1100
- dst[i] = *src;
1101
- }
1102
- // ******************************************************************** //
1103
- } else if (kind == StridedLinearBufferCopy::Kind::FillScatter) {
1104
- // Scatter `*src` into `dst`.
1105
- eigen_assert(src_stride == 0 && dst_stride != 1);
1106
- Packet p = pload1<Packet>(src);
1107
- for (; i <= vectorized_size; i += PacketSize) {
1108
- pscatter<Scalar, Packet>(dst + i * dst_stride, p, dst_stride);
1109
- }
1110
- for (; i < count; ++i) {
1111
- dst[i * dst_stride] = *src;
1112
- }
1113
- // ******************************************************************** //
1114
- } else if (kind == StridedLinearBufferCopy::Kind::Gather) {
1115
- // Gather from `src` into `dst`.
1116
- eigen_assert(dst_stride == 1);
1117
- for (; i <= vectorized_size; i += PacketSize) {
1118
- Packet p = pgather<Scalar, Packet>(src + i * src_stride, src_stride);
1119
- pstoreu<Scalar, Packet>(dst + i, p);
1120
- }
1121
- for (; i < count; ++i) {
1122
- dst[i] = src[i * src_stride];
1123
- }
1124
- // ******************************************************************** //
1125
- } else if (kind == StridedLinearBufferCopy::Kind::Random) {
1126
- // Random.
1127
- for (; i < count; ++i) {
1128
- dst[i * dst_stride] = src[i * src_stride];
1129
- }
1130
- } else {
1131
- eigen_assert(false);
1132
- }
1133
- }
1134
- };
1135
-
1136
- // -------------------------------------------------------------------------- //
1137
- // TensorBlockIO copies data from `src` tensor block, to the `dst` tensor block.
1138
- // It's possible to specify src->dst dimension mapping for the copy operation.
1139
- // Dimensions of `dst` specify how many elements have to be copied, for the
1140
- // `src` we need to know only stride to navigate through source memory buffer.
1141
-
1142
- template <typename Scalar, typename IndexType, int NumDims, int Layout>
1143
- class TensorBlockIO {
1144
- static const bool IsColMajor = (Layout == ColMajor);
1145
-
1146
- typedef StridedLinearBufferCopy<Scalar, IndexType> LinCopy;
1147
-
1148
- public:
1149
- typedef DSizes<IndexType, NumDims> Dimensions;
1150
- typedef DSizes<int, NumDims> DimensionsMap;
1151
-
1152
- struct Dst {
1153
- Dst(const Dimensions& dst_dims, const Dimensions& dst_strides, Scalar* dst,
1154
- IndexType dst_offset = 0)
1155
- : dims(dst_dims), strides(dst_strides), data(dst), offset(dst_offset) {}
1156
-
1157
- Dimensions dims;
1158
- Dimensions strides;
1159
- Scalar* data;
1160
- IndexType offset;
1161
- };
1162
-
1163
- struct Src {
1164
- Src(const Dimensions& src_strides, const Scalar* src,
1165
- IndexType src_offset = 0)
1166
- : strides(src_strides), data(src), offset(src_offset) {}
1167
-
1168
- Dimensions strides;
1169
- const Scalar* data;
1170
- IndexType offset;
1171
- };
1172
-
1173
- // Copies data to `dst` from `src`, using provided dimensions mapping:
1174
- //
1175
- // src_dimension_index = dst_to_src_dim_map[dst_dimension_index]
1176
- //
1177
- // Returns the number of copied elements.
1178
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE IndexType Copy(
1179
- const Dst& dst, const Src& src, const DimensionsMap& dst_to_src_dim_map) {
1180
- // Copy single scalar value from `src` to `dst`.
1181
- if (NumDims == 0) {
1182
- *(dst.data + dst.offset) = *(src.data + src.offset);
1183
- return 1;
1184
- }
1185
-
1186
- // Both `dst` and `src` must have contiguous innermost dimension. We also
1187
- // accept the special case with stride '0', because it's used as a trick to
1188
- // implement broadcasting.
1189
- {
1190
- int inner_dim = IsColMajor ? 0 : NumDims - 1;
1191
- EIGEN_UNUSED_VARIABLE(inner_dim);
1192
- eigen_assert(dst.strides[inner_dim] == 1 || dst.strides[inner_dim] == 0);
1193
- eigen_assert(src.strides[inner_dim] == 1 || src.strides[inner_dim] == 0);
1194
- }
1195
-
1196
- // Give a shorter name to `dst_to_src_dim_map`.
1197
- const DimensionsMap& dim_map = dst_to_src_dim_map;
1198
-
1199
- // Do not squeeze reordered inner dimensions.
1200
- int num_squeezable_dims = NumSqueezableInnerDims(dim_map);
1201
-
1202
- // NOTE: We find the innermost dimension (contiguous in memory) in the dst
1203
- // block, and we write data linearly into that dimension, reading it from
1204
- // the src. If dimensions are reordered, we might end up reading data from
1205
- // the src with `stride != 1`.
1206
- //
1207
- // NOTE: Random-Read/Linear-Write can be up to ~2X faster than
1208
- // Linear-Read/Random-Write: https://stackoverflow.com/a/54935680
1209
-
1210
- // Find the innermost dimension in the dst whose size is not 1. This is the
1211
- // effective inner dim.
1212
- int num_size_one_inner_dims = 0;
1213
- for (int i = 0; i < num_squeezable_dims; ++i) {
1214
- const int dst_dim = IsColMajor ? i : NumDims - i - 1;
1215
- if (dst.dims[dst_dim] != 1) break;
1216
- num_size_one_inner_dims++;
1217
- }
1218
-
1219
- // If all dimensions are of size 1, just copy a scalar from `src` to `dst`.
1220
- if (num_size_one_inner_dims == NumDims) {
1221
- *(dst.data + dst.offset) = *(src.data + src.offset);
1222
- return 1;
1223
- }
1224
-
1225
- // Outermost dimension in the dst with `stride == 1` (contiguous in memory).
1226
- const int dst_stride1_dim = IsColMajor
1227
- ? num_size_one_inner_dims
1228
- : NumDims - num_size_one_inner_dims - 1;
1229
-
1230
- // Dimension in the src that corresponds to the dst innermost dimension.
1231
- const int src_dim_for_dst_stride1_dim =
1232
- NumDims == 0 ? 1 : dim_map[dst_stride1_dim];
1233
-
1234
- // Size of the innermost dimension (length of contiguous blocks of memory).
1235
- IndexType dst_inner_dim_size = NumDims == 0 ? 1 : dst.dims[dst_stride1_dim];
1236
-
1237
- // Squeeze multiple inner dims into one if they are contiguous in `dst` and
1238
- // `src` memory, so we can do less linear copy calls.
1239
- for (int i = num_size_one_inner_dims + 1; i < num_squeezable_dims; ++i) {
1240
- const int dst_dim = IsColMajor ? i : NumDims - i - 1;
1241
- const IndexType dst_stride = dst.strides[dst_dim];
1242
- const IndexType src_stride = src.strides[dim_map[dst_dim]];
1243
- if (dst_inner_dim_size == dst_stride && dst_stride == src_stride) {
1244
- dst_inner_dim_size *= dst.dims[dst_dim];
1245
- ++num_size_one_inner_dims;
1246
- } else {
1247
- break;
1248
- }
1249
- }
1250
-
1251
- // Setup strides to read data from `src` and write to `dst`.
1252
- IndexType input_offset = src.offset;
1253
- IndexType output_offset = dst.offset;
1254
- IndexType input_stride =
1255
- NumDims == 0 ? 1 : src.strides[src_dim_for_dst_stride1_dim];
1256
- IndexType output_stride = NumDims == 0 ? 1 : dst.strides[dst_stride1_dim];
1257
-
1258
- const int at_least_1_dim = NumDims <= 1 ? 1 : NumDims - 1;
1259
- array<BlockIteratorState, at_least_1_dim> it;
1260
-
1261
- // Initialize block iterator state. Squeeze away any dimension of size 1.
1262
- int idx = 0; // currently initialized iterator state index
1263
- for (int i = num_size_one_inner_dims; i < NumDims - 1; ++i) {
1264
- const int dst_dim = IsColMajor ? i + 1 : NumDims - i - 2;
1265
- if (dst.dims[dst_dim] == 1) continue;
1266
-
1267
- it[idx].size = dst.dims[dst_dim];
1268
- it[idx].input_stride = src.strides[dim_map[dst_dim]];
1269
- it[idx].output_stride = dst.strides[dst_dim];
1270
-
1271
- it[idx].input_span = it[idx].input_stride * (it[idx].size - 1);
1272
- it[idx].output_span = it[idx].output_stride * (it[idx].size - 1);
1273
-
1274
- idx++;
1275
- }
1276
-
1277
- // Iterate copying data from src to dst.
1278
- const IndexType block_total_size = NumDims == 0 ? 1 : dst.dims.TotalSize();
1279
-
1280
- #define COPY_INNER_DIM(KIND) \
1281
- IndexType num_copied = 0; \
1282
- for (num_copied = 0; num_copied < block_total_size; \
1283
- num_copied += dst_inner_dim_size) { \
1284
- LinCopy::template Run<KIND>( \
1285
- typename LinCopy::Dst(output_offset, output_stride, dst.data), \
1286
- typename LinCopy::Src(input_offset, input_stride, src.data), \
1287
- dst_inner_dim_size); \
1288
- \
1289
- for (int j = 0; j < idx; ++j) { \
1290
- if (++it[j].count < it[j].size) { \
1291
- input_offset += it[j].input_stride; \
1292
- output_offset += it[j].output_stride; \
1293
- break; \
1294
- } \
1295
- it[j].count = 0; \
1296
- input_offset -= it[j].input_span; \
1297
- output_offset -= it[j].output_span; \
1298
- } \
1299
- } \
1300
- return num_copied;
1301
-
1302
- if (input_stride == 1 && output_stride == 1) {
1303
- COPY_INNER_DIM(LinCopy::Kind::Linear);
1304
- } else if (input_stride == 1 && output_stride != 1) {
1305
- COPY_INNER_DIM(LinCopy::Kind::Scatter);
1306
- } else if (input_stride == 0 && output_stride == 1) {
1307
- COPY_INNER_DIM(LinCopy::Kind::FillLinear);
1308
- } else if (input_stride == 0 && output_stride != 1) {
1309
- COPY_INNER_DIM(LinCopy::Kind::FillScatter);
1310
- } else if (output_stride == 1) {
1311
- COPY_INNER_DIM(LinCopy::Kind::Gather);
1312
- } else {
1313
- COPY_INNER_DIM(LinCopy::Kind::Random);
1314
- }
1315
-
1316
- #undef COPY_INNER_DIM
1317
- }
1318
-
1319
- // Copy from `src` to `dst` with an identity src->dst dimension map. Returns
1320
- // the number of copied elements.
1321
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE IndexType Copy(const Dst& dst,
1322
- const Src& src) {
1323
- DimensionsMap dst_to_src_map;
1324
- for (int i = 0; i < NumDims; ++i) dst_to_src_map[i] = i;
1325
- return Copy(dst, src, dst_to_src_map);
1326
- }
1327
-
1328
- private:
1329
- struct BlockIteratorState {
1330
- BlockIteratorState()
1331
- : size(0),
1332
- count(0),
1333
- input_stride(0),
1334
- output_stride(0),
1335
- input_span(0),
1336
- output_span(0) {}
1337
-
1338
- IndexType size;
1339
- IndexType count;
1340
- IndexType input_stride;
1341
- IndexType output_stride;
1342
- IndexType input_span;
1343
- IndexType output_span;
1344
- };
1345
-
1346
- // Compute how many inner dimensions it's allowed to squeeze when doing IO
1347
- // between two tensor blocks. It's safe to squeeze inner dimensions, only
1348
- // if they are not reordered.
1349
- static int NumSqueezableInnerDims(const DimensionsMap& dim_map) {
1350
- int num_squeezable_dims = 0;
1351
- for (int i = 0; i < NumDims; ++i) {
1352
- const int dim = IsColMajor ? i : NumDims - i - 1;
1353
- if (dim_map[dim] != dim) break;
1354
- num_squeezable_dims++;
1355
- }
1356
- return num_squeezable_dims;
1357
- }
1358
- };
1359
-
1360
- // -------------------------------------------------------------------------- //
1361
- // TensorBlockAssignment assigns a block expression of type `TensorBlockExpr` to
1362
- // a Tensor block defined by `desc`, backed by a memory buffer at `target`.
1363
- //
1364
- // Currently there is no way to write from a Tensor expression to a block of
1365
- // memory, if dimensions are reordered. If you need to do that, you should
1366
- // materialize a Tensor block expression into a memory buffer, and then use
1367
- // TensorBlockIO to copy data between two memory buffers with a custom
1368
- // `target->src` dimension map (see definition above).
1369
- //
1370
- // Also currently the innermost dimension of `target` must have a stride '1'
1371
- // (contiguous in memory). This restriction could be lifted with a `pscatter`,
1372
- // but in practice it's never needed, and there is a similar TensorBlockIO
1373
- // workaround for that.
1374
- //
1375
- // TODO(ezhulenev): TensorBlockAssignment is a special case of TensorBlockIO
1376
- // where `src` is a tensor expression. Explore if it is possible to rewrite IO
1377
- // to use expressions instead of pointers, and after that TensorBlockAssignment
1378
- // will become an alias to IO.
1379
- template <typename Scalar, int NumDims, typename TensorBlockExpr,
1380
- typename IndexType = Eigen::Index>
1381
- class TensorBlockAssignment {
1382
- // We will use coeff/packet path to evaluate block expressions.
1383
- typedef TensorEvaluator<const TensorBlockExpr, DefaultDevice>
1384
- TensorBlockEvaluator;
1385
-
1386
- typedef DSizes<IndexType, NumDims> Dimensions;
1387
-
1388
- enum {
1389
- Vectorizable = packet_traits<Scalar>::Vectorizable,
1390
- PacketSize = packet_traits<Scalar>::size
1391
- };
1392
-
1393
- template <bool Vectorizable, typename Evaluator>
1394
- struct InnerDimAssign {
1395
- EIGEN_ALWAYS_INLINE static void Run(Scalar* target, IndexType count,
1396
- const Evaluator& eval,
1397
- IndexType eval_offset) {
1398
- for (IndexType i = 0; i < count; ++i) {
1399
- target[i] = eval.coeff(eval_offset + i);
1400
- }
1401
- }
1402
- };
1403
-
1404
- template <typename Evaluator>
1405
- struct InnerDimAssign<true, Evaluator> {
1406
- EIGEN_ALWAYS_INLINE static void Run(Scalar* target, IndexType count,
1407
- const Evaluator& eval,
1408
- IndexType eval_offset) {
1409
- typedef typename packet_traits<Scalar>::type Packet;
1410
-
1411
- const IndexType unrolled_size = count - 4 * PacketSize;
1412
- const IndexType vectorized_size = count - PacketSize;
1413
- IndexType i = 0;
1414
-
1415
- for (; i <= unrolled_size; i += 4 * PacketSize) {
1416
- for (int j = 0; j < 4; ++j) {
1417
- const IndexType idx = eval_offset + i + j * PacketSize;
1418
- Packet p = eval.template packet<Unaligned>(idx);
1419
- pstoreu<Scalar>(target + i + j * PacketSize, p);
1420
- }
1421
- }
1422
-
1423
- for (; i <= vectorized_size; i += PacketSize) {
1424
- Packet p = eval.template packet<Unaligned>(eval_offset + i);
1425
- pstoreu<Scalar>(target + i, p);
1426
- }
1427
-
1428
- for (; i < count; ++i) {
1429
- target[i] = eval.coeff(eval_offset + i);
1430
- }
1431
- }
1432
- };
1433
-
1434
- public:
1435
- struct Target {
1436
- Target(const Dimensions& target_dims, const Dimensions& target_strides,
1437
- Scalar* target_data, IndexType target_offset = 0)
1438
- : dims(target_dims),
1439
- strides(target_strides),
1440
- data(target_data),
1441
- offset(target_offset) {}
1442
-
1443
- Dimensions dims;
1444
- Dimensions strides;
1445
- Scalar* data;
1446
- IndexType offset;
1447
- };
1448
-
1449
- static Target target(const Dimensions& target_dims,
1450
- const Dimensions& target_strides, Scalar* target_data,
1451
- IndexType target_offset = 0) {
1452
- return Target(target_dims, target_strides, target_data, target_offset);
1453
- }
1454
-
1455
- template <typename TargetDimsIndexType, typename TargetStridesIndexType>
1456
- static Target target(
1457
- const DSizes<TargetDimsIndexType, NumDims>& target_dims,
1458
- const DSizes<TargetStridesIndexType, NumDims>& target_strides,
1459
- Scalar* target_data, IndexType target_offset = 0) {
1460
- // DSizes constructor will do index type promotion if it's safe.
1461
- return Target(Dimensions(target_dims), Dimensions(target_strides),
1462
- target_data, target_offset);
1463
- }
1464
-
1465
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(
1466
- const Target& target, const TensorBlockExpr& expr) {
1467
- // Prepare evaluator for block expression.
1468
- DefaultDevice default_device;
1469
- TensorBlockEvaluator eval(expr, default_device);
1470
-
1471
- // Tensor block expression dimension should match destination dimensions.
1472
- eigen_assert(dimensions_match(target.dims, eval.dimensions()));
1473
-
1474
- static const int Layout = TensorBlockEvaluator::Layout;
1475
- static const bool is_col_major = Layout == ColMajor;
1476
-
1477
- // Initialize output inner dimension size based on a layout.
1478
- const IndexType output_size = NumDims == 0 ? 1 : target.dims.TotalSize();
1479
- const int inner_dim_idx = is_col_major ? 0 : NumDims - 1;
1480
- IndexType output_inner_dim_size = target.dims[inner_dim_idx];
1481
-
1482
- // Target inner dimension stride must be '1'.
1483
- eigen_assert(target.strides[inner_dim_idx] == 1);
1484
-
1485
- // Squeeze multiple inner dims into one if they are contiguous in `target`.
1486
- IndexType num_squeezed_dims = 0;
1487
- for (Index i = 1; i < NumDims; ++i) {
1488
- const Index dim = is_col_major ? i : NumDims - i - 1;
1489
- const IndexType target_stride = target.strides[dim];
1490
-
1491
- if (output_inner_dim_size == target_stride) {
1492
- output_inner_dim_size *= target.dims[dim];
1493
- num_squeezed_dims++;
1494
- } else {
1495
- break;
1496
- }
1497
- }
1498
-
1499
- // Initialize output block iterator state. Dimension in this array are
1500
- // always in inner_most -> outer_most order (col major layout).
1501
- array<BlockIteratorState, NumDims> it;
1502
-
1503
- int idx = 0; // currently initialized iterator state index
1504
- for (Index i = num_squeezed_dims; i < NumDims - 1; ++i) {
1505
- const Index dim = is_col_major ? i + 1 : NumDims - i - 2;
1506
-
1507
- it[idx].count = 0;
1508
- it[idx].size = target.dims[dim];
1509
- it[idx].output_stride = target.strides[dim];
1510
- it[idx].output_span = it[idx].output_stride * (it[idx].size - 1);
1511
- idx++;
1512
- }
1513
-
1514
- // We read block expression from the beginning, and start writing data to
1515
- // `target` at given offset.
1516
- IndexType input_offset = 0;
1517
- IndexType output_offset = target.offset;
1518
-
1519
- // Iterate copying data from `eval` to `target`.
1520
- for (IndexType i = 0; i < output_size; i += output_inner_dim_size) {
1521
- // Assign to `target` at current offset.
1522
- InnerDimAssign<Vectorizable && TensorBlockEvaluator::PacketAccess,
1523
- TensorBlockEvaluator>::Run(target.data + output_offset,
1524
- output_inner_dim_size, eval,
1525
- input_offset);
1526
-
1527
- // Move input offset forward by the number of assigned coefficients.
1528
- input_offset += output_inner_dim_size;
1529
-
1530
- // Update index.
1531
- for (int j = 0; j < idx; ++j) {
1532
- if (++it[j].count < it[j].size) {
1533
- output_offset += it[j].output_stride;
1534
- break;
1535
- }
1536
- it[j].count = 0;
1537
- output_offset -= it[j].output_span;
1538
- }
1539
- }
1540
- }
1541
-
1542
- private:
1543
- struct BlockIteratorState {
1544
- BlockIteratorState()
1545
- : count(0), size(0), output_stride(0), output_span(0) {}
1546
-
1547
- IndexType count;
1548
- IndexType size;
1549
- IndexType output_stride;
1550
- IndexType output_span;
1551
- };
1552
- };
1553
-
1554
- // -------------------------------------------------------------------------- //
1555
-
1556
- } // namespace internal
1557
- } // namespace Eigen
1558
-
1559
- #endif // EIGEN_CXX11_TENSOR_TENSOR_BLOCK_H