sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,703 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_EXECUTOR_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_EXECUTOR_H
12
-
13
- namespace Eigen {
14
-
15
- /**
16
- * \class TensorExecutor
17
- * \ingroup CXX11_Tensor_Module
18
- *
19
- * \brief The tensor executor class.
20
- *
21
- * This class is responsible for launch the evaluation of the expression on
22
- * the specified computing device.
23
- *
24
- * @tparam Vectorizable can use packet math (SSE/AVX/etc... registers and
25
- * instructions)
26
- * @tparam Tiling can use block based tensor evaluation
27
- * (see TensorBlock.h)
28
- */
29
- namespace internal {
30
-
31
- /**
32
- * Evaluating TensorBroadcastingOp via coefficient of packet path is extremely
33
- * expensive. If expression has at least one broadcast op in it, and it supports
34
- * block based evaluation, we always prefer it, even for the small tensors. For
35
- * all other tileable ops, block evaluation overhead for small tensors (fits
36
- * into L1) is too large, and we fallback on vectorized evaluation.
37
- */
38
-
39
- // TODO(ezhulenev): Add specializations for all other types of Tensor ops.
40
-
41
- template<typename Expression>
42
- struct ExpressionHasTensorBroadcastingOp {
43
- enum { value = false };
44
- };
45
-
46
- template<typename LhsXprType, typename RhsXprType>
47
- struct ExpressionHasTensorBroadcastingOp<
48
- const TensorAssignOp<LhsXprType, RhsXprType> > {
49
- enum { value = ExpressionHasTensorBroadcastingOp<RhsXprType>::value };
50
- };
51
-
52
- template<typename UnaryOp, typename XprType>
53
- struct ExpressionHasTensorBroadcastingOp<
54
- const TensorCwiseUnaryOp<UnaryOp, XprType> > {
55
- enum { value = ExpressionHasTensorBroadcastingOp<XprType>::value };
56
- };
57
-
58
- template<typename BinaryOp, typename LhsXprType, typename RhsXprType>
59
- struct ExpressionHasTensorBroadcastingOp<
60
- const TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType> > {
61
- enum {
62
- value = ExpressionHasTensorBroadcastingOp<LhsXprType>::value ||
63
- ExpressionHasTensorBroadcastingOp<RhsXprType>::value
64
- };
65
- };
66
-
67
- template<typename Broadcast, typename XprType>
68
- struct ExpressionHasTensorBroadcastingOp<
69
- const TensorBroadcastingOp<Broadcast, XprType> > {
70
- enum { value = true };
71
- };
72
-
73
- // -------------------------------------------------------------------------- //
74
-
75
- /**
76
- * Default strategy: the expression is evaluated sequentially with a single cpu
77
- * thread, without vectorization and block evaluation.
78
- */
79
- template <typename Expression, typename Device, bool Vectorizable,
80
- TiledEvaluation Tiling>
81
- class TensorExecutor {
82
- public:
83
- typedef typename Expression::Index StorageIndex;
84
-
85
- // Including `unsupported/Eigen/CXX11/Tensor` in different translation units
86
- // with/without `EIGEN_USE_THREADS` or `EIGEN_USE_GPU` is a potential ODR
87
- // violation. If this template is instantiated with a non-default device, it
88
- // means that this header file was included without defining
89
- // `EIGEN_USE_THREADS`, `EIGEN_USE_GPU` or `EIGEN_USE_SYCL`.
90
- static_assert(std::is_same<Device, DefaultDevice>::value,
91
- "Default executor instantiated with non-default device. "
92
- "You must #define EIGEN_USE_THREADS, EIGEN_USE_GPU or "
93
- "EIGEN_USE_SYCL before including Eigen headers.");
94
-
95
- EIGEN_DEVICE_FUNC
96
- static EIGEN_STRONG_INLINE void run(const Expression& expr,
97
- const Device& device = Device()) {
98
- TensorEvaluator<Expression, Device> evaluator(expr, device);
99
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(NULL);
100
- if (needs_assign) {
101
- const StorageIndex size = array_prod(evaluator.dimensions());
102
- for (StorageIndex i = 0; i < size; ++i) {
103
- evaluator.evalScalar(i);
104
- }
105
- }
106
- evaluator.cleanup();
107
- }
108
- };
109
-
110
- /**
111
- * Default async execution strategy is not implemented. Currently it's only
112
- * available for ThreadPoolDevice (see definition below).
113
- */
114
- template <typename Expression, typename Device, typename DoneCallback,
115
- bool Vectorizable, TiledEvaluation Tiling>
116
- class TensorAsyncExecutor {};
117
-
118
- /**
119
- * Process all the data with a single cpu thread, using vectorized instructions.
120
- */
121
- template <typename Expression>
122
- class TensorExecutor<Expression, DefaultDevice, /*Vectorizable=*/true,
123
- /*Tiling=*/TiledEvaluation::Off> {
124
- public:
125
- typedef typename Expression::Index StorageIndex;
126
-
127
- EIGEN_DEVICE_FUNC
128
- static EIGEN_STRONG_INLINE void run(
129
- const Expression& expr, const DefaultDevice& device = DefaultDevice()) {
130
- TensorEvaluator<Expression, DefaultDevice> evaluator(expr, device);
131
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(NULL);
132
- if (needs_assign) {
133
- const StorageIndex size = array_prod(evaluator.dimensions());
134
- const int PacketSize = unpacket_traits<typename TensorEvaluator<
135
- Expression, DefaultDevice>::PacketReturnType>::size;
136
-
137
- // Give compiler a strong possibility to unroll the loop. But don't insist
138
- // on unrolling, because if the function is expensive compiler should not
139
- // unroll the loop at the expense of inlining.
140
- const StorageIndex UnrolledSize =
141
- (size / (4 * PacketSize)) * 4 * PacketSize;
142
- for (StorageIndex i = 0; i < UnrolledSize; i += 4 * PacketSize) {
143
- for (StorageIndex j = 0; j < 4; j++) {
144
- evaluator.evalPacket(i + j * PacketSize);
145
- }
146
- }
147
- const StorageIndex VectorizedSize = (size / PacketSize) * PacketSize;
148
- for (StorageIndex i = UnrolledSize; i < VectorizedSize; i += PacketSize) {
149
- evaluator.evalPacket(i);
150
- }
151
- for (StorageIndex i = VectorizedSize; i < size; ++i) {
152
- evaluator.evalScalar(i);
153
- }
154
- }
155
- evaluator.cleanup();
156
- }
157
- };
158
-
159
- /**
160
- * Process all the data with a single cpu thread, using blocks of data. By
161
- * sizing a block to fit L1 cache we get better cache performance.
162
- */
163
- template <typename Expression, bool Vectorizable>
164
- class TensorExecutor<Expression, DefaultDevice, Vectorizable,
165
- /*Tiling=*/TiledEvaluation::On> {
166
- public:
167
- typedef typename traits<Expression>::Scalar Scalar;
168
- typedef typename remove_const<Scalar>::type ScalarNoConst;
169
-
170
- typedef TensorEvaluator<Expression, DefaultDevice> Evaluator;
171
- typedef typename traits<Expression>::Index StorageIndex;
172
-
173
- static const int NumDims = traits<Expression>::NumDimensions;
174
-
175
- EIGEN_DEVICE_FUNC
176
- static EIGEN_STRONG_INLINE void run(const Expression& expr,
177
- const DefaultDevice& device = DefaultDevice()) {
178
- typedef TensorBlockMapper<NumDims, Evaluator::Layout, StorageIndex>
179
- TensorBlockMapper;
180
-
181
- typedef internal::TensorBlockDescriptor<NumDims, StorageIndex>
182
- TensorBlockDesc;
183
- typedef internal::TensorBlockScratchAllocator<DefaultDevice>
184
- TensorBlockScratch;
185
-
186
- Evaluator evaluator(expr, device);
187
-
188
- // TODO(ezhulenev): Do not use tiling for small tensors?
189
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(NULL);
190
-
191
- if (needs_assign) {
192
- // Query expression tree for desired block size/shape.
193
- const TensorBlockResourceRequirements requirements =
194
- evaluator.getResourceRequirements();
195
-
196
- const TensorBlockMapper block_mapper(
197
- typename TensorBlockDesc::Dimensions(evaluator.dimensions()),
198
- requirements);
199
-
200
- // Share scratch memory allocator between all blocks.
201
- TensorBlockScratch scratch(device);
202
-
203
- const StorageIndex total_block_count = block_mapper.blockCount();
204
- for (StorageIndex i = 0; i < total_block_count; ++i) {
205
- TensorBlockDesc desc = block_mapper.blockDescriptor(i);
206
- evaluator.evalBlock(desc, scratch);
207
- scratch.reset();
208
- }
209
- }
210
- evaluator.cleanup();
211
- }
212
- };
213
-
214
- /**
215
- * Multicore strategy: the index space is partitioned and each partition is
216
- * executed on a single core.
217
- *
218
- * (1) TensorExecutor will submit work to the ThreadPoolDevice managed thread
219
- * pool, and will block the caller thread until all tasks are finished.
220
- *
221
- * (2) TensorAsyncExecutor is a non-blocking version, that will submit work to
222
- * the ThreadPoolDevice managed thread pool, and will return immediately.
223
- * It will call 'done' callback after all tasks are finished.
224
- */
225
- #ifdef EIGEN_USE_THREADS
226
-
227
- template <typename TensorBlockMapper>
228
- struct TensorExecutorTilingContext {
229
- TensorExecutorTilingContext() = default;
230
- TensorExecutorTilingContext(const TensorBlockMapper& b_mapper,
231
- const TensorOpCost& b_cost, size_t b_aligned_size)
232
- : block_mapper(b_mapper),
233
- cost(b_cost),
234
- aligned_blocksize(b_aligned_size) {}
235
-
236
- TensorBlockMapper block_mapper; // navigate through blocks
237
- TensorOpCost cost; // cost of computing a single block
238
- size_t aligned_blocksize; // block size after memory alignment
239
- };
240
-
241
- // Computes a block evaluation parameters, and allocates temporary memory buffer
242
- // for blocks. See TensorExecutor/TensorAsyncExecutor (Tiling=On) below.
243
- template <typename Evaluator, typename TensorBlockMapper, bool Vectorizable>
244
- TensorExecutorTilingContext<TensorBlockMapper> GetTensorExecutorTilingContext(
245
- const Evaluator& evaluator) {
246
- // Query expression tree for desired block size/shape.
247
- TensorBlockResourceRequirements requirements =
248
- evaluator.getResourceRequirements();
249
-
250
- // Update target block size based on cost model.
251
- double taskSize = TensorCostModel<ThreadPoolDevice>::taskSize(
252
- 1, requirements.cost_per_coeff);
253
- requirements.size = static_cast<size_t>(1.0 / taskSize);
254
-
255
- TensorBlockMapper block_mapper(
256
- typename TensorBlockMapper::Dimensions(evaluator.dimensions()),
257
- requirements);
258
-
259
- size_t block_size = block_mapper.blockTotalSize();
260
- const size_t align = numext::maxi(EIGEN_MAX_ALIGN_BYTES, 1);
261
- const size_t aligned_blocksize =
262
- align *
263
- divup<size_t>(block_size * sizeof(typename Evaluator::Scalar), align);
264
-
265
- return {block_mapper, requirements.cost_per_coeff * block_size,
266
- aligned_blocksize};
267
- }
268
-
269
- template <typename Evaluator, typename StorageIndex, bool Vectorizable>
270
- struct EvalRange {
271
- static void run(Evaluator* evaluator_in, const StorageIndex firstIdx,
272
- const StorageIndex lastIdx) {
273
- Evaluator evaluator = *evaluator_in;
274
- eigen_assert(lastIdx >= firstIdx);
275
- for (StorageIndex i = firstIdx; i < lastIdx; ++i) {
276
- evaluator.evalScalar(i);
277
- }
278
- }
279
-
280
- static StorageIndex alignBlockSize(StorageIndex size) { return size; }
281
- };
282
-
283
- template <typename Evaluator, typename StorageIndex>
284
- struct EvalRange<Evaluator, StorageIndex, /*Vectorizable*/ true> {
285
- static const int PacketSize =
286
- unpacket_traits<typename Evaluator::PacketReturnType>::size;
287
-
288
- static void run(Evaluator* evaluator_in, const StorageIndex firstIdx,
289
- const StorageIndex lastIdx) {
290
- Evaluator evaluator = *evaluator_in;
291
- eigen_assert(lastIdx >= firstIdx);
292
- StorageIndex i = firstIdx;
293
- if (lastIdx - firstIdx >= PacketSize) {
294
- eigen_assert(firstIdx % PacketSize == 0);
295
- StorageIndex last_chunk_offset = lastIdx - 4 * PacketSize;
296
- // Give compiler a strong possibility to unroll the loop. But don't insist
297
- // on unrolling, because if the function is expensive compiler should not
298
- // unroll the loop at the expense of inlining.
299
- for (; i <= last_chunk_offset; i += 4 * PacketSize) {
300
- for (StorageIndex j = 0; j < 4; j++) {
301
- evaluator.evalPacket(i + j * PacketSize);
302
- }
303
- }
304
- last_chunk_offset = lastIdx - PacketSize;
305
- for (; i <= last_chunk_offset; i += PacketSize) {
306
- evaluator.evalPacket(i);
307
- }
308
- }
309
- for (; i < lastIdx; ++i) {
310
- evaluator.evalScalar(i);
311
- }
312
- }
313
-
314
- static StorageIndex alignBlockSize(StorageIndex size) {
315
- // Align block size to packet size and account for unrolling in run above.
316
- if (size >= 16 * PacketSize) {
317
- return (size + 4 * PacketSize - 1) & ~(4 * PacketSize - 1);
318
- }
319
- // Aligning to 4 * PacketSize would increase block size by more than 25%.
320
- return (size + PacketSize - 1) & ~(PacketSize - 1);
321
- }
322
- };
323
-
324
- template <typename Expression, bool Vectorizable, TiledEvaluation Tiling>
325
- class TensorExecutor<Expression, ThreadPoolDevice, Vectorizable, Tiling> {
326
- public:
327
- typedef typename Expression::Index StorageIndex;
328
-
329
- static EIGEN_STRONG_INLINE void run(const Expression& expr,
330
- const ThreadPoolDevice& device) {
331
- typedef TensorEvaluator<Expression, ThreadPoolDevice> Evaluator;
332
- typedef EvalRange<Evaluator, StorageIndex, Vectorizable> EvalRange;
333
-
334
- Evaluator evaluator(expr, device);
335
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(nullptr);
336
- if (needs_assign) {
337
- const StorageIndex size = array_prod(evaluator.dimensions());
338
- device.parallelFor(size, evaluator.costPerCoeff(Vectorizable),
339
- EvalRange::alignBlockSize,
340
- [&evaluator](StorageIndex firstIdx, StorageIndex lastIdx) {
341
- EvalRange::run(&evaluator, firstIdx, lastIdx);
342
- });
343
- }
344
- evaluator.cleanup();
345
- }
346
- };
347
-
348
- template <typename Expression, bool Vectorizable>
349
- class TensorExecutor<Expression, ThreadPoolDevice, Vectorizable,
350
- /*Tiling=*/TiledEvaluation::On> {
351
- public:
352
- typedef typename traits<Expression>::Index IndexType;
353
- typedef typename traits<Expression>::Scalar Scalar;
354
- typedef typename remove_const<Scalar>::type ScalarNoConst;
355
-
356
- static const int NumDims = traits<Expression>::NumDimensions;
357
-
358
- typedef TensorEvaluator<Expression, ThreadPoolDevice> Evaluator;
359
- typedef TensorBlockMapper<NumDims, Evaluator::Layout, IndexType> BlockMapper;
360
- typedef TensorExecutorTilingContext<BlockMapper> TilingContext;
361
-
362
- typedef internal::TensorBlockDescriptor<NumDims, IndexType>
363
- TensorBlockDesc;
364
- typedef internal::TensorBlockScratchAllocator<ThreadPoolDevice>
365
- TensorBlockScratch;
366
-
367
- static EIGEN_STRONG_INLINE void run(const Expression& expr,
368
- const ThreadPoolDevice& device) {
369
- Evaluator evaluator(expr, device);
370
-
371
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(nullptr);
372
- if (needs_assign) {
373
- const TilingContext tiling =
374
- internal::GetTensorExecutorTilingContext<Evaluator, BlockMapper,
375
- Vectorizable>(evaluator);
376
-
377
- auto eval_block = [&device, &evaluator, &tiling](IndexType firstBlockIdx,
378
- IndexType lastBlockIdx) {
379
- TensorBlockScratch scratch(device);
380
-
381
- for (IndexType block_idx = firstBlockIdx; block_idx < lastBlockIdx;
382
- ++block_idx) {
383
- TensorBlockDesc desc = tiling.block_mapper.blockDescriptor(block_idx);
384
- evaluator.evalBlock(desc, scratch);
385
- scratch.reset();
386
- }
387
- };
388
-
389
- // Evaluate small expressions directly as a single block.
390
- if (tiling.block_mapper.blockCount() == 1) {
391
- TensorBlockScratch scratch(device);
392
- TensorBlockDesc desc(0, tiling.block_mapper.blockDimensions());
393
- evaluator.evalBlock(desc, scratch);
394
- } else {
395
- device.parallelFor(tiling.block_mapper.blockCount(), tiling.cost,
396
- eval_block);
397
- }
398
- }
399
- evaluator.cleanup();
400
- }
401
- };
402
-
403
- template <typename Expression, typename DoneCallback, bool Vectorizable,
404
- TiledEvaluation Tiling>
405
- class TensorAsyncExecutor<Expression, ThreadPoolDevice, DoneCallback,
406
- Vectorizable, Tiling> {
407
- public:
408
- typedef typename Expression::Index StorageIndex;
409
- typedef TensorEvaluator<Expression, ThreadPoolDevice> Evaluator;
410
-
411
- static EIGEN_STRONG_INLINE void runAsync(const Expression& expr,
412
- const ThreadPoolDevice& device,
413
- DoneCallback done) {
414
- TensorAsyncExecutorContext* const ctx =
415
- new TensorAsyncExecutorContext(expr, device, std::move(done));
416
-
417
- const auto on_eval_subexprs = [ctx, &device](bool need_assign) -> void {
418
- if (!need_assign) {
419
- delete ctx;
420
- return;
421
- }
422
-
423
- typedef EvalRange<Evaluator, StorageIndex, Vectorizable> EvalRange;
424
- const StorageIndex size = array_prod(ctx->evaluator.dimensions());
425
- device.parallelForAsync(
426
- size, ctx->evaluator.costPerCoeff(Vectorizable),
427
- EvalRange::alignBlockSize,
428
- [ctx](StorageIndex firstIdx, StorageIndex lastIdx) {
429
- EvalRange::run(&ctx->evaluator, firstIdx, lastIdx);
430
- },
431
- [ctx]() { delete ctx; });
432
- };
433
-
434
- ctx->evaluator.evalSubExprsIfNeededAsync(nullptr, on_eval_subexprs);
435
- }
436
-
437
- private:
438
- struct TensorAsyncExecutorContext {
439
- TensorAsyncExecutorContext(const Expression& expr,
440
- const ThreadPoolDevice& thread_pool,
441
- DoneCallback done)
442
- : evaluator(expr, thread_pool), on_done(std::move(done)) {}
443
-
444
- ~TensorAsyncExecutorContext() {
445
- evaluator.cleanup();
446
- on_done();
447
- }
448
-
449
- Evaluator evaluator;
450
-
451
- private:
452
- DoneCallback on_done;
453
- };
454
- };
455
-
456
- template <typename Expression, typename DoneCallback, bool Vectorizable>
457
- class TensorAsyncExecutor<Expression, ThreadPoolDevice, DoneCallback,
458
- Vectorizable, /*Tileable*/ TiledEvaluation::On> {
459
- public:
460
- typedef typename traits<Expression>::Index IndexType;
461
- typedef typename traits<Expression>::Scalar Scalar;
462
- typedef typename remove_const<Scalar>::type ScalarNoConst;
463
-
464
- static const int NumDims = traits<Expression>::NumDimensions;
465
-
466
- typedef TensorEvaluator<Expression, ThreadPoolDevice> Evaluator;
467
- typedef TensorBlockMapper<NumDims, Evaluator::Layout, IndexType> BlockMapper;
468
- typedef TensorExecutorTilingContext<BlockMapper> TilingContext;
469
-
470
- typedef internal::TensorBlockDescriptor<NumDims, IndexType> TensorBlockDesc;
471
- typedef internal::TensorBlockScratchAllocator<ThreadPoolDevice>
472
- TensorBlockScratch;
473
-
474
- static EIGEN_STRONG_INLINE void runAsync(const Expression& expr,
475
- const ThreadPoolDevice& device,
476
- DoneCallback done) {
477
-
478
- TensorAsyncExecutorContext* const ctx =
479
- new TensorAsyncExecutorContext(expr, device, std::move(done));
480
-
481
- const auto on_eval_subexprs = [ctx](bool need_assign) -> void {
482
- if (!need_assign) {
483
- delete ctx;
484
- return;
485
- }
486
-
487
- ctx->tiling = internal::GetTensorExecutorTilingContext<
488
- Evaluator, BlockMapper, Vectorizable>(ctx->evaluator);
489
-
490
- auto eval_block = [ctx](IndexType firstBlockIdx, IndexType lastBlockIdx) {
491
- TensorBlockScratch scratch(ctx->device);
492
-
493
- for (IndexType block_idx = firstBlockIdx; block_idx < lastBlockIdx;
494
- ++block_idx) {
495
- TensorBlockDesc desc =
496
- ctx->tiling.block_mapper.blockDescriptor(block_idx);
497
- ctx->evaluator.evalBlock(desc, scratch);
498
- scratch.reset();
499
- }
500
- };
501
-
502
- // Evaluate small expressions directly as a single block.
503
- if (ctx->tiling.block_mapper.blockCount() == 1) {
504
- TensorBlockScratch scratch(ctx->device);
505
- TensorBlockDesc desc(0, ctx->tiling.block_mapper.blockDimensions());
506
- ctx->evaluator.evalBlock(desc, scratch);
507
- delete ctx;
508
- } else {
509
- ctx->device.parallelForAsync(ctx->tiling.block_mapper.blockCount(),
510
- ctx->tiling.cost, eval_block,
511
- [ctx]() { delete ctx; });
512
- }
513
- };
514
-
515
- ctx->evaluator.evalSubExprsIfNeededAsync(nullptr, on_eval_subexprs);
516
- }
517
-
518
- private:
519
- struct TensorAsyncExecutorContext {
520
- TensorAsyncExecutorContext(const Expression& expr,
521
- const ThreadPoolDevice& thread_pool,
522
- DoneCallback done)
523
- : device(thread_pool),
524
- evaluator(expr, thread_pool),
525
- on_done(std::move(done)) {}
526
-
527
- ~TensorAsyncExecutorContext() {
528
- evaluator.cleanup();
529
- on_done();
530
- }
531
-
532
- const ThreadPoolDevice& device;
533
- Evaluator evaluator;
534
- TilingContext tiling;
535
-
536
- private:
537
- DoneCallback on_done;
538
- };
539
- };
540
-
541
- #endif // EIGEN_USE_THREADS
542
-
543
- // GPU: the evaluation of the expression is offloaded to a GPU.
544
- #if defined(EIGEN_USE_GPU)
545
-
546
- template <typename Expression, bool Vectorizable, TiledEvaluation Tiling>
547
- class TensorExecutor<Expression, GpuDevice, Vectorizable, Tiling> {
548
- public:
549
- typedef typename Expression::Index StorageIndex;
550
- static void run(const Expression& expr, const GpuDevice& device);
551
- };
552
-
553
- #if defined(EIGEN_GPUCC)
554
- template <typename Evaluator, typename StorageIndex, bool Vectorizable>
555
- struct EigenMetaKernelEval {
556
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
557
- void run(Evaluator& eval, StorageIndex firstIdx, StorageIndex lastIdx, StorageIndex step_size) {
558
- for (StorageIndex i = firstIdx; i < lastIdx; i += step_size) {
559
- eval.evalScalar(i);
560
- }
561
- }
562
- };
563
-
564
- template <typename Evaluator, typename StorageIndex>
565
- struct EigenMetaKernelEval<Evaluator, StorageIndex, true> {
566
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
567
- void run(Evaluator& eval, StorageIndex firstIdx, StorageIndex lastIdx, StorageIndex step_size) {
568
- const StorageIndex PacketSize = unpacket_traits<typename Evaluator::PacketReturnType>::size;
569
- const StorageIndex vectorized_size = (lastIdx / PacketSize) * PacketSize;
570
- const StorageIndex vectorized_step_size = step_size * PacketSize;
571
-
572
- // Use the vector path
573
- for (StorageIndex i = firstIdx * PacketSize; i < vectorized_size;
574
- i += vectorized_step_size) {
575
- eval.evalPacket(i);
576
- }
577
- for (StorageIndex i = vectorized_size + firstIdx; i < lastIdx; i += step_size) {
578
- eval.evalScalar(i);
579
- }
580
- }
581
- };
582
-
583
- template <typename Evaluator, typename StorageIndex>
584
- __global__ void
585
- __launch_bounds__(1024)
586
- EigenMetaKernel(Evaluator eval, StorageIndex size) {
587
-
588
- const StorageIndex first_index = blockIdx.x * blockDim.x + threadIdx.x;
589
- const StorageIndex step_size = blockDim.x * gridDim.x;
590
-
591
- const bool vectorizable = Evaluator::PacketAccess & Evaluator::IsAligned;
592
- EigenMetaKernelEval<Evaluator, StorageIndex, vectorizable>::run(eval, first_index, size, step_size);
593
- }
594
-
595
- /*static*/
596
- template <typename Expression, bool Vectorizable, TiledEvaluation Tiling>
597
- EIGEN_STRONG_INLINE void TensorExecutor<Expression, GpuDevice, Vectorizable, Tiling>::run(
598
- const Expression& expr, const GpuDevice& device) {
599
- TensorEvaluator<Expression, GpuDevice> evaluator(expr, device);
600
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(nullptr);
601
- if (needs_assign) {
602
-
603
- const int block_size = device.maxGpuThreadsPerBlock();
604
- const int max_blocks = device.getNumGpuMultiProcessors() *
605
- device.maxGpuThreadsPerMultiProcessor() / block_size;
606
- const StorageIndex size = array_prod(evaluator.dimensions());
607
- // Create a least one block to ensure we won't crash when tensorflow calls with tensors of size 0.
608
- const int num_blocks = numext::maxi<int>(numext::mini<int>(max_blocks, divup<int>(size, block_size)), 1);
609
-
610
- LAUNCH_GPU_KERNEL(
611
- (EigenMetaKernel<TensorEvaluator<Expression, GpuDevice>, StorageIndex>),
612
- num_blocks, block_size, 0, device, evaluator, size);
613
- }
614
- evaluator.cleanup();
615
- }
616
-
617
- #endif // EIGEN_GPUCC
618
- #endif // EIGEN_USE_GPU
619
-
620
- // SYCL Executor policy
621
- #ifdef EIGEN_USE_SYCL
622
-
623
- template <typename Evaluator>
624
- struct ExecExprFunctorKernel {
625
- typedef typename Evaluator::Index Index;
626
- Evaluator evaluator;
627
- const Index range;
628
- template <typename Scratch>
629
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE ExecExprFunctorKernel(
630
- const Scratch, Evaluator evaluator_, const Index range_)
631
- : evaluator(evaluator_), range(range_) {}
632
-
633
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void operator()(
634
- cl::sycl::nd_item<1> itemID) {
635
- compute(itemID);
636
- }
637
- template <bool is_vec = Evaluator::PacketAccess>
638
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename std::enable_if<!is_vec>::type
639
- compute(const cl::sycl::nd_item<1>& itemID) {
640
- Index gId = static_cast<Index>(itemID.get_global_linear_id());
641
- Index total_threads = itemID.get_global_range(0);
642
-
643
- for (Index i = gId; i < range; i += total_threads) {
644
- evaluator.evalScalar(i);
645
- }
646
- }
647
- template <bool is_vec = Evaluator::PacketAccess>
648
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename std::enable_if<is_vec>::type
649
- compute(const cl::sycl::nd_item<1>& itemID) {
650
- const Index vectorizedRange =
651
- (range / Evaluator::PacketSize) * Evaluator::PacketSize;
652
- Index gId = static_cast<Index>(itemID.get_global_linear_id());
653
- const Index step = Evaluator::PacketSize * itemID.get_global_range(0);
654
- const Index start = Evaluator::PacketSize * gId;
655
- for (Index i = start; i < vectorizedRange; i += step) {
656
- evaluator.evalPacket(i);
657
- }
658
- gId += vectorizedRange;
659
- for (Index i = gId; i < range; i += itemID.get_global_range(0)) {
660
- evaluator.evalScalar(i);
661
- }
662
- }
663
- };
664
-
665
- template <typename Expression, bool Vectorizable, TiledEvaluation Tiling>
666
- class TensorExecutor<Expression, Eigen::SyclDevice, Vectorizable, Tiling> {
667
- public:
668
- typedef typename Expression::Index Index;
669
- static EIGEN_STRONG_INLINE void run(const Expression& expr,
670
- const Eigen::SyclDevice& dev) {
671
- typedef Eigen::TensorEvaluator<Expression, Eigen::SyclDevice> Evaluator;
672
- Evaluator evaluator(expr, dev);
673
- const bool needs_assign = evaluator.evalSubExprsIfNeeded(NULL);
674
- if (needs_assign) {
675
- Index range, GRange, tileSize;
676
- Index total_size = ::Eigen::internal::array_prod(evaluator.dimensions());
677
- total_size = (total_size == 0) ? 1 : total_size;
678
- const int PacketSize =
679
- Eigen::PacketType<typename Evaluator::CoeffReturnType,
680
- Eigen::SyclDevice>::size;
681
- Index vectorizable_threads = static_cast<Index>(total_size / PacketSize);
682
- dev.parallel_for_setup(vectorizable_threads, tileSize, range, GRange);
683
- range = total_size;
684
-
685
- dev.template nullary_kernel_launcher<
686
- typename Evaluator::CoeffReturnType,
687
- ExecExprFunctorKernel<Evaluator> >(
688
- evaluator,
689
- cl::sycl::nd_range<1>(cl::sycl::range<1>(GRange),
690
- cl::sycl::range<1>(tileSize)),
691
- Index(1), range);
692
- }
693
- evaluator.cleanup();
694
- }
695
- };
696
-
697
- #endif
698
-
699
- } // end namespace internal
700
-
701
- } // end namespace Eigen
702
-
703
- #endif // EIGEN_CXX11_TENSOR_TENSOR_EXECUTOR_H