sequenzo 0.1.17__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-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 +155 -155
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-311-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-311-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 +155 -155
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-311-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-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
@@ -1,582 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
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- // Mehdi Goli Codeplay Software Ltd.
5
- // Ralph Potter Codeplay Software Ltd.
6
- // Luke Iwanski Codeplay Software Ltd.
7
- // Contact: <eigen@codeplay.com>
8
- //
9
- // This Source Code Form is subject to the terms of the Mozilla
10
- // Public License v. 2.0. If a copy of the MPL was not distributed
11
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
12
-
13
- /*****************************************************************
14
- * TensorReductionSycl.h
15
- *
16
- * \brief:
17
- * This is the specialization of the reduction operation. Two phase reduction approach
18
- * is used since the GPU does not have Global Synchronization for global memory among
19
- * different work-group/thread block. To solve the problem, we need to create two kernels
20
- * to reduce the data, where the first kernel reduce the data locally and each local
21
- * workgroup/thread-block save the input data into global memory. In the second phase (global reduction)
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- * one work-group uses one work-group/thread-block to reduces the intermediate data into one single element.
23
- * Here is an NVIDIA presentation explaining the optimized two phase reduction algorithm on GPU:
24
- * https://developer.download.nvidia.com/assets/cuda/files/reduction.pdf
25
- *
26
- *****************************************************************/
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-
28
- #ifndef UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_REDUCTION_SYCL_HPP
29
- #define UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_REDUCTION_SYCL_HPP
30
- namespace Eigen {
31
- namespace TensorSycl {
32
- namespace internal {
33
-
34
- template <typename Op, typename CoeffReturnType, typename Index, bool Vectorizable>
35
- struct OpDefiner {
36
- typedef typename Vectorise<CoeffReturnType, Eigen::SyclDevice, Vectorizable>::PacketReturnType PacketReturnType;
37
- typedef Op type;
38
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE type get_op(Op &op) { return op; }
39
-
40
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType finalise_op(const PacketReturnType &accumulator,
41
- const Index &) {
42
- return accumulator;
43
- }
44
- };
45
-
46
- template <typename CoeffReturnType, typename Index>
47
- struct OpDefiner<Eigen::internal::MeanReducer<CoeffReturnType>, CoeffReturnType, Index, false> {
48
- typedef Eigen::internal::SumReducer<CoeffReturnType> type;
49
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE type get_op(Eigen::internal::MeanReducer<CoeffReturnType> &) {
50
- return type();
51
- }
52
-
53
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType finalise_op(const CoeffReturnType &accumulator,
54
- const Index &scale) {
55
- ::Eigen::internal::scalar_quotient_op<CoeffReturnType> quotient_op;
56
- return quotient_op(accumulator, CoeffReturnType(scale));
57
- }
58
- };
59
-
60
- template <typename CoeffReturnType, typename Index>
61
- struct OpDefiner<Eigen::internal::MeanReducer<CoeffReturnType>, CoeffReturnType, Index, true> {
62
- typedef typename Vectorise<CoeffReturnType, Eigen::SyclDevice, true>::PacketReturnType PacketReturnType;
63
- typedef Eigen::internal::SumReducer<CoeffReturnType> type;
64
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE type get_op(Eigen::internal::MeanReducer<CoeffReturnType> &) {
65
- return type();
66
- }
67
-
68
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType finalise_op(const PacketReturnType &accumulator,
69
- const Index &scale) {
70
- return ::Eigen::internal::pdiv(accumulator, ::Eigen::internal::pset1<PacketReturnType>(CoeffReturnType(scale)));
71
- }
72
- };
73
-
74
- template <typename CoeffReturnType, typename OpType, typename InputAccessor, typename OutputAccessor, typename Index,
75
- Index local_range>
76
- struct SecondStepFullReducer {
77
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
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- LocalAccessor;
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- typedef OpDefiner<OpType, CoeffReturnType, Index, true> OpDef;
80
- typedef typename OpDef::type Op;
81
- LocalAccessor scratch;
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- InputAccessor aI;
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- OutputAccessor outAcc;
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- Op op;
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- SecondStepFullReducer(LocalAccessor scratch_, InputAccessor aI_, OutputAccessor outAcc_, OpType op_)
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- : scratch(scratch_), aI(aI_), outAcc(outAcc_), op(OpDef::get_op(op_)) {}
87
-
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- void operator()(cl::sycl::nd_item<1> itemID) {
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- // Our empirical research shows that the best performance will be achieved
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- // when there is only one element per thread to reduce in the second step.
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- // in this step the second step reduction time is almost negligible.
92
- // Hence, in the second step of reduction the input size is fixed to the
93
- // local size, thus, there is only one element read per thread. The
94
- // algorithm must be changed if the number of reduce per thread in the
95
- // second step is greater than 1. Otherwise, the result will be wrong.
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- const Index localid = itemID.get_local_id(0);
97
- auto aInPtr = aI.get_pointer() + localid;
98
- auto aOutPtr = outAcc.get_pointer();
99
- CoeffReturnType *scratchptr = scratch.get_pointer();
100
- CoeffReturnType accumulator = *aInPtr;
101
-
102
- scratchptr[localid] = op.finalize(accumulator);
103
- for (Index offset = itemID.get_local_range(0) / 2; offset > 0; offset /= 2) {
104
- itemID.barrier(cl::sycl::access::fence_space::local_space);
105
- if (localid < offset) {
106
- op.reduce(scratchptr[localid + offset], &accumulator);
107
- scratchptr[localid] = op.finalize(accumulator);
108
- }
109
- }
110
- if (localid == 0) *aOutPtr = op.finalize(accumulator);
111
- }
112
- };
113
-
114
- // Full reduction first phase. In this version the vectorization is true and the reduction accept
115
- // any generic reducerOp e.g( max, min, sum, mean, iamax, iamin, etc ).
116
- template <typename Evaluator, typename OpType, typename Evaluator::Index local_range>
117
- class FullReductionKernelFunctor {
118
- public:
119
- typedef typename Evaluator::CoeffReturnType CoeffReturnType;
120
- typedef typename Evaluator::Index Index;
121
- typedef OpDefiner<OpType, typename Evaluator::CoeffReturnType, Index,
122
- (Evaluator::ReducerTraits::PacketAccess & Evaluator::InputPacketAccess)>
123
- OpDef;
124
-
125
- typedef typename OpDef::type Op;
126
- typedef typename Evaluator::EvaluatorPointerType EvaluatorPointerType;
127
- typedef typename Evaluator::PacketReturnType PacketReturnType;
128
- typedef
129
- typename ::Eigen::internal::conditional<(Evaluator::ReducerTraits::PacketAccess & Evaluator::InputPacketAccess),
130
- PacketReturnType, CoeffReturnType>::type OutType;
131
- typedef cl::sycl::accessor<OutType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
132
- LocalAccessor;
133
- LocalAccessor scratch;
134
- Evaluator evaluator;
135
- EvaluatorPointerType final_output;
136
- Index rng;
137
- Op op;
138
-
139
- FullReductionKernelFunctor(LocalAccessor scratch_, Evaluator evaluator_, EvaluatorPointerType final_output_,
140
- Index rng_, OpType op_)
141
- : scratch(scratch_), evaluator(evaluator_), final_output(final_output_), rng(rng_), op(OpDef::get_op(op_)) {}
142
-
143
- void operator()(cl::sycl::nd_item<1> itemID) { compute_reduction(itemID); }
144
-
145
- template <bool Vect = (Evaluator::ReducerTraits::PacketAccess & Evaluator::InputPacketAccess)>
146
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE typename ::Eigen::internal::enable_if<Vect>::type compute_reduction(
147
- const cl::sycl::nd_item<1> &itemID) {
148
- auto output_ptr = final_output.get_pointer();
149
- Index VectorizedRange = (rng / Evaluator::PacketSize) * Evaluator::PacketSize;
150
- Index globalid = itemID.get_global_id(0);
151
- Index localid = itemID.get_local_id(0);
152
- Index step = Evaluator::PacketSize * itemID.get_global_range(0);
153
- Index start = Evaluator::PacketSize * globalid;
154
- // vectorizable parts
155
- PacketReturnType packetAccumulator = op.template initializePacket<PacketReturnType>();
156
- for (Index i = start; i < VectorizedRange; i += step) {
157
- op.template reducePacket<PacketReturnType>(evaluator.impl().template packet<Unaligned>(i), &packetAccumulator);
158
- }
159
- globalid += VectorizedRange;
160
- // non vectorizable parts
161
- for (Index i = globalid; i < rng; i += itemID.get_global_range(0)) {
162
- op.template reducePacket<PacketReturnType>(
163
- ::Eigen::TensorSycl::internal::PacketWrapper<PacketReturnType, Evaluator::PacketSize>::convert_to_packet_type(
164
- evaluator.impl().coeff(i), op.initialize()),
165
- &packetAccumulator);
166
- }
167
- scratch[localid] = packetAccumulator =
168
- OpDef::finalise_op(op.template finalizePacket<PacketReturnType>(packetAccumulator), rng);
169
- // reduction parts // Local size is always power of 2
170
- EIGEN_UNROLL_LOOP
171
- for (Index offset = local_range / 2; offset > 0; offset /= 2) {
172
- itemID.barrier(cl::sycl::access::fence_space::local_space);
173
- if (localid < offset) {
174
- op.template reducePacket<PacketReturnType>(scratch[localid + offset], &packetAccumulator);
175
- scratch[localid] = op.template finalizePacket<PacketReturnType>(packetAccumulator);
176
- }
177
- }
178
- if (localid == 0) {
179
- output_ptr[itemID.get_group(0)] =
180
- op.finalizeBoth(op.initialize(), op.template finalizePacket<PacketReturnType>(packetAccumulator));
181
- }
182
- }
183
-
184
- template <bool Vect = (Evaluator::ReducerTraits::PacketAccess & Evaluator::InputPacketAccess)>
185
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE typename ::Eigen::internal::enable_if<!Vect>::type compute_reduction(
186
- const cl::sycl::nd_item<1> &itemID) {
187
- auto output_ptr = final_output.get_pointer();
188
- Index globalid = itemID.get_global_id(0);
189
- Index localid = itemID.get_local_id(0);
190
- // vectorizable parts
191
- CoeffReturnType accumulator = op.initialize();
192
- // non vectorizable parts
193
- for (Index i = globalid; i < rng; i += itemID.get_global_range(0)) {
194
- op.reduce(evaluator.impl().coeff(i), &accumulator);
195
- }
196
- scratch[localid] = accumulator = OpDef::finalise_op(op.finalize(accumulator), rng);
197
-
198
- // reduction parts. the local size is always power of 2
199
- EIGEN_UNROLL_LOOP
200
- for (Index offset = local_range / 2; offset > 0; offset /= 2) {
201
- itemID.barrier(cl::sycl::access::fence_space::local_space);
202
- if (localid < offset) {
203
- op.reduce(scratch[localid + offset], &accumulator);
204
- scratch[localid] = op.finalize(accumulator);
205
- }
206
- }
207
- if (localid == 0) {
208
- output_ptr[itemID.get_group(0)] = op.finalize(accumulator);
209
- }
210
- }
211
- };
212
-
213
- template <typename Evaluator, typename OpType>
214
- class GenericNondeterministicReducer {
215
- public:
216
- typedef typename Evaluator::CoeffReturnType CoeffReturnType;
217
- typedef typename Evaluator::EvaluatorPointerType EvaluatorPointerType;
218
- typedef typename Evaluator::Index Index;
219
- typedef OpDefiner<OpType, CoeffReturnType, Index, false> OpDef;
220
- typedef typename OpDef::type Op;
221
- template <typename Scratch>
222
- GenericNondeterministicReducer(Scratch, Evaluator evaluator_, EvaluatorPointerType output_accessor_, OpType functor_,
223
- Index range_, Index num_values_to_reduce_)
224
- : evaluator(evaluator_),
225
- output_accessor(output_accessor_),
226
- functor(OpDef::get_op(functor_)),
227
- range(range_),
228
- num_values_to_reduce(num_values_to_reduce_) {}
229
-
230
- void operator()(cl::sycl::nd_item<1> itemID) {
231
- auto output_accessor_ptr = output_accessor.get_pointer();
232
- /// const cast added as a naive solution to solve the qualifier drop error
233
- Index globalid = static_cast<Index>(itemID.get_global_linear_id());
234
- if (globalid < range) {
235
- CoeffReturnType accum = functor.initialize();
236
- Eigen::internal::GenericDimReducer<Evaluator::NumReducedDims - 1, Evaluator, Op>::reduce(
237
- evaluator, evaluator.firstInput(globalid), functor, &accum);
238
- output_accessor_ptr[globalid] = OpDef::finalise_op(functor.finalize(accum), num_values_to_reduce);
239
- }
240
- }
241
-
242
- private:
243
- Evaluator evaluator;
244
- EvaluatorPointerType output_accessor;
245
- Op functor;
246
- Index range;
247
- Index num_values_to_reduce;
248
- };
249
-
250
- enum class reduction_dim { inner_most, outer_most };
251
- // default is preserver
252
- template <typename Evaluator, typename OpType, typename PannelParameters, reduction_dim rt>
253
- struct PartialReductionKernel {
254
- typedef typename Evaluator::CoeffReturnType CoeffReturnType;
255
- typedef typename Evaluator::EvaluatorPointerType EvaluatorPointerType;
256
- typedef typename Evaluator::Index Index;
257
- typedef OpDefiner<OpType, CoeffReturnType, Index, false> OpDef;
258
- typedef typename OpDef::type Op;
259
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
260
- ScratchAcc;
261
- ScratchAcc scratch;
262
- Evaluator evaluator;
263
- EvaluatorPointerType output_accessor;
264
- Op op;
265
- const Index preserve_elements_num_groups;
266
- const Index reduce_elements_num_groups;
267
- const Index num_coeffs_to_preserve;
268
- const Index num_coeffs_to_reduce;
269
-
270
- PartialReductionKernel(ScratchAcc scratch_, Evaluator evaluator_, EvaluatorPointerType output_accessor_, OpType op_,
271
- const Index preserve_elements_num_groups_, const Index reduce_elements_num_groups_,
272
- const Index num_coeffs_to_preserve_, const Index num_coeffs_to_reduce_)
273
- : scratch(scratch_),
274
- evaluator(evaluator_),
275
- output_accessor(output_accessor_),
276
- op(OpDef::get_op(op_)),
277
- preserve_elements_num_groups(preserve_elements_num_groups_),
278
- reduce_elements_num_groups(reduce_elements_num_groups_),
279
- num_coeffs_to_preserve(num_coeffs_to_preserve_),
280
- num_coeffs_to_reduce(num_coeffs_to_reduce_) {}
281
-
282
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void element_wise_reduce(Index globalRId, Index globalPId,
283
- CoeffReturnType &accumulator) {
284
- if (globalPId >= num_coeffs_to_preserve) {
285
- return;
286
- }
287
- Index global_offset = rt == reduction_dim::outer_most ? globalPId + (globalRId * num_coeffs_to_preserve)
288
- : globalRId + (globalPId * num_coeffs_to_reduce);
289
- Index localOffset = globalRId;
290
-
291
- const Index per_thread_local_stride = PannelParameters::LocalThreadSizeR * reduce_elements_num_groups;
292
- const Index per_thread_global_stride =
293
- rt == reduction_dim::outer_most ? num_coeffs_to_preserve * per_thread_local_stride : per_thread_local_stride;
294
- for (Index i = globalRId; i < num_coeffs_to_reduce; i += per_thread_local_stride) {
295
- op.reduce(evaluator.impl().coeff(global_offset), &accumulator);
296
- localOffset += per_thread_local_stride;
297
- global_offset += per_thread_global_stride;
298
- }
299
- }
300
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(cl::sycl::nd_item<1> itemID) {
301
- const Index linearLocalThreadId = itemID.get_local_id(0);
302
- Index pLocalThreadId = rt == reduction_dim::outer_most ? linearLocalThreadId % PannelParameters::LocalThreadSizeP
303
- : linearLocalThreadId / PannelParameters::LocalThreadSizeR;
304
- Index rLocalThreadId = rt == reduction_dim::outer_most ? linearLocalThreadId / PannelParameters::LocalThreadSizeP
305
- : linearLocalThreadId % PannelParameters::LocalThreadSizeR;
306
- const Index pGroupId = rt == reduction_dim::outer_most ? itemID.get_group(0) % preserve_elements_num_groups
307
- : itemID.get_group(0) / reduce_elements_num_groups;
308
- const Index rGroupId = rt == reduction_dim::outer_most ? itemID.get_group(0) / preserve_elements_num_groups
309
- : itemID.get_group(0) % reduce_elements_num_groups;
310
-
311
- Index globalPId = pGroupId * PannelParameters::LocalThreadSizeP + pLocalThreadId;
312
- const Index globalRId = rGroupId * PannelParameters::LocalThreadSizeR + rLocalThreadId;
313
- auto scratchPtr = scratch.get_pointer().get();
314
- auto outPtr =
315
- output_accessor.get_pointer() + (reduce_elements_num_groups > 1 ? rGroupId * num_coeffs_to_preserve : 0);
316
- CoeffReturnType accumulator = op.initialize();
317
-
318
- element_wise_reduce(globalRId, globalPId, accumulator);
319
-
320
- accumulator = OpDef::finalise_op(op.finalize(accumulator), num_coeffs_to_reduce);
321
- scratchPtr[pLocalThreadId + rLocalThreadId * (PannelParameters::LocalThreadSizeP + PannelParameters::BC)] =
322
- accumulator;
323
- if (rt == reduction_dim::inner_most) {
324
- pLocalThreadId = linearLocalThreadId % PannelParameters::LocalThreadSizeP;
325
- rLocalThreadId = linearLocalThreadId / PannelParameters::LocalThreadSizeP;
326
- globalPId = pGroupId * PannelParameters::LocalThreadSizeP + pLocalThreadId;
327
- }
328
-
329
- /* Apply the reduction operation between the current local
330
- * id and the one on the other half of the vector. */
331
- auto out_scratch_ptr =
332
- scratchPtr + (pLocalThreadId + (rLocalThreadId * (PannelParameters::LocalThreadSizeP + PannelParameters::BC)));
333
- itemID.barrier(cl::sycl::access::fence_space::local_space);
334
- if (rt == reduction_dim::inner_most) {
335
- accumulator = *out_scratch_ptr;
336
- }
337
- // The Local LocalThreadSizeR is always power of 2
338
- EIGEN_UNROLL_LOOP
339
- for (Index offset = PannelParameters::LocalThreadSizeR >> 1; offset > 0; offset >>= 1) {
340
- if (rLocalThreadId < offset) {
341
- op.reduce(out_scratch_ptr[(PannelParameters::LocalThreadSizeP + PannelParameters::BC) * offset], &accumulator);
342
- // The result has already been divided for mean reducer in the
343
- // previous reduction so no need to divide furthermore
344
- *out_scratch_ptr = op.finalize(accumulator);
345
- }
346
- /* All threads collectively read from global memory into local.
347
- * The barrier ensures all threads' IO is resolved before
348
- * execution continues (strictly speaking, all threads within
349
- * a single work-group - there is no co-ordination between
350
- * work-groups, only work-items). */
351
- itemID.barrier(cl::sycl::access::fence_space::local_space);
352
- }
353
-
354
- if (rLocalThreadId == 0 && (globalPId < num_coeffs_to_preserve)) {
355
- outPtr[globalPId] = op.finalize(accumulator);
356
- }
357
- }
358
- };
359
-
360
- template <typename OutScalar, typename Index, typename InputAccessor, typename OutputAccessor, typename OpType>
361
- struct SecondStepPartialReduction {
362
- typedef OpDefiner<OpType, OutScalar, Index, false> OpDef;
363
- typedef typename OpDef::type Op;
364
- typedef cl::sycl::accessor<OutScalar, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
365
- ScratchAccessor;
366
- InputAccessor input_accessor;
367
- OutputAccessor output_accessor;
368
- Op op;
369
- const Index num_coeffs_to_preserve;
370
- const Index num_coeffs_to_reduce;
371
-
372
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE SecondStepPartialReduction(ScratchAccessor, InputAccessor input_accessor_,
373
- OutputAccessor output_accessor_, OpType op_,
374
- const Index num_coeffs_to_preserve_,
375
- const Index num_coeffs_to_reduce_)
376
- : input_accessor(input_accessor_),
377
- output_accessor(output_accessor_),
378
- op(OpDef::get_op(op_)),
379
- num_coeffs_to_preserve(num_coeffs_to_preserve_),
380
- num_coeffs_to_reduce(num_coeffs_to_reduce_) {}
381
-
382
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(cl::sycl::nd_item<1> itemID) {
383
- const Index globalId = itemID.get_global_id(0);
384
-
385
- if (globalId >= num_coeffs_to_preserve) return;
386
-
387
- auto in_ptr = input_accessor.get_pointer() + globalId;
388
-
389
- OutScalar accumulator = op.initialize();
390
- // num_coeffs_to_reduce is not bigger that 256
391
- for (Index i = 0; i < num_coeffs_to_reduce; i++) {
392
- op.reduce(*in_ptr, &accumulator);
393
- in_ptr += num_coeffs_to_preserve;
394
- }
395
- output_accessor.get_pointer()[globalId] = op.finalize(accumulator);
396
- }
397
- }; // namespace internal
398
-
399
- template <typename Index, Index LTP, Index LTR, bool BC_>
400
- struct ReductionPannel {
401
- static EIGEN_CONSTEXPR Index LocalThreadSizeP = LTP;
402
- static EIGEN_CONSTEXPR Index LocalThreadSizeR = LTR;
403
- static EIGEN_CONSTEXPR bool BC = BC_;
404
- };
405
-
406
- template <typename Self, typename Op, TensorSycl::internal::reduction_dim rt>
407
- struct PartialReducerLauncher {
408
- typedef typename Self::EvaluatorPointerType EvaluatorPointerType;
409
- typedef typename Self::CoeffReturnType CoeffReturnType;
410
- typedef typename Self::Storage Storage;
411
- typedef typename Self::Index Index;
412
- typedef ReductionPannel<typename Self::Index, EIGEN_SYCL_LOCAL_THREAD_DIM0, EIGEN_SYCL_LOCAL_THREAD_DIM1, true>
413
- PannelParameters;
414
-
415
- typedef PartialReductionKernel<Self, Op, PannelParameters, rt> SyclReducerKerneType;
416
-
417
- static bool run(const Self &self, const Op &reducer, const Eigen::SyclDevice &dev, EvaluatorPointerType output,
418
- Index num_coeffs_to_reduce, Index num_coeffs_to_preserve) {
419
- Index roundUpP = roundUp(num_coeffs_to_preserve, PannelParameters::LocalThreadSizeP);
420
-
421
- // getPowerOfTwo makes sure local range is power of 2 and <=
422
- // maxSyclThreadPerBlock this will help us to avoid extra check on the
423
- // kernel
424
- static_assert(!((PannelParameters::LocalThreadSizeP * PannelParameters::LocalThreadSizeR) &
425
- (PannelParameters::LocalThreadSizeP * PannelParameters::LocalThreadSizeR - 1)),
426
- "The Local thread size must be a power of 2 for the reduction "
427
- "operation");
428
-
429
- EIGEN_CONSTEXPR Index localRange = PannelParameters::LocalThreadSizeP * PannelParameters::LocalThreadSizeR;
430
- // In this step, we force the code not to be more than 2-step reduction:
431
- // Our empirical research shows that if each thread reduces at least 64
432
- // elemnts individually, we get better performance. However, this can change
433
- // on different platforms. In this step we force the code not to be
434
- // morthan step reduction: Our empirical research shows that for inner_most
435
- // dim reducer, it is better to have 8 group in a reduce dimension for sizes
436
- // > 1024 to achieve the best performance.
437
- const Index reductionPerThread = 64;
438
- Index cu = dev.getPowerOfTwo(dev.getNumSyclMultiProcessors(), true);
439
- const Index pNumGroups = roundUpP / PannelParameters::LocalThreadSizeP;
440
- Index rGroups = (cu + pNumGroups - 1) / pNumGroups;
441
- const Index rNumGroups = num_coeffs_to_reduce > reductionPerThread * localRange ? std::min(rGroups, localRange) : 1;
442
- const Index globalRange = pNumGroups * rNumGroups * localRange;
443
-
444
- EIGEN_CONSTEXPR Index scratchSize =
445
- PannelParameters::LocalThreadSizeR * (PannelParameters::LocalThreadSizeP + PannelParameters::BC);
446
- auto thread_range = cl::sycl::nd_range<1>(cl::sycl::range<1>(globalRange), cl::sycl::range<1>(localRange));
447
- if (rNumGroups > 1) {
448
- CoeffReturnType *temp_pointer = static_cast<CoeffReturnType *>(
449
- dev.allocate_temp(num_coeffs_to_preserve * rNumGroups * sizeof(CoeffReturnType)));
450
- EvaluatorPointerType temp_accessor = dev.get(temp_pointer);
451
- dev.template unary_kernel_launcher<CoeffReturnType, SyclReducerKerneType>(
452
- self, temp_accessor, thread_range, scratchSize, reducer, pNumGroups, rNumGroups, num_coeffs_to_preserve,
453
- num_coeffs_to_reduce);
454
-
455
- typedef SecondStepPartialReduction<CoeffReturnType, Index, EvaluatorPointerType, EvaluatorPointerType, Op>
456
- SecondStepPartialReductionKernel;
457
-
458
- dev.template unary_kernel_launcher<CoeffReturnType, SecondStepPartialReductionKernel>(
459
- temp_accessor, output,
460
- cl::sycl::nd_range<1>(cl::sycl::range<1>(pNumGroups * localRange), cl::sycl::range<1>(localRange)), Index(1),
461
- reducer, num_coeffs_to_preserve, rNumGroups);
462
-
463
- self.device().deallocate_temp(temp_pointer);
464
- } else {
465
- dev.template unary_kernel_launcher<CoeffReturnType, SyclReducerKerneType>(
466
- self, output, thread_range, scratchSize, reducer, pNumGroups, rNumGroups, num_coeffs_to_preserve,
467
- num_coeffs_to_reduce);
468
- }
469
- return false;
470
- }
471
- };
472
- } // namespace internal
473
- } // namespace TensorSycl
474
-
475
- namespace internal {
476
-
477
- template <typename Self, typename Op, bool Vectorizable>
478
- struct FullReducer<Self, Op, Eigen::SyclDevice, Vectorizable> {
479
- typedef typename Self::CoeffReturnType CoeffReturnType;
480
- typedef typename Self::EvaluatorPointerType EvaluatorPointerType;
481
- static EIGEN_CONSTEXPR bool HasOptimizedImplementation = true;
482
- static EIGEN_CONSTEXPR int PacketSize = Self::PacketAccess ? Self::PacketSize : 1;
483
- static void run(const Self &self, Op &reducer, const Eigen::SyclDevice &dev, EvaluatorPointerType data) {
484
- typedef typename conditional<Self::PacketAccess, typename Self::PacketReturnType, CoeffReturnType>::type OutType;
485
- static_assert(!((EIGEN_SYCL_LOCAL_THREAD_DIM0 * EIGEN_SYCL_LOCAL_THREAD_DIM1) &
486
- (EIGEN_SYCL_LOCAL_THREAD_DIM0 * EIGEN_SYCL_LOCAL_THREAD_DIM1 - 1)),
487
- "The Local thread size must be a power of 2 for the reduction "
488
- "operation");
489
- EIGEN_CONSTEXPR Index local_range = EIGEN_SYCL_LOCAL_THREAD_DIM0 * EIGEN_SYCL_LOCAL_THREAD_DIM1;
490
-
491
- typename Self::Index inputSize = self.impl().dimensions().TotalSize();
492
- // In this step we force the code not to be more than 2-step reduction:
493
- // Our empirical research shows that if each thread reduces at least 512
494
- // elemnts individually, we get better performance.
495
- const Index reductionPerThread = 2048;
496
- // const Index num_work_group =
497
- Index reductionGroup = dev.getPowerOfTwo(
498
- (inputSize + (reductionPerThread * local_range - 1)) / (reductionPerThread * local_range), true);
499
- const Index num_work_group = std::min(reductionGroup, local_range);
500
- // 1
501
- // ? local_range
502
- // : 1);
503
- const Index global_range = num_work_group * local_range;
504
-
505
- auto thread_range = cl::sycl::nd_range<1>(cl::sycl::range<1>(global_range), cl::sycl::range<1>(local_range));
506
- typedef TensorSycl::internal::FullReductionKernelFunctor<Self, Op, local_range> reduction_kernel_t;
507
- if (num_work_group > 1) {
508
- CoeffReturnType *temp_pointer =
509
- static_cast<CoeffReturnType *>(dev.allocate_temp(num_work_group * sizeof(CoeffReturnType)));
510
- typename Self::EvaluatorPointerType tmp_global_accessor = dev.get(temp_pointer);
511
- dev.template unary_kernel_launcher<OutType, reduction_kernel_t>(self, tmp_global_accessor, thread_range,
512
- local_range, inputSize, reducer);
513
-
514
- typedef TensorSycl::internal::SecondStepFullReducer<CoeffReturnType, Op, EvaluatorPointerType,
515
- EvaluatorPointerType, Index, local_range>
516
- GenericRKernel;
517
- dev.template unary_kernel_launcher<CoeffReturnType, GenericRKernel>(
518
- tmp_global_accessor, data,
519
- cl::sycl::nd_range<1>(cl::sycl::range<1>(num_work_group), cl::sycl::range<1>(num_work_group)), num_work_group,
520
- reducer);
521
-
522
- dev.deallocate_temp(temp_pointer);
523
- } else {
524
- dev.template unary_kernel_launcher<OutType, reduction_kernel_t>(self, data, thread_range, local_range, inputSize,
525
- reducer);
526
- }
527
- }
528
- };
529
- // vectorizable inner_most most dim preserver
530
- // col reduction
531
- template <typename Self, typename Op>
532
- struct OuterReducer<Self, Op, Eigen::SyclDevice> {
533
- static EIGEN_CONSTEXPR bool HasOptimizedImplementation = true;
534
-
535
- static bool run(const Self &self, const Op &reducer, const Eigen::SyclDevice &dev,
536
- typename Self::EvaluatorPointerType output, typename Self::Index num_coeffs_to_reduce,
537
- typename Self::Index num_coeffs_to_preserve) {
538
- return ::Eigen::TensorSycl::internal::PartialReducerLauncher<
539
- Self, Op, ::Eigen::TensorSycl::internal::reduction_dim::outer_most>::run(self, reducer, dev, output,
540
- num_coeffs_to_reduce,
541
- num_coeffs_to_preserve);
542
- }
543
- };
544
- // row reduction
545
- template <typename Self, typename Op>
546
- struct InnerReducer<Self, Op, Eigen::SyclDevice> {
547
- static EIGEN_CONSTEXPR bool HasOptimizedImplementation = true;
548
-
549
- static bool run(const Self &self, const Op &reducer, const Eigen::SyclDevice &dev,
550
- typename Self::EvaluatorPointerType output, typename Self::Index num_coeffs_to_reduce,
551
- typename Self::Index num_coeffs_to_preserve) {
552
- return ::Eigen::TensorSycl::internal::PartialReducerLauncher<
553
- Self, Op, ::Eigen::TensorSycl::internal::reduction_dim::inner_most>::run(self, reducer, dev, output,
554
- num_coeffs_to_reduce,
555
- num_coeffs_to_preserve);
556
- }
557
- };
558
-
559
- // ArmgMax uses this kernel for partial reduction//
560
- // TODO(@mehdi.goli) come up with a better kernel
561
- // generic partial reduction
562
- template <typename Self, typename Op>
563
- struct GenericReducer<Self, Op, Eigen::SyclDevice> {
564
- static EIGEN_CONSTEXPR bool HasOptimizedImplementation = false;
565
- static bool run(const Self &self, const Op &reducer, const Eigen::SyclDevice &dev,
566
- typename Self::EvaluatorPointerType output, typename Self::Index num_values_to_reduce,
567
- typename Self::Index num_coeffs_to_preserve) {
568
- typename Self::Index range, GRange, tileSize;
569
- dev.parallel_for_setup(num_coeffs_to_preserve, tileSize, range, GRange);
570
-
571
- dev.template unary_kernel_launcher<typename Self::CoeffReturnType,
572
- TensorSycl::internal::GenericNondeterministicReducer<Self, Op>>(
573
- self, output, cl::sycl::nd_range<1>(cl::sycl::range<1>(GRange), cl::sycl::range<1>(tileSize)), Index(1),
574
- reducer, range, (num_values_to_reduce != 0) ? num_values_to_reduce : static_cast<Index>(1));
575
- return false;
576
- }
577
- };
578
-
579
- } // namespace internal
580
- } // namespace Eigen
581
-
582
- #endif // UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_REDUCTION_SYCL_HPP