sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sequenzo might be problematic. Click here for more details.

Files changed (475) hide show
  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 +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  214. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  215. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  216. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  217. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  218. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  219. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  220. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  221. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  222. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  223. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  224. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  225. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  226. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  227. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  228. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  229. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  230. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  231. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  232. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  233. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  234. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  235. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  236. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  237. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  238. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  239. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  240. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  241. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  242. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  243. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  244. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  245. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  246. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  247. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  248. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  249. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  250. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  251. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  252. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  253. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  254. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  255. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  256. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  257. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  258. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  259. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  260. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  261. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  262. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  263. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  264. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  265. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  266. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  267. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  268. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  269. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  270. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  271. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  272. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  273. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  274. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  275. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  276. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  277. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  278. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  279. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  280. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  281. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  282. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  283. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  284. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  285. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  286. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  287. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  288. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  289. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  290. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  291. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  292. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
  293. sequenzo/dissimilarity_measures/src/eigen/test/main.h +0 -857
  294. sequenzo/dissimilarity_measures/src/eigen/test/packetmath_test_shared.h +0 -275
  295. sequenzo/dissimilarity_measures/src/eigen/test/product.h +0 -259
  296. sequenzo/dissimilarity_measures/src/eigen/test/random_without_cast_overflow.h +0 -152
  297. sequenzo/dissimilarity_measures/src/eigen/test/solverbase.h +0 -36
  298. sequenzo/dissimilarity_measures/src/eigen/test/sparse.h +0 -204
  299. sequenzo/dissimilarity_measures/src/eigen/test/sparse_solver.h +0 -699
  300. sequenzo/dissimilarity_measures/src/eigen/test/split_test_helper.h +0 -5994
  301. sequenzo/dissimilarity_measures/src/eigen/test/svd_common.h +0 -521
  302. sequenzo/dissimilarity_measures/src/eigen/test/svd_fill.h +0 -118
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  393. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  394. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  395. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  396. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  397. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  398. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  399. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  400. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  401. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  402. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,582 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // 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)
22
- * 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
- *****************************************************************/
27
-
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>
78
- LocalAccessor;
79
- typedef OpDefiner<OpType, CoeffReturnType, Index, true> OpDef;
80
- typedef typename OpDef::type Op;
81
- LocalAccessor scratch;
82
- InputAccessor aI;
83
- OutputAccessor outAcc;
84
- Op op;
85
- SecondStepFullReducer(LocalAccessor scratch_, InputAccessor aI_, OutputAccessor outAcc_, OpType op_)
86
- : scratch(scratch_), aI(aI_), outAcc(outAcc_), op(OpDef::get_op(op_)) {}
87
-
88
- void operator()(cl::sycl::nd_item<1> itemID) {
89
- // Our empirical research shows that the best performance will be achieved
90
- // when there is only one element per thread to reduce in the second step.
91
- // 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.
96
- 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