sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__cp310-cp310-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +107 -5
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  13. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  15. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  17. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  18. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  19. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  20. sequenzo/multidomain/cat.py +0 -53
  21. sequenzo/multidomain/idcd.py +0 -1
  22. sequenzo/openmp_setup.py +233 -0
  23. sequenzo/visualization/plot_transition_matrix.py +21 -22
  24. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  25. sequenzo-0.1.19.dist-info/RECORD +272 -0
  26. sequenzo/dissimilarity_measures/setup.py +0 -35
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  169. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  171. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  172. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  173. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  174. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  175. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  176. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  177. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  178. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  179. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  180. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  181. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  182. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  183. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  184. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  185. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  186. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  187. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  188. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  189. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  190. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  191. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  192. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  197. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  198. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  199. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  200. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  201. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  202. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  203. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  206. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  207. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  208. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  209. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  210. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  211. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  212. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
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  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Mehdi Goli Codeplay Software Ltd.
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- // Ralph Potter Codeplay Software Ltd.
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- // Luke Iwanski Codeplay Software Ltd.
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- // Contact: <eigen@codeplay.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- /*****************************************************************
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- * TensorScanSycl.h
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- *
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- * \brief:
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- * Tensor Scan Sycl implement the extend version of
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- * "Efficient parallel scan algorithms for GPUs." .for Tensor operations.
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- * The algorithm requires up to 3 stage (consequently 3 kernels) depending on
20
- * the size of the tensor. In the first kernel (ScanKernelFunctor), each
21
- * threads within the work-group individually reduces the allocated elements per
22
- * thread in order to reduces the total number of blocks. In the next step all
23
- * thread within the work-group will reduce the associated blocks into the
24
- * temporary buffers. In the next kernel(ScanBlockKernelFunctor), the temporary
25
- * buffer is given as an input and all the threads within a work-group scan and
26
- * reduces the boundaries between the blocks (generated from the previous
27
- * kernel). and write the data on the temporary buffer. If the second kernel is
28
- * required, the third and final kerenl (ScanAdjustmentKernelFunctor) will
29
- * adjust the final result into the output buffer.
30
- * The original algorithm for the parallel prefix sum can be found here:
31
- *
32
- * Sengupta, Shubhabrata, Mark Harris, and Michael Garland. "Efficient parallel
33
- * scan algorithms for GPUs." NVIDIA, Santa Clara, CA, Tech. Rep. NVR-2008-003
34
- *1, no. 1 (2008): 1-17.
35
- *****************************************************************/
36
-
37
- #ifndef UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_SYCL_SYCL_HPP
38
- #define UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_SYCL_SYCL_HPP
39
-
40
- namespace Eigen {
41
- namespace TensorSycl {
42
- namespace internal {
43
-
44
- #ifndef EIGEN_SYCL_MAX_GLOBAL_RANGE
45
- #define EIGEN_SYCL_MAX_GLOBAL_RANGE (EIGEN_SYCL_LOCAL_THREAD_DIM0 * EIGEN_SYCL_LOCAL_THREAD_DIM1 * 4)
46
- #endif
47
-
48
- template <typename index_t>
49
- struct ScanParameters {
50
- // must be power of 2
51
- static EIGEN_CONSTEXPR index_t ScanPerThread = 8;
52
- const index_t total_size;
53
- const index_t non_scan_size;
54
- const index_t scan_size;
55
- const index_t non_scan_stride;
56
- const index_t scan_stride;
57
- const index_t panel_threads;
58
- const index_t group_threads;
59
- const index_t block_threads;
60
- const index_t elements_per_group;
61
- const index_t elements_per_block;
62
- const index_t loop_range;
63
-
64
- ScanParameters(index_t total_size_, index_t non_scan_size_, index_t scan_size_, index_t non_scan_stride_,
65
- index_t scan_stride_, index_t panel_threads_, index_t group_threads_, index_t block_threads_,
66
- index_t elements_per_group_, index_t elements_per_block_, index_t loop_range_)
67
- : total_size(total_size_),
68
- non_scan_size(non_scan_size_),
69
- scan_size(scan_size_),
70
- non_scan_stride(non_scan_stride_),
71
- scan_stride(scan_stride_),
72
- panel_threads(panel_threads_),
73
- group_threads(group_threads_),
74
- block_threads(block_threads_),
75
- elements_per_group(elements_per_group_),
76
- elements_per_block(elements_per_block_),
77
- loop_range(loop_range_) {}
78
- };
79
-
80
- enum class scan_step { first, second };
81
- template <typename Evaluator, typename CoeffReturnType, typename OutAccessor, typename Op, typename Index,
82
- scan_step stp>
83
- struct ScanKernelFunctor {
84
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
85
- LocalAccessor;
86
- static EIGEN_CONSTEXPR int PacketSize = ScanParameters<Index>::ScanPerThread / 2;
87
-
88
- LocalAccessor scratch;
89
- Evaluator dev_eval;
90
- OutAccessor out_accessor;
91
- OutAccessor temp_accessor;
92
- const ScanParameters<Index> scanParameters;
93
- Op accumulator;
94
- const bool inclusive;
95
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE ScanKernelFunctor(LocalAccessor scratch_, const Evaluator dev_eval_,
96
- OutAccessor out_accessor_, OutAccessor temp_accessor_,
97
- const ScanParameters<Index> scanParameters_, Op accumulator_,
98
- const bool inclusive_)
99
- : scratch(scratch_),
100
- dev_eval(dev_eval_),
101
- out_accessor(out_accessor_),
102
- temp_accessor(temp_accessor_),
103
- scanParameters(scanParameters_),
104
- accumulator(accumulator_),
105
- inclusive(inclusive_) {}
106
-
107
- template <scan_step sst = stp, typename Input>
108
- typename ::Eigen::internal::enable_if<sst == scan_step::first, CoeffReturnType>::type EIGEN_DEVICE_FUNC
109
- EIGEN_STRONG_INLINE
110
- read(const Input &inpt, Index global_id) {
111
- return inpt.coeff(global_id);
112
- }
113
-
114
- template <scan_step sst = stp, typename Input>
115
- typename ::Eigen::internal::enable_if<sst != scan_step::first, CoeffReturnType>::type EIGEN_DEVICE_FUNC
116
- EIGEN_STRONG_INLINE
117
- read(const Input &inpt, Index global_id) {
118
- return inpt[global_id];
119
- }
120
-
121
- template <scan_step sst = stp, typename InclusiveOp>
122
- typename ::Eigen::internal::enable_if<sst == scan_step::first>::type EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
123
- first_step_inclusive_Operation(InclusiveOp inclusive_op) {
124
- inclusive_op();
125
- }
126
-
127
- template <scan_step sst = stp, typename InclusiveOp>
128
- typename ::Eigen::internal::enable_if<sst != scan_step::first>::type EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
129
- first_step_inclusive_Operation(InclusiveOp) {}
130
-
131
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(cl::sycl::nd_item<1> itemID) {
132
- auto out_ptr = out_accessor.get_pointer();
133
- auto tmp_ptr = temp_accessor.get_pointer();
134
- auto scratch_ptr = scratch.get_pointer().get();
135
-
136
- for (Index loop_offset = 0; loop_offset < scanParameters.loop_range; loop_offset++) {
137
- Index data_offset = (itemID.get_global_id(0) + (itemID.get_global_range(0) * loop_offset));
138
- Index tmp = data_offset % scanParameters.panel_threads;
139
- const Index panel_id = data_offset / scanParameters.panel_threads;
140
- const Index group_id = tmp / scanParameters.group_threads;
141
- tmp = tmp % scanParameters.group_threads;
142
- const Index block_id = tmp / scanParameters.block_threads;
143
- const Index local_id = tmp % scanParameters.block_threads;
144
- // we put one element per packet in scratch_mem
145
- const Index scratch_stride = scanParameters.elements_per_block / PacketSize;
146
- const Index scratch_offset = (itemID.get_local_id(0) / scanParameters.block_threads) * scratch_stride;
147
- CoeffReturnType private_scan[ScanParameters<Index>::ScanPerThread];
148
- CoeffReturnType inclusive_scan;
149
- // the actual panel size is scan_size * non_scan_size.
150
- // elements_per_panel is roundup to power of 2 for binary tree
151
- const Index panel_offset = panel_id * scanParameters.scan_size * scanParameters.non_scan_size;
152
- const Index group_offset = group_id * scanParameters.non_scan_stride;
153
- // This will be effective when the size is bigger than elements_per_block
154
- const Index block_offset = block_id * scanParameters.elements_per_block * scanParameters.scan_stride;
155
- const Index thread_offset = (ScanParameters<Index>::ScanPerThread * local_id * scanParameters.scan_stride);
156
- const Index global_offset = panel_offset + group_offset + block_offset + thread_offset;
157
- Index next_elements = 0;
158
- EIGEN_UNROLL_LOOP
159
- for (int i = 0; i < ScanParameters<Index>::ScanPerThread; i++) {
160
- Index global_id = global_offset + next_elements;
161
- private_scan[i] = ((((block_id * scanParameters.elements_per_block) +
162
- (ScanParameters<Index>::ScanPerThread * local_id) + i) < scanParameters.scan_size) &&
163
- (global_id < scanParameters.total_size))
164
- ? read(dev_eval, global_id)
165
- : accumulator.initialize();
166
- next_elements += scanParameters.scan_stride;
167
- }
168
- first_step_inclusive_Operation([&]() EIGEN_DEVICE_FUNC {
169
- if (inclusive) {
170
- inclusive_scan = private_scan[ScanParameters<Index>::ScanPerThread - 1];
171
- }
172
- });
173
- // This for loop must be 2
174
- EIGEN_UNROLL_LOOP
175
- for (int packetIndex = 0; packetIndex < ScanParameters<Index>::ScanPerThread; packetIndex += PacketSize) {
176
- Index private_offset = 1;
177
- // build sum in place up the tree
178
- EIGEN_UNROLL_LOOP
179
- for (Index d = PacketSize >> 1; d > 0; d >>= 1) {
180
- EIGEN_UNROLL_LOOP
181
- for (Index l = 0; l < d; l++) {
182
- Index ai = private_offset * (2 * l + 1) - 1 + packetIndex;
183
- Index bi = private_offset * (2 * l + 2) - 1 + packetIndex;
184
- CoeffReturnType accum = accumulator.initialize();
185
- accumulator.reduce(private_scan[ai], &accum);
186
- accumulator.reduce(private_scan[bi], &accum);
187
- private_scan[bi] = accumulator.finalize(accum);
188
- }
189
- private_offset *= 2;
190
- }
191
- scratch_ptr[2 * local_id + (packetIndex / PacketSize) + scratch_offset] =
192
- private_scan[PacketSize - 1 + packetIndex];
193
- private_scan[PacketSize - 1 + packetIndex] = accumulator.initialize();
194
- // traverse down tree & build scan
195
- EIGEN_UNROLL_LOOP
196
- for (Index d = 1; d < PacketSize; d *= 2) {
197
- private_offset >>= 1;
198
- EIGEN_UNROLL_LOOP
199
- for (Index l = 0; l < d; l++) {
200
- Index ai = private_offset * (2 * l + 1) - 1 + packetIndex;
201
- Index bi = private_offset * (2 * l + 2) - 1 + packetIndex;
202
- CoeffReturnType accum = accumulator.initialize();
203
- accumulator.reduce(private_scan[ai], &accum);
204
- accumulator.reduce(private_scan[bi], &accum);
205
- private_scan[ai] = private_scan[bi];
206
- private_scan[bi] = accumulator.finalize(accum);
207
- }
208
- }
209
- }
210
-
211
- Index offset = 1;
212
- // build sum in place up the tree
213
- for (Index d = scratch_stride >> 1; d > 0; d >>= 1) {
214
- // Synchronise
215
- itemID.barrier(cl::sycl::access::fence_space::local_space);
216
- if (local_id < d) {
217
- Index ai = offset * (2 * local_id + 1) - 1 + scratch_offset;
218
- Index bi = offset * (2 * local_id + 2) - 1 + scratch_offset;
219
- CoeffReturnType accum = accumulator.initialize();
220
- accumulator.reduce(scratch_ptr[ai], &accum);
221
- accumulator.reduce(scratch_ptr[bi], &accum);
222
- scratch_ptr[bi] = accumulator.finalize(accum);
223
- }
224
- offset *= 2;
225
- }
226
- // Synchronise
227
- itemID.barrier(cl::sycl::access::fence_space::local_space);
228
- // next step optimisation
229
- if (local_id == 0) {
230
- if (((scanParameters.elements_per_group / scanParameters.elements_per_block) > 1)) {
231
- const Index temp_id = panel_id * (scanParameters.elements_per_group / scanParameters.elements_per_block) *
232
- scanParameters.non_scan_size +
233
- group_id * (scanParameters.elements_per_group / scanParameters.elements_per_block) +
234
- block_id;
235
- tmp_ptr[temp_id] = scratch_ptr[scratch_stride - 1 + scratch_offset];
236
- }
237
- // clear the last element
238
- scratch_ptr[scratch_stride - 1 + scratch_offset] = accumulator.initialize();
239
- }
240
- // traverse down tree & build scan
241
- for (Index d = 1; d < scratch_stride; d *= 2) {
242
- offset >>= 1;
243
- // Synchronise
244
- itemID.barrier(cl::sycl::access::fence_space::local_space);
245
- if (local_id < d) {
246
- Index ai = offset * (2 * local_id + 1) - 1 + scratch_offset;
247
- Index bi = offset * (2 * local_id + 2) - 1 + scratch_offset;
248
- CoeffReturnType accum = accumulator.initialize();
249
- accumulator.reduce(scratch_ptr[ai], &accum);
250
- accumulator.reduce(scratch_ptr[bi], &accum);
251
- scratch_ptr[ai] = scratch_ptr[bi];
252
- scratch_ptr[bi] = accumulator.finalize(accum);
253
- }
254
- }
255
- // Synchronise
256
- itemID.barrier(cl::sycl::access::fence_space::local_space);
257
- // This for loop must be 2
258
- EIGEN_UNROLL_LOOP
259
- for (int packetIndex = 0; packetIndex < ScanParameters<Index>::ScanPerThread; packetIndex += PacketSize) {
260
- EIGEN_UNROLL_LOOP
261
- for (Index i = 0; i < PacketSize; i++) {
262
- CoeffReturnType accum = private_scan[packetIndex + i];
263
- accumulator.reduce(scratch_ptr[2 * local_id + (packetIndex / PacketSize) + scratch_offset], &accum);
264
- private_scan[packetIndex + i] = accumulator.finalize(accum);
265
- }
266
- }
267
- first_step_inclusive_Operation([&]() EIGEN_DEVICE_FUNC {
268
- if (inclusive) {
269
- accumulator.reduce(private_scan[ScanParameters<Index>::ScanPerThread - 1], &inclusive_scan);
270
- private_scan[0] = accumulator.finalize(inclusive_scan);
271
- }
272
- });
273
- next_elements = 0;
274
- // right the first set of private param
275
- EIGEN_UNROLL_LOOP
276
- for (Index i = 0; i < ScanParameters<Index>::ScanPerThread; i++) {
277
- Index global_id = global_offset + next_elements;
278
- if ((((block_id * scanParameters.elements_per_block) + (ScanParameters<Index>::ScanPerThread * local_id) + i) <
279
- scanParameters.scan_size) &&
280
- (global_id < scanParameters.total_size)) {
281
- Index private_id = (i * !inclusive) + (((i + 1) % ScanParameters<Index>::ScanPerThread) * (inclusive));
282
- out_ptr[global_id] = private_scan[private_id];
283
- }
284
- next_elements += scanParameters.scan_stride;
285
- }
286
- } // end for loop
287
- }
288
- };
289
-
290
- template <typename CoeffReturnType, typename InAccessor, typename OutAccessor, typename Op, typename Index>
291
- struct ScanAdjustmentKernelFunctor {
292
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
293
- LocalAccessor;
294
- static EIGEN_CONSTEXPR int PacketSize = ScanParameters<Index>::ScanPerThread / 2;
295
- InAccessor in_accessor;
296
- OutAccessor out_accessor;
297
- const ScanParameters<Index> scanParameters;
298
- Op accumulator;
299
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE ScanAdjustmentKernelFunctor(LocalAccessor, InAccessor in_accessor_,
300
- OutAccessor out_accessor_,
301
- const ScanParameters<Index> scanParameters_,
302
- Op accumulator_)
303
- : in_accessor(in_accessor_),
304
- out_accessor(out_accessor_),
305
- scanParameters(scanParameters_),
306
- accumulator(accumulator_) {}
307
-
308
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(cl::sycl::nd_item<1> itemID) {
309
- auto in_ptr = in_accessor.get_pointer();
310
- auto out_ptr = out_accessor.get_pointer();
311
-
312
- for (Index loop_offset = 0; loop_offset < scanParameters.loop_range; loop_offset++) {
313
- Index data_offset = (itemID.get_global_id(0) + (itemID.get_global_range(0) * loop_offset));
314
- Index tmp = data_offset % scanParameters.panel_threads;
315
- const Index panel_id = data_offset / scanParameters.panel_threads;
316
- const Index group_id = tmp / scanParameters.group_threads;
317
- tmp = tmp % scanParameters.group_threads;
318
- const Index block_id = tmp / scanParameters.block_threads;
319
- const Index local_id = tmp % scanParameters.block_threads;
320
-
321
- // the actual panel size is scan_size * non_scan_size.
322
- // elements_per_panel is roundup to power of 2 for binary tree
323
- const Index panel_offset = panel_id * scanParameters.scan_size * scanParameters.non_scan_size;
324
- const Index group_offset = group_id * scanParameters.non_scan_stride;
325
- // This will be effective when the size is bigger than elements_per_block
326
- const Index block_offset = block_id * scanParameters.elements_per_block * scanParameters.scan_stride;
327
- const Index thread_offset = ScanParameters<Index>::ScanPerThread * local_id * scanParameters.scan_stride;
328
-
329
- const Index global_offset = panel_offset + group_offset + block_offset + thread_offset;
330
- const Index block_size = scanParameters.elements_per_group / scanParameters.elements_per_block;
331
- const Index in_id = (panel_id * block_size * scanParameters.non_scan_size) + (group_id * block_size) + block_id;
332
- CoeffReturnType adjust_val = in_ptr[in_id];
333
-
334
- Index next_elements = 0;
335
- EIGEN_UNROLL_LOOP
336
- for (Index i = 0; i < ScanParameters<Index>::ScanPerThread; i++) {
337
- Index global_id = global_offset + next_elements;
338
- if ((((block_id * scanParameters.elements_per_block) + (ScanParameters<Index>::ScanPerThread * local_id) + i) <
339
- scanParameters.scan_size) &&
340
- (global_id < scanParameters.total_size)) {
341
- CoeffReturnType accum = adjust_val;
342
- accumulator.reduce(out_ptr[global_id], &accum);
343
- out_ptr[global_id] = accumulator.finalize(accum);
344
- }
345
- next_elements += scanParameters.scan_stride;
346
- }
347
- }
348
- }
349
- };
350
-
351
- template <typename Index>
352
- struct ScanInfo {
353
- const Index &total_size;
354
- const Index &scan_size;
355
- const Index &panel_size;
356
- const Index &non_scan_size;
357
- const Index &scan_stride;
358
- const Index &non_scan_stride;
359
-
360
- Index max_elements_per_block;
361
- Index block_size;
362
- Index panel_threads;
363
- Index group_threads;
364
- Index block_threads;
365
- Index elements_per_group;
366
- Index elements_per_block;
367
- Index loop_range;
368
- Index global_range;
369
- Index local_range;
370
- const Eigen::SyclDevice &dev;
371
- EIGEN_STRONG_INLINE ScanInfo(const Index &total_size_, const Index &scan_size_, const Index &panel_size_,
372
- const Index &non_scan_size_, const Index &scan_stride_, const Index &non_scan_stride_,
373
- const Eigen::SyclDevice &dev_)
374
- : total_size(total_size_),
375
- scan_size(scan_size_),
376
- panel_size(panel_size_),
377
- non_scan_size(non_scan_size_),
378
- scan_stride(scan_stride_),
379
- non_scan_stride(non_scan_stride_),
380
- dev(dev_) {
381
- // must be power of 2
382
- local_range = std::min(Index(dev.getNearestPowerOfTwoWorkGroupSize()),
383
- Index(EIGEN_SYCL_LOCAL_THREAD_DIM0 * EIGEN_SYCL_LOCAL_THREAD_DIM1));
384
-
385
- max_elements_per_block = local_range * ScanParameters<Index>::ScanPerThread;
386
-
387
- elements_per_group =
388
- dev.getPowerOfTwo(Index(roundUp(Index(scan_size), ScanParameters<Index>::ScanPerThread)), true);
389
- const Index elements_per_panel = elements_per_group * non_scan_size;
390
- elements_per_block = std::min(Index(elements_per_group), Index(max_elements_per_block));
391
- panel_threads = elements_per_panel / ScanParameters<Index>::ScanPerThread;
392
- group_threads = elements_per_group / ScanParameters<Index>::ScanPerThread;
393
- block_threads = elements_per_block / ScanParameters<Index>::ScanPerThread;
394
- block_size = elements_per_group / elements_per_block;
395
- #ifdef EIGEN_SYCL_MAX_GLOBAL_RANGE
396
- const Index max_threads = std::min(Index(panel_threads * panel_size), Index(EIGEN_SYCL_MAX_GLOBAL_RANGE));
397
- #else
398
- const Index max_threads = panel_threads * panel_size;
399
- #endif
400
- global_range = roundUp(max_threads, local_range);
401
- loop_range = Index(
402
- std::ceil(double(elements_per_panel * panel_size) / (global_range * ScanParameters<Index>::ScanPerThread)));
403
- }
404
- inline ScanParameters<Index> get_scan_parameter() {
405
- return ScanParameters<Index>(total_size, non_scan_size, scan_size, non_scan_stride, scan_stride, panel_threads,
406
- group_threads, block_threads, elements_per_group, elements_per_block, loop_range);
407
- }
408
- inline cl::sycl::nd_range<1> get_thread_range() {
409
- return cl::sycl::nd_range<1>(cl::sycl::range<1>(global_range), cl::sycl::range<1>(local_range));
410
- }
411
- };
412
-
413
- template <typename EvaluatorPointerType, typename CoeffReturnType, typename Reducer, typename Index>
414
- struct SYCLAdjustBlockOffset {
415
- EIGEN_STRONG_INLINE static void adjust_scan_block_offset(EvaluatorPointerType in_ptr, EvaluatorPointerType out_ptr,
416
- Reducer &accumulator, const Index total_size,
417
- const Index scan_size, const Index panel_size,
418
- const Index non_scan_size, const Index scan_stride,
419
- const Index non_scan_stride, const Eigen::SyclDevice &dev) {
420
- auto scan_info =
421
- ScanInfo<Index>(total_size, scan_size, panel_size, non_scan_size, scan_stride, non_scan_stride, dev);
422
-
423
- typedef ScanAdjustmentKernelFunctor<CoeffReturnType, EvaluatorPointerType, EvaluatorPointerType, Reducer, Index>
424
- AdjustFuctor;
425
- dev.template unary_kernel_launcher<CoeffReturnType, AdjustFuctor>(in_ptr, out_ptr, scan_info.get_thread_range(),
426
- scan_info.max_elements_per_block,
427
- scan_info.get_scan_parameter(), accumulator);
428
- }
429
- };
430
-
431
- template <typename CoeffReturnType, scan_step stp>
432
- struct ScanLauncher_impl {
433
- template <typename Input, typename EvaluatorPointerType, typename Reducer, typename Index>
434
- EIGEN_STRONG_INLINE static void scan_block(Input in_ptr, EvaluatorPointerType out_ptr, Reducer &accumulator,
435
- const Index total_size, const Index scan_size, const Index panel_size,
436
- const Index non_scan_size, const Index scan_stride,
437
- const Index non_scan_stride, const bool inclusive,
438
- const Eigen::SyclDevice &dev) {
439
- auto scan_info =
440
- ScanInfo<Index>(total_size, scan_size, panel_size, non_scan_size, scan_stride, non_scan_stride, dev);
441
- const Index temp_pointer_size = scan_info.block_size * non_scan_size * panel_size;
442
- const Index scratch_size = scan_info.max_elements_per_block / (ScanParameters<Index>::ScanPerThread / 2);
443
- CoeffReturnType *temp_pointer =
444
- static_cast<CoeffReturnType *>(dev.allocate_temp(temp_pointer_size * sizeof(CoeffReturnType)));
445
- EvaluatorPointerType tmp_global_accessor = dev.get(temp_pointer);
446
-
447
- typedef ScanKernelFunctor<Input, CoeffReturnType, EvaluatorPointerType, Reducer, Index, stp> ScanFunctor;
448
- dev.template binary_kernel_launcher<CoeffReturnType, ScanFunctor>(
449
- in_ptr, out_ptr, tmp_global_accessor, scan_info.get_thread_range(), scratch_size,
450
- scan_info.get_scan_parameter(), accumulator, inclusive);
451
-
452
- if (scan_info.block_size > 1) {
453
- ScanLauncher_impl<CoeffReturnType, scan_step::second>::scan_block(
454
- tmp_global_accessor, tmp_global_accessor, accumulator, temp_pointer_size, scan_info.block_size, panel_size,
455
- non_scan_size, Index(1), scan_info.block_size, false, dev);
456
-
457
- SYCLAdjustBlockOffset<EvaluatorPointerType, CoeffReturnType, Reducer, Index>::adjust_scan_block_offset(
458
- tmp_global_accessor, out_ptr, accumulator, total_size, scan_size, panel_size, non_scan_size, scan_stride,
459
- non_scan_stride, dev);
460
- }
461
- dev.deallocate_temp(temp_pointer);
462
- }
463
- };
464
-
465
- } // namespace internal
466
- } // namespace TensorSycl
467
- namespace internal {
468
- template <typename Self, typename Reducer, bool vectorize>
469
- struct ScanLauncher<Self, Reducer, Eigen::SyclDevice, vectorize> {
470
- typedef typename Self::Index Index;
471
- typedef typename Self::CoeffReturnType CoeffReturnType;
472
- typedef typename Self::Storage Storage;
473
- typedef typename Self::EvaluatorPointerType EvaluatorPointerType;
474
- void operator()(Self &self, EvaluatorPointerType data) {
475
- const Index total_size = internal::array_prod(self.dimensions());
476
- const Index scan_size = self.size();
477
- const Index scan_stride = self.stride();
478
- // this is the scan op (can be sum or ...)
479
- auto accumulator = self.accumulator();
480
- auto inclusive = !self.exclusive();
481
- auto consume_dim = self.consume_dim();
482
- auto dev = self.device();
483
-
484
- auto dims = self.inner().dimensions();
485
-
486
- Index non_scan_size = 1;
487
- Index panel_size = 1;
488
- if (static_cast<int>(Self::Layout) == static_cast<int>(ColMajor)) {
489
- for (int i = 0; i < consume_dim; i++) {
490
- non_scan_size *= dims[i];
491
- }
492
- for (int i = consume_dim + 1; i < Self::NumDims; i++) {
493
- panel_size *= dims[i];
494
- }
495
- } else {
496
- for (int i = Self::NumDims - 1; i > consume_dim; i--) {
497
- non_scan_size *= dims[i];
498
- }
499
- for (int i = consume_dim - 1; i >= 0; i--) {
500
- panel_size *= dims[i];
501
- }
502
- }
503
- const Index non_scan_stride = (scan_stride > 1) ? 1 : scan_size;
504
- auto eval_impl = self.inner();
505
- TensorSycl::internal::ScanLauncher_impl<CoeffReturnType, TensorSycl::internal::scan_step::first>::scan_block(
506
- eval_impl, data, accumulator, total_size, scan_size, panel_size, non_scan_size, scan_stride, non_scan_stride,
507
- inclusive, dev);
508
- }
509
- };
510
- } // namespace internal
511
- } // namespace Eigen
512
-
513
- #endif // UNSUPPORTED_EIGEN_CXX11_SRC_TENSOR_TENSOR_SYCL_SYCL_HPP