sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-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.cp312-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp312-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp312-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp312-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp312-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp312-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp312-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp312-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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- // 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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- // Copyright (C) 2016 Benoit Steiner <benoit.steiner.goog@gmail.com>
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-
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_CONVOLUTION_SYCL_H
16
- #define EIGEN_CXX11_TENSOR_TENSOR_CONVOLUTION_SYCL_H
17
-
18
- namespace Eigen {
19
-
20
- /** \class TensorConvolution
21
- * \ingroup CXX11_Tensor_Module
22
- *
23
- * \brief Tensor convolution class.
24
- *
25
- *
26
- */
27
-
28
- enum class convolution_type { CONV1D, CONV2D, CONV3D };
29
- template <typename Evaluator, typename CoeffReturnType, typename KernelType, typename Index, typename InputDims,
30
- typename Kernel_accessor, typename Buffer_accessor, convolution_type Conv_Dim>
31
- struct EigenConvolutionKernel;
32
- template <typename Evaluator, typename CoeffReturnType, typename KernelType, typename Index, typename InputDims,
33
- typename Kernel_accessor, typename Buffer_accessor>
34
- struct EigenConvolutionKernel<Evaluator, CoeffReturnType, KernelType, Index, InputDims, Kernel_accessor,
35
- Buffer_accessor, convolution_type::CONV1D> {
36
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
37
- Local_accessor;
38
- Local_accessor local_acc;
39
- Evaluator device_evaluator;
40
- Kernel_accessor kernel_filter;
41
- Buffer_accessor buffer_acc;
42
- internal::IndexMapper<Index, InputDims, 1, Evaluator::Layout> indexMapper;
43
- const size_t kernelSize;
44
- const cl::sycl::range<2> input_range;
45
- EigenConvolutionKernel(Local_accessor local_acc_, Evaluator device_evaluator_, Kernel_accessor kernel_filter_,
46
- Buffer_accessor buffer_acc_,
47
- internal::IndexMapper<Index, InputDims, 1, Evaluator::Layout> indexMapper_,
48
- const size_t kernelSize_, const cl::sycl::range<2> input_range_)
49
- : local_acc(local_acc_),
50
- device_evaluator(device_evaluator_),
51
- kernel_filter(kernel_filter_),
52
- buffer_acc(buffer_acc_),
53
- indexMapper(indexMapper_),
54
- kernelSize(kernelSize_),
55
- input_range(input_range_) {}
56
-
57
- template <typename BooleanDim2>
58
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool boundary_check(const BooleanDim2 boolean_check) {
59
- return (boolean_check[0] && boolean_check[1]);
60
- }
61
- void operator()(cl::sycl::nd_item<2> itemID) {
62
- auto buffer_ptr = buffer_acc.get_pointer();
63
- auto kernel_ptr = kernel_filter.get_pointer();
64
- // the required row to be calculated for the for each plane in shered memory
65
- const size_t num_input = (itemID.get_local_range()[0] + kernelSize - 1);
66
- const size_t plane_kernel_offset = itemID.get_local_id(1) * num_input;
67
- const size_t input_offset = itemID.get_group(0) * itemID.get_local_range()[0];
68
- const size_t plane_tensor_offset = indexMapper.mapGpuInputPlaneToTensorInputOffset(itemID.get_global_id(1));
69
- /// fill the shared memory
70
- for (size_t i = itemID.get_local_id(0); i < num_input; i += itemID.get_local_range()[0]) {
71
- const size_t local_index = i + plane_kernel_offset;
72
- const size_t tensor_index =
73
- plane_tensor_offset + indexMapper.mapGpuInputKernelToTensorInputOffset(i + input_offset);
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-
75
- local_acc[local_index] =
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- (((i + input_offset) < (input_range[0] + kernelSize - 1)) && itemID.get_global_id(1) < input_range[1])
77
- ? device_evaluator.coeff(tensor_index)
78
- : CoeffReturnType(0);
79
- }
80
-
81
- itemID.barrier(cl::sycl::access::fence_space::local_space);
82
-
83
- // calculate the convolution // output start x
84
- const size_t first_output_start = itemID.get_group(0) * (itemID.get_local_range()[0]);
85
- if (boundary_check(itemID.get_global_id() < input_range)) {
86
- CoeffReturnType result = static_cast<CoeffReturnType>(0);
87
- const size_t index = plane_kernel_offset + itemID.get_local_id(0);
88
- for (size_t k = 0; k < kernelSize; ++k) {
89
- result += (local_acc[k + index] * kernel_ptr[k]);
90
- }
91
- const size_t tensor_index =
92
- indexMapper.mapGpuOutputPlaneToTensorOutputOffset(itemID.get_global_id(1)) +
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- indexMapper.mapGpuOutputKernelToTensorOutputOffset(itemID.get_local_id(0) + first_output_start);
94
- buffer_ptr[tensor_index] = result;
95
- }
96
- }
97
- };
98
-
99
- template <typename Evaluator, typename CoeffReturnType, typename KernelType, typename Index, typename InputDims,
100
- typename Kernel_accessor, typename Buffer_accessor>
101
- struct EigenConvolutionKernel<Evaluator, CoeffReturnType, KernelType, Index, InputDims, Kernel_accessor,
102
- Buffer_accessor, convolution_type::CONV2D> {
103
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
104
- Local_accessor;
105
- Local_accessor local_acc;
106
- Evaluator device_evaluator;
107
- Kernel_accessor kernel_filter;
108
- Buffer_accessor buffer_acc;
109
- internal::IndexMapper<Index, InputDims, 2, Evaluator::Layout> indexMapper;
110
- const cl::sycl::range<2> kernel_size;
111
- const cl::sycl::range<3> input_range;
112
- EigenConvolutionKernel(Local_accessor local_acc_, Evaluator device_evaluator_, Kernel_accessor kernel_filter_,
113
- Buffer_accessor buffer_acc_,
114
- internal::IndexMapper<Index, InputDims, 2, Evaluator::Layout> indexMapper_,
115
- const cl::sycl::range<2> kernel_size_, const cl::sycl::range<3> input_range_)
116
- : local_acc(local_acc_),
117
- device_evaluator(device_evaluator_),
118
- kernel_filter(kernel_filter_),
119
- buffer_acc(buffer_acc_),
120
- indexMapper(indexMapper_),
121
- kernel_size(kernel_size_),
122
- input_range(input_range_) {}
123
- template <typename BooleanDim3>
124
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool boundary_check(const BooleanDim3 boolean_check) {
125
- return (boolean_check[0] && boolean_check[1] && boolean_check[2]);
126
- }
127
-
128
- void operator()(cl::sycl::nd_item<3> itemID) {
129
- auto buffer_ptr = buffer_acc.get_pointer();
130
- auto kernel_ptr = kernel_filter.get_pointer();
131
- // the required row to be calculated for the for each plane in shered memory
132
- const auto num_input = cl::sycl::range<2>{
133
- (cl::sycl::range<2>(itemID.get_local_range()[0], itemID.get_local_range()[1]) + kernel_size - 1)};
134
-
135
- const size_t plane_input_offset = indexMapper.mapGpuInputPlaneToTensorInputOffset(itemID.get_global_id(2));
136
- const size_t plane_kernel_offset = itemID.get_local_id(2) * num_input[1];
137
-
138
- const auto input_offset = cl::sycl::range<2>{itemID.get_group(0) * itemID.get_local_range()[0],
139
- itemID.get_group(1) * itemID.get_local_range()[1]};
140
-
141
- // fill the local memory
142
- bool in_range_dim2 = itemID.get_global_id(2) < input_range[2];
143
- for (size_t j = itemID.get_local_id(1); j < num_input[1]; j += itemID.get_local_range()[1]) {
144
- const size_t local_input_offset = num_input[0] * (j + plane_kernel_offset);
145
- bool in_range_dim1 = ((j + input_offset[1]) < (input_range[1] + kernel_size[1] - 1));
146
- for (size_t i = itemID.get_local_id(0); i < num_input[0]; i += itemID.get_local_range()[0]) {
147
- const size_t local_index = i + local_input_offset;
148
- const size_t tensor_index = plane_input_offset + indexMapper.mapGpuInputKernelToTensorInputOffset(
149
- i + input_offset[0], j + input_offset[1]);
150
- local_acc[local_index] = (((i + input_offset[0]) < (input_range[0] + kernel_size[0] - 1)) &&
151
- in_range_dim1 && in_range_dim2)
152
- ? device_evaluator.coeff(tensor_index)
153
- : CoeffReturnType(0);
154
- }
155
- }
156
-
157
- itemID.barrier(cl::sycl::access::fence_space::local_space);
158
-
159
- // output offset start for each thread
160
- const auto output_offset = cl::sycl::range<2>{itemID.get_group(0) * itemID.get_local_range()[0],
161
- itemID.get_group(1) * itemID.get_local_range()[1]};
162
-
163
- if (boundary_check(itemID.get_global_id() < input_range)) {
164
- CoeffReturnType result = static_cast<CoeffReturnType>(0);
165
-
166
- for (size_t j = 0; j < kernel_size[1]; j++) {
167
- size_t kernel_offset = kernel_size[0] * j;
168
- const size_t index =
169
- (num_input[0] * (plane_kernel_offset + j + itemID.get_local_id(1))) + itemID.get_local_id(0);
170
- for (size_t i = 0; i < kernel_size[0]; i++) {
171
- result += (local_acc[i + index] * kernel_ptr[i + kernel_offset]);
172
- }
173
- }
174
- const size_t tensor_index =
175
- indexMapper.mapGpuOutputPlaneToTensorOutputOffset(itemID.get_global_id(2)) +
176
- indexMapper.mapGpuOutputKernelToTensorOutputOffset(itemID.get_local_id(0) + output_offset[0],
177
- itemID.get_local_id(1) + output_offset[1]);
178
-
179
- buffer_ptr[tensor_index] = result;
180
- }
181
- }
182
- };
183
-
184
- template <typename Evaluator, typename CoeffReturnType, typename KernelType, typename Index, typename InputDims,
185
- typename Kernel_accessor, typename Buffer_accessor>
186
- struct EigenConvolutionKernel<Evaluator, CoeffReturnType, KernelType, Index, InputDims, Kernel_accessor,
187
- Buffer_accessor, convolution_type::CONV3D> {
188
- typedef cl::sycl::accessor<CoeffReturnType, 1, cl::sycl::access::mode::read_write, cl::sycl::access::target::local>
189
- Local_accessor;
190
- Local_accessor local_acc;
191
- Evaluator device_evaluator;
192
- Kernel_accessor kernel_filter;
193
- Buffer_accessor buffer_acc;
194
- internal::IndexMapper<Index, InputDims, 3, Evaluator::Layout> indexMapper;
195
- const cl::sycl::range<3> kernel_size;
196
- const cl::sycl::range<3> input_range;
197
- const size_t numP;
198
-
199
- EigenConvolutionKernel(Local_accessor local_acc_, Evaluator device_evaluator_, Kernel_accessor kernel_filter_,
200
- Buffer_accessor buffer_acc_,
201
- internal::IndexMapper<Index, InputDims, 3, Evaluator::Layout> indexMapper_,
202
- const cl::sycl::range<3> kernel_size_, const cl::sycl::range<3> input_range_,
203
- const size_t numP_)
204
- : local_acc(local_acc_),
205
- device_evaluator(device_evaluator_),
206
- kernel_filter(kernel_filter_),
207
- buffer_acc(buffer_acc_),
208
- indexMapper(indexMapper_),
209
- kernel_size(kernel_size_),
210
- input_range(input_range_),
211
- numP(numP_) {}
212
- template <typename BooleanDim3>
213
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool boundary_check(const BooleanDim3 boolean_check) {
214
- return (boolean_check[0] && boolean_check[1] && boolean_check[2]);
215
- }
216
- void operator()(cl::sycl::nd_item<3> itemID) {
217
- auto buffer_ptr = buffer_acc.get_pointer();
218
- auto kernel_ptr = kernel_filter.get_pointer();
219
- const auto num_input = cl::sycl::range<3>{itemID.get_local_range() + kernel_size - 1};
220
-
221
- const auto input_offset = cl::sycl::range<3>{itemID.get_group().get_id() * itemID.get_local_range()};
222
-
223
- const auto output_offset =
224
- cl::sycl::range<3>{itemID.get_group().get_id() * itemID.get_local_range() + itemID.get_local_id()};
225
-
226
- for (size_t p = 0; p < numP; p++) {
227
- /// fill the shared memory
228
- const size_t plane_input_offset = indexMapper.mapGpuInputPlaneToTensorInputOffset(p);
229
- for (size_t k = itemID.get_local_id(2); k < num_input[2]; k += itemID.get_local_range()[2]) {
230
- size_t local_index_dim2 = num_input[0] * num_input[1] * k;
231
- bool cond_k_dim = (k + input_offset[2] < (input_range[2] + kernel_size[2] - 1));
232
- for (size_t j = itemID.get_local_id(1); j < num_input[1]; j += itemID.get_local_range()[1]) {
233
- bool cond_j_dim = cond_k_dim && (j + input_offset[1] < (input_range[1] + kernel_size[1] - 1));
234
- size_t local_index_dim1 = (num_input[0] * j) + local_index_dim2;
235
- for (size_t i = itemID.get_local_id(0); i < num_input[0]; i += itemID.get_local_range()[0]) {
236
- bool conds = cond_j_dim && (i + input_offset[0] < (input_range[0] + kernel_size[0] - 1));
237
- const size_t local_index = local_index_dim1 + i;
238
- const size_t tensor_index =
239
- plane_input_offset + indexMapper.mapGpuInputKernelToTensorInputOffset(
240
- i + input_offset[0], j + input_offset[1], k + input_offset[2]);
241
- local_acc[local_index] = conds ? device_evaluator.coeff(tensor_index) : CoeffReturnType(0);
242
- }
243
- }
244
- }
245
- itemID.barrier(cl::sycl::access::fence_space::local_space);
246
-
247
- // calculate the convolution
248
-
249
- if (boundary_check(itemID.get_global_id() < input_range)) {
250
- CoeffReturnType result = static_cast<CoeffReturnType>(0);
251
- for (size_t k = 0; k < kernel_size[2]; k++) {
252
- for (size_t j = 0; j < kernel_size[1]; j++) {
253
- for (size_t i = 0; i < kernel_size[0]; i++) {
254
- const size_t kernel_index = i + kernel_size[0] * (j + kernel_size[1] * k);
255
- const size_t local_index =
256
- ((i + itemID.get_local_id(0)) +
257
- num_input[0] * ((j + itemID.get_local_id(1)) + num_input[1] * (k + itemID.get_local_id(2))));
258
-
259
- result += (local_acc[local_index] * kernel_ptr[kernel_index]);
260
- }
261
- }
262
- }
263
- const size_t tensor_index =
264
- indexMapper.mapGpuOutputPlaneToTensorOutputOffset(p) +
265
- indexMapper.mapGpuOutputKernelToTensorOutputOffset(output_offset[0], output_offset[1], output_offset[2]);
266
- buffer_ptr[tensor_index] = result;
267
- }
268
-
269
- itemID.barrier(cl::sycl::access::fence_space::local_space);
270
- }
271
- }
272
- };
273
-
274
- template <typename Indices, typename InputArgType, typename KernelArgType>
275
- struct TensorEvaluator<const TensorConvolutionOp<Indices, InputArgType, KernelArgType>, Eigen::SyclDevice> {
276
- typedef TensorConvolutionOp<Indices, InputArgType, KernelArgType> XprType;
277
-
278
- static const int NumDims =
279
- internal::array_size<typename TensorEvaluator<InputArgType, Eigen::SyclDevice>::Dimensions>::value;
280
- static const int NumKernelDims = internal::array_size<Indices>::value;
281
- typedef typename XprType::Index Index;
282
- typedef DSizes<Index, NumDims> Dimensions;
283
- typedef typename TensorEvaluator<KernelArgType, Eigen::SyclDevice>::Dimensions KernelDimensions;
284
- typedef const Eigen::SyclDevice Device;
285
- typedef typename XprType::CoeffReturnType CoeffReturnType;
286
- typedef typename PacketType<CoeffReturnType, Eigen::SyclDevice>::type PacketReturnType;
287
- typedef typename InputArgType::Scalar Scalar;
288
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
289
- typedef StorageMemory<CoeffReturnType, Eigen::SyclDevice> Storage;
290
- typedef typename Storage::Type EvaluatorPointerType;
291
- typedef StorageMemory<const CoeffReturnType, Eigen::SyclDevice> KernelStorage;
292
-
293
- enum {
294
- IsAligned = TensorEvaluator<InputArgType, Eigen::SyclDevice>::IsAligned &
295
- TensorEvaluator<KernelArgType, Eigen::SyclDevice>::IsAligned,
296
- PacketAccess = false,
297
- BlockAccess = false,
298
- PreferBlockAccess = false,
299
- Layout = TensorEvaluator<InputArgType, Eigen::SyclDevice>::Layout,
300
- CoordAccess = false, // to be implemented
301
- RawAccess = false
302
- };
303
-
304
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
305
- typedef internal::TensorBlockNotImplemented TensorBlock;
306
- //===--------------------------------------------------------------------===//
307
-
308
- TensorEvaluator(const XprType &op, const Eigen::SyclDevice &device)
309
- : m_inputImpl(op.inputExpression(), device),
310
- m_kernelArg(op.kernelExpression()),
311
- m_kernelImpl(op.kernelExpression(), device),
312
- m_indices(op.indices()),
313
- m_buf(NULL),
314
- m_kernel(NULL),
315
- m_local_kernel(false),
316
- m_device(device) {
317
- EIGEN_STATIC_ASSERT((static_cast<int>(TensorEvaluator<InputArgType, Eigen::SyclDevice>::Layout) ==
318
- static_cast<int>(TensorEvaluator<KernelArgType, Eigen::SyclDevice>::Layout)),
319
- YOU_MADE_A_PROGRAMMING_MISTAKE);
320
-
321
- const typename TensorEvaluator<InputArgType, Eigen::SyclDevice>::Dimensions &input_dims = m_inputImpl.dimensions();
322
- const typename TensorEvaluator<KernelArgType, Eigen::SyclDevice>::Dimensions &kernel_dims =
323
- m_kernelImpl.dimensions();
324
-
325
- m_dimensions = m_inputImpl.dimensions();
326
- for (int i = 0; i < NumKernelDims; ++i) {
327
- const Index index = op.indices()[i];
328
- const Index input_dim = input_dims[index];
329
- const Index kernel_dim = kernel_dims[i];
330
- const Index result_dim = input_dim - kernel_dim + 1;
331
- m_dimensions[index] = result_dim;
332
- }
333
- }
334
-
335
- EIGEN_DEVICE_FUNC const Dimensions &dimensions() const { return m_dimensions; }
336
-
337
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
338
- preloadKernel();
339
- m_inputImpl.evalSubExprsIfNeeded(NULL);
340
- if (data) {
341
- executeEval(data);
342
- return false;
343
- } else {
344
- m_buf = (EvaluatorPointerType)m_device.get(
345
- (Scalar *)m_device.allocate_temp(dimensions().TotalSize() * sizeof(Scalar)));
346
- executeEval(m_buf);
347
- return true;
348
- }
349
- }
350
-
351
- EIGEN_STRONG_INLINE void cleanup() {
352
- m_inputImpl.cleanup();
353
- if (m_buf) {
354
- m_device.deallocate_temp(m_buf);
355
- m_buf = NULL;
356
- }
357
- if (m_local_kernel) {
358
- m_device.deallocate_temp(m_kernel);
359
- m_local_kernel = false;
360
- }
361
- m_kernel = NULL;
362
- }
363
- /// used by sycl in order to build the sycl buffer
364
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Device &device() const { return m_device; }
365
- /// used by sycl in order to build the sycl buffer
366
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE EvaluatorPointerType data() const { return m_buf; }
367
-
368
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void preloadKernel() {
369
- // Don't make a local copy of the kernel unless we have to (i.e. it's an
370
- // expression that needs to be evaluated)
371
- typename KernelStorage::Type in_place = m_kernelImpl.data();
372
- if (in_place) {
373
- m_kernel = in_place;
374
- m_local_kernel = false;
375
- } else {
376
- ptrdiff_t kernel_sz = m_kernelImpl.dimensions().TotalSize() * sizeof(Scalar);
377
- EvaluatorPointerType local = (EvaluatorPointerType)m_device.get((Scalar *)m_device.allocate_temp(kernel_sz));
378
- typedef TensorEvalToOp<const KernelArgType> EvalTo;
379
- EvalTo evalToTmp(m_device.get(local), m_kernelArg);
380
- const bool PacketAccess = internal::IsVectorizable<Eigen::SyclDevice, KernelArgType>::value;
381
- internal::TensorExecutor<const EvalTo, Eigen::SyclDevice, PacketAccess>::run(evalToTmp, m_device);
382
- m_kernel = local;
383
- m_local_kernel = true;
384
- }
385
- }
386
-
387
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void executeEval(EvaluatorPointerType data) const {
388
- typedef TensorEvaluator<InputArgType, Eigen::SyclDevice> InputEvaluator;
389
- typedef typename InputEvaluator::Dimensions InputDims;
390
- switch (NumKernelDims) {
391
- case 1: {
392
- const size_t numX = dimensions()[m_indices[0]];
393
- const size_t numP = dimensions().TotalSize() / numX;
394
- const auto input_dim = std::array<size_t, 2>{numX, numP};
395
- auto global_range = cl::sycl::range<2>{};
396
- auto local_range = cl::sycl::range<2>{};
397
- const size_t kernel_size = m_kernelImpl.dimensions().TotalSize();
398
-
399
- m_device.parallel_for_setup(input_dim, global_range, local_range);
400
- const size_t local_memory_size = (local_range[0] + kernel_size - 1) * (local_range[1]);
401
- gpu_assert(static_cast<unsigned long>(local_memory_size) <= m_device.sharedMemPerBlock());
402
- const array<Index, 1> indices{{m_indices[0]}};
403
- const array<Index, 1> kernel_dims{{m_kernelImpl.dimensions()[0]}};
404
- internal::IndexMapper<Index, InputDims, 1, Layout> indexMapper(m_inputImpl.dimensions(), kernel_dims, indices);
405
-
406
- typedef EigenConvolutionKernel<InputEvaluator, CoeffReturnType, Scalar, Index, InputDims,
407
- typename KernelStorage::Type, EvaluatorPointerType, convolution_type::CONV1D>
408
- ConvKernel;
409
-
410
- m_device.template binary_kernel_launcher<CoeffReturnType, ConvKernel>(
411
- m_inputImpl, m_kernel, data, cl::sycl::nd_range<2>(global_range, local_range), local_memory_size,
412
- indexMapper, kernel_size, cl::sycl::range<2>(input_dim[0], input_dim[1]));
413
- break;
414
- }
415
-
416
- case 2: {
417
- auto kernel_index = std::array<size_t, 2>{static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : 1,
418
- static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 1 : 0};
419
- auto kernel_size = cl::sycl::range<2>{(size_t)m_kernelImpl.dimensions()[kernel_index[0]],
420
- (size_t)m_kernelImpl.dimensions()[kernel_index[1]]};
421
- const size_t numX = dimensions()[m_indices[kernel_index[0]]];
422
- const size_t numY = dimensions()[m_indices[kernel_index[1]]];
423
- const size_t numP = dimensions().TotalSize() / (numX * numY);
424
- auto input_dim = std::array<size_t, 3>{numX, numY, numP};
425
-
426
- auto global_range = cl::sycl::range<3>{};
427
- auto local_range = cl::sycl::range<3>{};
428
-
429
- m_device.parallel_for_setup(input_dim, global_range, local_range);
430
-
431
- const size_t local_memory_size =
432
- (local_range[0] + kernel_size[0] - 1) * (local_range[1] + kernel_size[1] - 1) * local_range[2];
433
- gpu_assert(static_cast<unsigned long>(local_memory_size) <= m_device.sharedMemPerBlock());
434
- const array<Index, 2> indices{{m_indices[kernel_index[0]], m_indices[kernel_index[1]]}};
435
- const array<Index, 2> kernel_dims{
436
- {m_kernelImpl.dimensions()[kernel_index[0]], m_kernelImpl.dimensions()[kernel_index[1]]}};
437
- internal::IndexMapper<Index, InputDims, 2, Layout> indexMapper(m_inputImpl.dimensions(), kernel_dims, indices);
438
- typedef EigenConvolutionKernel<InputEvaluator, CoeffReturnType, Scalar, Index, InputDims,
439
- typename KernelStorage::Type, EvaluatorPointerType, convolution_type::CONV2D>
440
- ConvKernel;
441
- m_device.template binary_kernel_launcher<CoeffReturnType, ConvKernel>(
442
- m_inputImpl, m_kernel, data, cl::sycl::nd_range<3>(global_range, local_range), local_memory_size,
443
- indexMapper, kernel_size, cl::sycl::range<3>{input_dim[0], input_dim[1], input_dim[2]});
444
- break;
445
- }
446
-
447
- case 3: {
448
- auto kernel_index = std::array<size_t, 3>{static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : 2,
449
- static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 1 : 1,
450
- static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 2 : 0};
451
-
452
- auto kernel_size = cl::sycl::range<3>{(size_t)m_kernelImpl.dimensions()[kernel_index[0]],
453
- (size_t)m_kernelImpl.dimensions()[kernel_index[1]],
454
- (size_t)m_kernelImpl.dimensions()[kernel_index[2]]};
455
-
456
- const size_t numX = dimensions()[m_indices[kernel_index[0]]];
457
- const size_t numY = dimensions()[m_indices[kernel_index[1]]];
458
- const size_t numZ = dimensions()[m_indices[kernel_index[2]]];
459
- auto input_dim = std::array<size_t, 3>{numX, numY, numZ};
460
- const size_t numP = dimensions().TotalSize() / (numX * numY * numZ);
461
-
462
- const array<Index, 3> indices{
463
- {m_indices[kernel_index[0]], m_indices[kernel_index[1]], m_indices[kernel_index[2]]}};
464
- const array<Index, 3> kernel_dims{{m_kernelImpl.dimensions()[kernel_index[0]],
465
- m_kernelImpl.dimensions()[kernel_index[1]],
466
- m_kernelImpl.dimensions()[kernel_index[2]]}};
467
-
468
- internal::IndexMapper<Index, InputDims, 3, Layout> indexMapper(m_inputImpl.dimensions(), kernel_dims, indices);
469
-
470
- auto global_range = cl::sycl::range<3>{};
471
- auto local_range = cl::sycl::range<3>{};
472
-
473
- m_device.parallel_for_setup(input_dim, global_range, local_range);
474
- auto local_memory_range = (local_range + kernel_size - 1);
475
- const size_t local_memory_size = local_memory_range[0] * local_memory_range[1] * local_memory_range[2];
476
-
477
- gpu_assert(static_cast<unsigned long>(local_memory_size) <= m_device.sharedMemPerBlock());
478
- typedef EigenConvolutionKernel<InputEvaluator, CoeffReturnType, Scalar, Index, InputDims,
479
- typename KernelStorage::Type, EvaluatorPointerType, convolution_type::CONV3D>
480
- ConvKernel;
481
- m_device.template binary_kernel_launcher<CoeffReturnType, ConvKernel>(
482
- m_inputImpl, m_kernel, data, cl::sycl::nd_range<3>(global_range, local_range), local_memory_size,
483
- indexMapper, kernel_size, cl::sycl::range<3>(input_dim[0], input_dim[1], input_dim[2]), numP);
484
- break;
485
- }
486
-
487
- default: {
488
- EIGEN_STATIC_ASSERT((NumKernelDims >= 1 && NumKernelDims <= 3),
489
- THIS_METHOD_IS_ONLY_FOR_OBJECTS_OF_A_SPECIFIC_SIZE);
490
- }
491
- }
492
- }
493
-
494
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const {
495
- eigen_assert(m_buf != NULL);
496
- eigen_assert(index < m_dimensions.TotalSize());
497
- return m_buf[index];
498
- }
499
-
500
- template <int LoadMode>
501
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(const Index index) const {
502
- eigen_assert(m_buf != NULL);
503
- eigen_assert(index < m_dimensions.TotalSize());
504
- return internal::ploadt<PacketReturnType, LoadMode>(m_buf + index);
505
- }
506
-
507
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
508
- // TODO(rmlarsen): FIXME: For now, this is just a copy of the CPU cost
509
- // model.
510
- const double kernel_size = m_kernelImpl.dimensions().TotalSize();
511
- // We ignore the use of fused multiply-add.
512
- const double convolve_compute_cost = TensorOpCost::AddCost<Scalar>() + TensorOpCost::MulCost<Scalar>();
513
- const double firstIndex_compute_cost =
514
- NumDims *
515
- (2 * TensorOpCost::AddCost<Index>() + 2 * TensorOpCost::MulCost<Index>() + TensorOpCost::DivCost<Index>());
516
- return TensorOpCost(0, 0, firstIndex_compute_cost, vectorized, PacketSize) +
517
- kernel_size * (m_inputImpl.costPerCoeff(vectorized) + m_kernelImpl.costPerCoeff(vectorized) +
518
- TensorOpCost(0, 0, convolve_compute_cost, vectorized, PacketSize));
519
- }
520
- // binding placeholder accessors to a command group handler for SYCL
521
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
522
- m_kernelImpl.bind(cgh);
523
- m_inputImpl.bind(cgh);
524
- m_buf.bind(cgh);
525
- m_kernel.bind(cgh);
526
- }
527
-
528
- private:
529
- // No assignment (copies are needed by the kernels)
530
- TensorEvaluator &operator=(const TensorEvaluator &);
531
- TensorEvaluator<InputArgType, Eigen::SyclDevice> m_inputImpl;
532
- KernelArgType m_kernelArg;
533
- TensorEvaluator<KernelArgType, Eigen::SyclDevice> m_kernelImpl;
534
- Indices m_indices;
535
- Dimensions m_dimensions;
536
- EvaluatorPointerType m_buf;
537
- typename KernelStorage::Type m_kernel;
538
- bool m_local_kernel;
539
- const Eigen::SyclDevice EIGEN_DEVICE_REF m_device;
540
- }; // namespace Eigen
541
-
542
- } // end namespace Eigen
543
-
544
- #endif // EIGEN_CXX11_TENSOR_TENSOR_CONVOLUTION_H