nmatrix-lapacke 0.2.0

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Files changed (185) hide show
  1. checksums.yaml +7 -0
  2. data/ext/nmatrix/data/complex.h +364 -0
  3. data/ext/nmatrix/data/data.h +638 -0
  4. data/ext/nmatrix/data/meta.h +64 -0
  5. data/ext/nmatrix/data/ruby_object.h +389 -0
  6. data/ext/nmatrix/math/asum.h +120 -0
  7. data/ext/nmatrix/math/cblas_enums.h +36 -0
  8. data/ext/nmatrix/math/cblas_templates_core.h +507 -0
  9. data/ext/nmatrix/math/gemm.h +241 -0
  10. data/ext/nmatrix/math/gemv.h +178 -0
  11. data/ext/nmatrix/math/getrf.h +255 -0
  12. data/ext/nmatrix/math/getrs.h +121 -0
  13. data/ext/nmatrix/math/imax.h +79 -0
  14. data/ext/nmatrix/math/laswp.h +165 -0
  15. data/ext/nmatrix/math/long_dtype.h +49 -0
  16. data/ext/nmatrix/math/math.h +744 -0
  17. data/ext/nmatrix/math/nrm2.h +160 -0
  18. data/ext/nmatrix/math/rot.h +117 -0
  19. data/ext/nmatrix/math/rotg.h +106 -0
  20. data/ext/nmatrix/math/scal.h +71 -0
  21. data/ext/nmatrix/math/trsm.h +332 -0
  22. data/ext/nmatrix/math/util.h +148 -0
  23. data/ext/nmatrix/nm_memory.h +60 -0
  24. data/ext/nmatrix/nmatrix.h +408 -0
  25. data/ext/nmatrix/ruby_constants.h +106 -0
  26. data/ext/nmatrix/storage/common.h +176 -0
  27. data/ext/nmatrix/storage/dense/dense.h +128 -0
  28. data/ext/nmatrix/storage/list/list.h +137 -0
  29. data/ext/nmatrix/storage/storage.h +98 -0
  30. data/ext/nmatrix/storage/yale/class.h +1139 -0
  31. data/ext/nmatrix/storage/yale/iterators/base.h +142 -0
  32. data/ext/nmatrix/storage/yale/iterators/iterator.h +130 -0
  33. data/ext/nmatrix/storage/yale/iterators/row.h +449 -0
  34. data/ext/nmatrix/storage/yale/iterators/row_stored.h +139 -0
  35. data/ext/nmatrix/storage/yale/iterators/row_stored_nd.h +168 -0
  36. data/ext/nmatrix/storage/yale/iterators/stored_diagonal.h +123 -0
  37. data/ext/nmatrix/storage/yale/math/transpose.h +110 -0
  38. data/ext/nmatrix/storage/yale/yale.h +202 -0
  39. data/ext/nmatrix/types.h +54 -0
  40. data/ext/nmatrix/util/io.h +115 -0
  41. data/ext/nmatrix/util/sl_list.h +143 -0
  42. data/ext/nmatrix/util/util.h +78 -0
  43. data/ext/nmatrix_lapacke/extconf.rb +200 -0
  44. data/ext/nmatrix_lapacke/lapacke.cpp +100 -0
  45. data/ext/nmatrix_lapacke/lapacke/include/lapacke.h +16445 -0
  46. data/ext/nmatrix_lapacke/lapacke/include/lapacke_config.h +119 -0
  47. data/ext/nmatrix_lapacke/lapacke/include/lapacke_mangling.h +17 -0
  48. data/ext/nmatrix_lapacke/lapacke/include/lapacke_mangling_with_flags.h +17 -0
  49. data/ext/nmatrix_lapacke/lapacke/include/lapacke_utils.h +579 -0
  50. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgeev.c +89 -0
  51. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgeev_work.c +141 -0
  52. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgesdd.c +106 -0
  53. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgesdd_work.c +158 -0
  54. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgesvd.c +94 -0
  55. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgesvd_work.c +149 -0
  56. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetrf.c +51 -0
  57. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetrf_work.c +83 -0
  58. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetri.c +77 -0
  59. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetri_work.c +89 -0
  60. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetrs.c +56 -0
  61. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cgetrs_work.c +102 -0
  62. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotrf.c +50 -0
  63. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotrf_work.c +82 -0
  64. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotri.c +50 -0
  65. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotri_work.c +82 -0
  66. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotrs.c +55 -0
  67. data/ext/nmatrix_lapacke/lapacke/src/lapacke_cpotrs_work.c +101 -0
  68. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgeev.c +78 -0
  69. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgeev_work.c +136 -0
  70. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgesdd.c +88 -0
  71. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgesdd_work.c +153 -0
  72. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgesvd.c +83 -0
  73. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgesvd_work.c +144 -0
  74. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetrf.c +50 -0
  75. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetrf_work.c +81 -0
  76. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetri.c +75 -0
  77. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetri_work.c +87 -0
  78. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetrs.c +55 -0
  79. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dgetrs_work.c +99 -0
  80. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotrf.c +50 -0
  81. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotrf_work.c +81 -0
  82. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotri.c +50 -0
  83. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotri_work.c +81 -0
  84. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotrs.c +54 -0
  85. data/ext/nmatrix_lapacke/lapacke/src/lapacke_dpotrs_work.c +97 -0
  86. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgeev.c +78 -0
  87. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgeev_work.c +134 -0
  88. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgesdd.c +88 -0
  89. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgesdd_work.c +152 -0
  90. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgesvd.c +83 -0
  91. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgesvd_work.c +143 -0
  92. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetrf.c +50 -0
  93. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetrf_work.c +81 -0
  94. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetri.c +75 -0
  95. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetri_work.c +87 -0
  96. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetrs.c +55 -0
  97. data/ext/nmatrix_lapacke/lapacke/src/lapacke_sgetrs_work.c +99 -0
  98. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotrf.c +50 -0
  99. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotrf_work.c +81 -0
  100. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotri.c +50 -0
  101. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotri_work.c +81 -0
  102. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotrs.c +54 -0
  103. data/ext/nmatrix_lapacke/lapacke/src/lapacke_spotrs_work.c +97 -0
  104. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgeev.c +89 -0
  105. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgeev_work.c +141 -0
  106. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgesdd.c +106 -0
  107. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgesdd_work.c +158 -0
  108. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgesvd.c +94 -0
  109. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgesvd_work.c +149 -0
  110. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetrf.c +51 -0
  111. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetrf_work.c +83 -0
  112. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetri.c +77 -0
  113. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetri_work.c +89 -0
  114. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetrs.c +56 -0
  115. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zgetrs_work.c +102 -0
  116. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotrf.c +50 -0
  117. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotrf_work.c +82 -0
  118. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotri.c +50 -0
  119. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotri_work.c +82 -0
  120. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotrs.c +55 -0
  121. data/ext/nmatrix_lapacke/lapacke/src/lapacke_zpotrs_work.c +101 -0
  122. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_cge_nancheck.c +62 -0
  123. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_cge_trans.c +65 -0
  124. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_cpo_nancheck.c +43 -0
  125. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_cpo_trans.c +45 -0
  126. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_ctr_nancheck.c +85 -0
  127. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_ctr_trans.c +85 -0
  128. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dge_nancheck.c +62 -0
  129. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dge_trans.c +65 -0
  130. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dpo_nancheck.c +43 -0
  131. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dpo_trans.c +45 -0
  132. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dtr_nancheck.c +85 -0
  133. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_dtr_trans.c +85 -0
  134. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_lsame.c +41 -0
  135. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_sge_nancheck.c +62 -0
  136. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_sge_trans.c +65 -0
  137. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_spo_nancheck.c +43 -0
  138. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_spo_trans.c +45 -0
  139. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_str_nancheck.c +85 -0
  140. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_str_trans.c +85 -0
  141. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_xerbla.c +46 -0
  142. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_zge_nancheck.c +62 -0
  143. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_zge_trans.c +65 -0
  144. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_zpo_nancheck.c +43 -0
  145. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_zpo_trans.c +45 -0
  146. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_ztr_nancheck.c +85 -0
  147. data/ext/nmatrix_lapacke/lapacke/utils/lapacke_ztr_trans.c +85 -0
  148. data/ext/nmatrix_lapacke/lapacke_nmatrix.h +16 -0
  149. data/ext/nmatrix_lapacke/make_lapacke_cpp.rb +9 -0
  150. data/ext/nmatrix_lapacke/math_lapacke.cpp +967 -0
  151. data/ext/nmatrix_lapacke/math_lapacke/cblas_local.h +576 -0
  152. data/ext/nmatrix_lapacke/math_lapacke/cblas_templates_lapacke.h +51 -0
  153. data/ext/nmatrix_lapacke/math_lapacke/lapacke_templates.h +356 -0
  154. data/ext/nmatrix_lapacke/nmatrix_lapacke.cpp +42 -0
  155. data/lib/nmatrix/lapack_ext_common.rb +69 -0
  156. data/lib/nmatrix/lapacke.rb +213 -0
  157. data/spec/00_nmatrix_spec.rb +730 -0
  158. data/spec/01_enum_spec.rb +190 -0
  159. data/spec/02_slice_spec.rb +389 -0
  160. data/spec/03_nmatrix_monkeys_spec.rb +78 -0
  161. data/spec/2x2_dense_double.mat +0 -0
  162. data/spec/4x4_sparse.mat +0 -0
  163. data/spec/4x5_dense.mat +0 -0
  164. data/spec/blas_spec.rb +193 -0
  165. data/spec/elementwise_spec.rb +303 -0
  166. data/spec/homogeneous_spec.rb +99 -0
  167. data/spec/io/fortran_format_spec.rb +88 -0
  168. data/spec/io/harwell_boeing_spec.rb +98 -0
  169. data/spec/io/test.rua +9 -0
  170. data/spec/io_spec.rb +149 -0
  171. data/spec/lapack_core_spec.rb +482 -0
  172. data/spec/leakcheck.rb +16 -0
  173. data/spec/math_spec.rb +730 -0
  174. data/spec/nmatrix_yale_resize_test_associations.yaml +2802 -0
  175. data/spec/nmatrix_yale_spec.rb +286 -0
  176. data/spec/plugins/lapacke/lapacke_spec.rb +303 -0
  177. data/spec/rspec_monkeys.rb +56 -0
  178. data/spec/rspec_spec.rb +34 -0
  179. data/spec/shortcuts_spec.rb +310 -0
  180. data/spec/slice_set_spec.rb +157 -0
  181. data/spec/spec_helper.rb +140 -0
  182. data/spec/stat_spec.rb +203 -0
  183. data/spec/test.pcd +20 -0
  184. data/spec/utm5940.mtx +83844 -0
  185. metadata +262 -0
@@ -0,0 +1,286 @@
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+ # = NMatrix
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+ #
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+ # A linear algebra library for scientific computation in Ruby.
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+ # NMatrix is part of SciRuby.
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+ #
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+ # NMatrix was originally inspired by and derived from NArray, by
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+ # Masahiro Tanaka: http://narray.rubyforge.org
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+ #
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+ # == Copyright Information
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+ #
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+ # SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ # NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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+ #
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+ # Please see LICENSE.txt for additional copyright notices.
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+ #
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+ # == Contributing
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+ #
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+ # By contributing source code to SciRuby, you agree to be bound by
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+ # our Contributor Agreement:
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+ #
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+ # * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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+ #
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+ # == nmatrix_yale_spec.rb
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+ #
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+ # Basic tests for NMatrix's Yale storage type.
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+ #
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+ require 'spec_helper'
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+ require "./lib/nmatrix"
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+
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+ describe NMatrix do
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+ context :yale do
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+
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+ it "compares two empty matrices" do
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+ n = NMatrix.new(4, stype: :yale, dtype: :float64)
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+ m = NMatrix.new(4, stype: :yale, dtype: :float64)
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+ expect(n).to eq(m)
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+ end
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+
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+ it "compares two matrices following basic assignments" do
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+ n = NMatrix.new(2, stype: :yale, dtype: :float64)
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+ m = NMatrix.new(2, stype: :yale, dtype: :float64)
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+
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+ m[0,0] = 1
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+ m[0,1] = 1
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+ expect(n).not_to eq(m)
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+ n[0,0] = 1
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+ expect(n).not_to eq(m)
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+ n[0,1] = 1
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+ expect(n).to eq(m)
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+ end
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+
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+ it "compares two matrices following elementwise operations" do
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+ n = NMatrix.new(2, stype: :yale, dtype: :float64)
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+ m = NMatrix.new(2, stype: :yale, dtype: :float64)
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+ n[0,1] = 1
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+ m[0,1] = -1
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+ x = n+m
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+ expect(n+m).to eq(NMatrix.new(2, 0.0, stype: :yale))
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+ end
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+
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+ it "sets diagonal values" do
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+ n = NMatrix.new([2,3], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[1,1] = 0.1
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+ n[0,0] = 0.2
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+ expect(n.yale_d).to eq([0.2, 0.1])
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+ end
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+
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+ it "gets non-diagonal rows as hashes" do
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+ n = NMatrix.new([4,6], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[0,0] = 0.1
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+ n[0,2] = 0.2
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+ n[0,3] = 0.3
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+ n[1,5] = 0.4
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+ h = n.yale_nd_row(0, :hash)
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+ expect(h).to eq({2 => 0.2, 3 => 0.3})
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+ end
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+
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+ it "gets non-diagonal occupied column indices for a given row" do
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+ n = NMatrix.new([4,6], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[0,0] = 0.1
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+ n[0,2] = 0.2
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+ n[0,3] = 0.3
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+ n[1,5] = 0.4
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+ a = n.yale_nd_row(0, :array)
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+ expect(a).to eq([2,3])
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+ end
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+
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+ it "does not resize until necessary" do
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+ n = NMatrix.new([2,3], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ expect(n.yale_size).to eq(3)
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+ expect(n.capacity).to eq(5)
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+ n[0,0] = 0.1
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+ n[0,1] = 0.2
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+ n[1,0] = 0.3
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+ expect(n.yale_size).to eq(5)
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+ expect(n.capacity).to eq(5)
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+ end
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+
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+
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+ it "sets when not resizing" do
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+ n = NMatrix.new([2,3], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[0,0] = 0.1
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+ n[0,1] = 0.2
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+ n[1,0] = 0.3
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+ expect(n.yale_a).to eq([0.1, 0.0, 0.0, 0.2, 0.3])
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+ expect(n.yale_ija).to eq([3,4,5,1,0])
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+ end
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+
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+ it "sets when resizing" do
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+ n = NMatrix.new([2,3], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[0,0] = 0.01
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+ n[1,1] = 0.1
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+ n[0,1] = 0.2
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+ n[1,0] = 0.3
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+ n[1,2] = 0.4
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+ expect(n.yale_d).to eq([0.01, 0.1])
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+ expect(n.yale_ia).to eq([3,4,6])
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+ expect(n.yale_ja).to eq([1,0,2,nil])
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+ expect(n.yale_lu).to eq([0.2, 0.3, 0.4, nil])
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+ end
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+
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+ it "resizes without erasing values" do
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+ require 'yaml'
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+
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+ associations = File.open('spec/nmatrix_yale_resize_test_associations.yaml') { |y| YAML::load(y) }
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+
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+ n = NMatrix.new([618,2801], stype: :yale, dtype: :byte, capacity: associations.size)
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+ #n = NMatrix.new(:yale, [618, 2801], associations.size, :byte)
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+
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+ associations.each_pair do |j,i|
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+ n[i,j] = 1
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+ expect(n[i,j]).to be(1), "Value at #{i},#{j} not inserted correctly!"
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+ end
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+
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+ associations.each_pair do |j,i|
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+ expect(n[i,j]).to be(1), "Value at #{i},#{j} erased during resize!"
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+ end
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+ end
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+
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+ it "sets values within rows" do
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+ n = NMatrix.new([3,20], stype: :yale, dtype: :float64)
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+ n.extend(NMatrix::YaleFunctions)
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+ n[2,1] = 1.0
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+ n[2,0] = 1.5
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+ n[2,15] = 2.0
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+ expect(n.yale_lu).to eq([1.5, 1.0, 2.0])
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+ expect(n.yale_ja).to eq([0, 1, 15])
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+ end
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+
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+ it "gets values within rows" do
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+ n = NMatrix.new([3,20], stype: :yale, dtype: :float64)
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+ n[2,1] = 1.0
159
+ n[2,0] = 1.5
160
+ n[2,15] = 2.0
161
+ expect(n[2,1]).to eq(1.0)
162
+ expect(n[2,0]).to eq(1.5)
163
+ expect(n[2,15]).to eq(2.0)
164
+ end
165
+
166
+ it "sets values within large rows" do
167
+ n = NMatrix.new([10,300], stype: :yale, dtype: :float64)
168
+ n.extend(NMatrix::YaleFunctions)
169
+ n[5,1] = 1.0
170
+ n[5,0] = 1.5
171
+ n[5,15] = 2.0
172
+ n[5,291] = 3.0
173
+ n[5,292] = 4.0
174
+ n[5,289] = 5.0
175
+ n[5,290] = 6.0
176
+ n[5,293] = 2.0
177
+ n[5,299] = 7.0
178
+ n[5,100] = 8.0
179
+ expect(n.yale_lu).to eq([1.5, 1.0, 2.0, 8.0, 5.0, 6.0, 3.0, 4.0, 2.0, 7.0])
180
+ expect(n.yale_ja).to eq([0, 1, 15, 100, 289, 290, 291, 292, 293, 299])
181
+ end
182
+
183
+ it "gets values within large rows" do
184
+ n = NMatrix.new([10,300], stype: :yale, dtype: :float64)
185
+ n.extend(NMatrix::YaleFunctions)
186
+ n[5,1] = 1.0
187
+ n[5,0] = 1.5
188
+ n[5,15] = 2.0
189
+ n[5,291] = 3.0
190
+ n[5,292] = 4.0
191
+ n[5,289] = 5.0
192
+ n[5,290] = 6.0
193
+ n[5,293] = 2.0
194
+ n[5,299] = 7.0
195
+ n[5,100] = 8.0
196
+
197
+ n.yale_ja.each_index do |idx|
198
+ j = n.yale_ja[idx]
199
+ expect(n[5,j]).to eq(n.yale_lu[idx])
200
+ end
201
+ end
202
+
203
+ it "dots two identical matrices" do
204
+ a = NMatrix.new(4, stype: :yale, dtype: :float64)
205
+ a[0,1] = 4.0
206
+ a[1,2] = 1.0
207
+ a[1,3] = 1.0
208
+ a[3,1] = 2.0
209
+
210
+ b = a.dup
211
+ c = a.dot b
212
+
213
+ d = NMatrix.new(4, [0,0,4,4, 0,2,0,0, 0,0,0,0, 0,0,2,2], dtype: :float64, stype: :yale)
214
+
215
+ expect(c).to eq(d)
216
+ end
217
+
218
+ it "dots two identical matrices where a positive and negative partial sum cancel on the diagonal" do
219
+ a = NMatrix.new(4, 0.0, stype: :yale)
220
+
221
+ a[0,0] = 1.0
222
+ a[0,1] = 4.0
223
+ a[1,2] = 2.0
224
+ a[1,3] = -4.0
225
+ a[3,1] = 4.0
226
+ a[3,3] = 4.0
227
+
228
+ b = a.dup
229
+ c = a.dot b
230
+
231
+ c.extend(NMatrix::YaleFunctions)
232
+
233
+ expect(c.yale_ija.reject { |i| i.nil? }).to eq([5,8,9,9,11,1,2,3,3,1,2])
234
+ expect(c.yale_a.reject { |i| i.nil? }).to eq([1.0, -16.0, 0.0, 0.0, 0.0, 4.0, 8.0, -16.0, -16.0, 16.0, 8.0])
235
+
236
+ end
237
+
238
+ it "dots two vectors" do
239
+ n = NMatrix.new([16,1], 0, stype: :yale)
240
+ m = NMatrix.new([1,16], 0, stype: :yale)
241
+
242
+ n[0] = m[0] = 1
243
+ n[1] = m[1] = 2
244
+ n[2] = m[2] = 3
245
+ n[3] = m[3] = 4
246
+ n[4] = m[4] = 5
247
+ n[5] = m[5] = 6
248
+ n[6] = m[6] = 7
249
+ n[7] = m[7] = 8
250
+ n[8] = m[8] = 9
251
+ n[15] = m[15] = 16
252
+
253
+ nm = n.dot(m)
254
+
255
+ # Perform the same multiplication with dense
256
+ nmr = n.cast(:dense, :int64).dot(m.cast(:dense, :int64)).cast(:yale, :int64)
257
+
258
+ nm.extend(NMatrix::YaleFunctions)
259
+ nmr.extend(NMatrix::YaleFunctions)
260
+
261
+ # We want to do a structure comparison to ensure multiplication is occurring properly, but more importantly, to
262
+ # ensure that insertion sort is occurring as it should. If the row has more than four entries, it'll run quicksort
263
+ # instead. Quicksort calls insertion sort for small rows, so we test both with this particular multiplication.
264
+ expect(nm.yale_ija[0...107]).to eq(nmr.yale_ija[0...107])
265
+ expect(nm.yale_a[0...107]).to eq(nmr.yale_a[0...107])
266
+
267
+ mn = m.dot(n)
268
+ expect(mn[0,0]).to eq(541)
269
+ end
270
+
271
+ it "calculates the row key intersections of two matrices" do
272
+ a = NMatrix.new([3,9], [0,1], stype: :yale, dtype: :byte, default: 0)
273
+ b = NMatrix.new([3,9], [0,0,1,0,1], stype: :yale, dtype: :byte, default: 0)
274
+ a.extend NMatrix::YaleFunctions
275
+ b.extend NMatrix::YaleFunctions
276
+
277
+ (0...3).each do |ai|
278
+ (0...3).each do |bi|
279
+ STDERR.puts (a.yale_ja_d_keys_at(ai) & b.yale_ja_d_keys_at(bi)).inspect
280
+ expect(a.yale_ja_d_keys_at(ai) & b.yale_ja_d_keys_at(bi)).to eq(a.yale_row_keys_intersection(ai, b, bi))
281
+ end
282
+ end
283
+
284
+ end
285
+ end
286
+ end
@@ -0,0 +1,303 @@
1
+ # = NMatrix
2
+ #
3
+ # A linear algebra library for scientific computation in Ruby.
4
+ # NMatrix is part of SciRuby.
5
+ #
6
+ # NMatrix was originally inspired by and derived from NArray, by
7
+ # Masahiro Tanaka: http://narray.rubyforge.org
8
+ #
9
+ # == Copyright Information
10
+ #
11
+ # SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
12
+ # NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
13
+ #
14
+ # Please see LICENSE.txt for additional copyright notices.
15
+ #
16
+ # == Contributing
17
+ #
18
+ # By contributing source code to SciRuby, you agree to be bound by
19
+ # our Contributor Agreement:
20
+ #
21
+ # * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
22
+ #
23
+ # == lapacke_spec.rb
24
+ #
25
+ # Tests for interfaces that are only exposed by nmatrix-lapacke
26
+ #
27
+
28
+ require 'spec_helper'
29
+ require "./lib/nmatrix/lapacke"
30
+
31
+ describe "NMatrix::LAPACK functions implemented with LAPACKE interface" do
32
+ [:float32, :float64, :complex64, :complex128].each do |dtype|
33
+ context dtype do
34
+ it "exposes lapacke_getrf" do
35
+ a = NMatrix.new([3,4], GETRF_EXAMPLE_ARRAY, dtype: dtype)
36
+ ipiv = NMatrix::LAPACK.lapacke_getrf(:row, 3, 4, a, 4)
37
+ b = NMatrix.new([3,4], GETRF_SOLUTION_ARRAY, dtype: dtype)
38
+ ipiv_true = [2,3,3]
39
+
40
+ # delta varies for different dtypes
41
+ err = case dtype
42
+ when :float32, :complex64
43
+ 1e-6
44
+ when :float64, :complex128
45
+ 1e-14
46
+ end
47
+
48
+ expect(a).to be_within(err).of(b)
49
+ expect(ipiv).to eq(ipiv_true)
50
+ end
51
+
52
+ it "exposes lapacke_getri" do
53
+ a = NMatrix.new(:dense, 3, [1,0,4,1,1,6,-3,0,-10], dtype)
54
+ ipiv = NMatrix::LAPACK::lapacke_getrf(:row, 3, 3, a, 3) # get pivot from getrf, use for getri
55
+
56
+ # delta varies for different dtypes
57
+ err = case dtype
58
+ when :float32, :complex64
59
+ 1e-5
60
+ when :float64, :complex128
61
+ 1e-14
62
+ end
63
+
64
+ NMatrix::LAPACK::lapacke_getri(:row, 3, a, 3, ipiv)
65
+
66
+ b = NMatrix.new(:dense, 3, [-5,0,-2,-4,1,-1,1.5,0,0.5], dtype)
67
+ expect(a).to be_within(err).of(b)
68
+ end
69
+
70
+ it "exposes lapacke_getrs with vector solutions" do
71
+ a = NMatrix.new(3, [-2,4,-3,3,-2,1,0,-4,3], dtype: dtype)
72
+ ipiv = NMatrix::LAPACK::lapacke_getrf(:row, 3, 3, a, 3)
73
+ b = NMatrix.new([3,1], [-1, 17, -9], dtype: dtype)
74
+
75
+ #be careful! the leading dimenension (lda,ldb) is the number of rows for row-major in LAPACKE. Different from CLAPACK convention!
76
+ NMatrix::LAPACK::lapacke_getrs(:row, false, 3, 1, a, 3, ipiv, b, 1)
77
+
78
+ # delta varies for different dtypes
79
+ err = case dtype
80
+ when :float32, :complex64
81
+ 1e-5
82
+ when :float64, :complex128
83
+ 1e-13
84
+ end
85
+
86
+ expect(b[0]).to be_within(err).of(5)
87
+ expect(b[1]).to be_within(err).of(-15.0/2)
88
+ expect(b[2]).to be_within(err).of(-13)
89
+ end
90
+
91
+ it "exposes lapacke_getrs with matrix solutions" do
92
+ a = NMatrix.new(3, [-2,4,-3,3,-2,1,0,-4,3], dtype: dtype)
93
+ ipiv = NMatrix::LAPACK::lapacke_getrf(:row, 3, 3, a, 3)
94
+ b = NMatrix.new([3,2], [-1, 2, 17, 10, -9, 1], dtype: dtype)
95
+
96
+ #be careful! the leading dimenension (lda,ldb) is the number of rows for row-major in LAPACKE. Different from CLAPACK convention!
97
+ NMatrix::LAPACK::lapacke_getrs(:row, false, 3, 2, a, 3, ipiv, b, 2)
98
+
99
+ # delta varies for different dtypes
100
+ err = case dtype
101
+ when :float32, :complex64
102
+ 1e-4
103
+ when :float64, :complex128
104
+ 1e-13
105
+ end
106
+
107
+ x = NMatrix.new([3,2], [5, -1.5, -7.5, -21.25, -13, -28], dtype: dtype)
108
+ expect(b).to be_within(err).of(x)
109
+ end
110
+
111
+ it "exposes lapacke_potrf" do
112
+ # first do upper
113
+ begin
114
+ a = NMatrix.new(:dense, 3, [25,15,-5, 0,18,0, 0,0,11], dtype)
115
+ NMatrix::LAPACK::lapacke_potrf(:row, :upper, 3, a, 3)
116
+ b = NMatrix.new(:dense, 3, [5,3,-1, 0,3,1, 0,0,3], dtype)
117
+ expect(a).to eq(b)
118
+ end
119
+
120
+ # then do lower
121
+ a = NMatrix.new(:dense, 3, [25,0,0, 15,18,0,-5,0,11], dtype)
122
+ NMatrix::LAPACK::lapacke_potrf(:row, :lower, 3, a, 3)
123
+ b = NMatrix.new(:dense, 3, [5,0,0, 3,3,0, -1,1,3], dtype)
124
+ expect(a).to eq(b)
125
+ end
126
+
127
+ it "exposes lapacke_potri" do
128
+ a = NMatrix.new(3, [4, 0,-1,
129
+ 0, 2, 1,
130
+ 0, 0, 1], dtype: dtype)
131
+ NMatrix::LAPACK::lapacke_potrf(:row, :upper, 3, a, 3)
132
+ NMatrix::LAPACK::lapacke_potri(:row, :upper, 3, a, 3)
133
+ b = NMatrix.new(3, [0.5, -0.5, 1, 0, 1.5, -2, 0, 0, 4], dtype: dtype)
134
+ err = case dtype
135
+ when :float32, :complex64
136
+ 1e-6
137
+ when :float64, :complex128
138
+ 1e-14
139
+ end
140
+ expect(a).to be_within(err).of(b)
141
+ end
142
+
143
+ it "exposes lapacke_potrs with vector solution" do
144
+ a = NMatrix.new(3, [4, 0,-1,
145
+ 0, 2, 1,
146
+ 0, 0, 1], dtype: dtype)
147
+ b = NMatrix.new([3,1], [3,0,2], dtype: dtype)
148
+
149
+ NMatrix::LAPACK::lapacke_potrf(:row, :upper, 3, a, 3)
150
+ #ldb is different from CLAPACK versions
151
+ NMatrix::LAPACK::lapacke_potrs(:row, :upper, 3, 1, a, 3, b, 1)
152
+
153
+ x = NMatrix.new([3,1], [3.5, -5.5, 11], dtype: dtype)
154
+
155
+ err = case dtype
156
+ when :float32, :complex64
157
+ 1e-5
158
+ when :float64, :complex128
159
+ 1e-14
160
+ end
161
+
162
+ expect(b).to be_within(err).of(x)
163
+ end
164
+
165
+ it "exposes lapacke_potrs with matrix solution" do
166
+ a = NMatrix.new(3, [4, 0,-1,
167
+ 0, 2, 1,
168
+ 0, 0, 1], dtype: dtype)
169
+ b = NMatrix.new([3,2], [3,4,
170
+ 0,4,
171
+ 2,0], dtype: dtype)
172
+
173
+ NMatrix::LAPACK::lapacke_potrf(:row, :upper, 3, a, 3)
174
+ #ldb is different from CLAPACK versions
175
+ NMatrix::LAPACK::lapacke_potrs(:row, :upper, 3, 2, a, 3, b, 2)
176
+
177
+ x = NMatrix.new([3,2], [3.5, 0,
178
+ -5.5, 4,
179
+ 11, -4], dtype: dtype)
180
+
181
+ err = case dtype
182
+ when :float32, :complex64
183
+ 1e-5
184
+ when :float64, :complex128
185
+ 1e-14
186
+ end
187
+
188
+ expect(b).to be_within(err).of(x)
189
+ end
190
+
191
+ it "calculates the singular value decomposition with lapacke_gesvd" do
192
+ #example from Wikipedia
193
+ m = 4
194
+ n = 5
195
+ mn_min = [m,n].min
196
+ a = NMatrix.new([m,n],[1,0,0,0,2, 0,0,3,0,0, 0,0,0,0,0, 0,4,0,0,0], dtype: dtype)
197
+ s = NMatrix.new([mn_min], 0, dtype: a.abs_dtype) #s is always real and always returned as float/double, never as complex
198
+ u = NMatrix.new([m,m], 0, dtype: dtype)
199
+ vt = NMatrix.new([n,n], 0, dtype: dtype)
200
+ superb = NMatrix.new([mn_min-1], dtype: a.abs_dtype)
201
+
202
+ NMatrix::LAPACK.lapacke_gesvd(:row, :a, :a, m, n, a, n, s, u, m, vt, n, superb)
203
+
204
+ s_true = NMatrix.new([mn_min], [4,3,Math.sqrt(5),0], dtype: a.abs_dtype)
205
+ u_true = NMatrix.new([m,m], [0,0,1,0, 0,1,0,0, 0,0,0,-1, 1,0,0,0], dtype: dtype)
206
+ vt_true = NMatrix.new([n,n], [0,1,0,0,0, 0,0,1,0,0, Math.sqrt(0.2),0,0,0,Math.sqrt(0.8), 0,0,0,1,0, -Math.sqrt(0.8),0,0,0,Math.sqrt(0.2)], dtype: dtype)
207
+
208
+ err = case dtype
209
+ when :float32, :complex64
210
+ 1e-5
211
+ when :float64, :complex128
212
+ 1e-14
213
+ end
214
+
215
+ expect(s).to be_within(err).of(s_true)
216
+ expect(u).to be_within(err).of(u_true)
217
+ expect(vt).to be_within(err).of(vt_true)
218
+ end
219
+
220
+ it "calculates the singular value decomposition with lapacke_gesdd" do
221
+ #example from Wikipedia
222
+ m = 4
223
+ n = 5
224
+ mn_min = [m,n].min
225
+ a = NMatrix.new([m,n],[1,0,0,0,2, 0,0,3,0,0, 0,0,0,0,0, 0,4,0,0,0], dtype: dtype)
226
+ s = NMatrix.new([mn_min], 0, dtype: a.abs_dtype) #s is always real and always returned as float/double, never as complex
227
+ u = NMatrix.new([m,m], 0, dtype: dtype)
228
+ vt = NMatrix.new([n,n], 0, dtype: dtype)
229
+
230
+ NMatrix::LAPACK.lapacke_gesdd(:row, :a, m, n, a, n, s, u, m, vt, n)
231
+
232
+ s_true = NMatrix.new([mn_min], [4,3,Math.sqrt(5),0], dtype: a.abs_dtype)
233
+ u_true = NMatrix.new([m,m], [0,0,1,0, 0,1,0,0, 0,0,0,-1, 1,0,0,0], dtype: dtype)
234
+ vt_true = NMatrix.new([n,n], [0,1,0,0,0, 0,0,1,0,0, Math.sqrt(0.2),0,0,0,Math.sqrt(0.8), 0,0,0,1,0, -Math.sqrt(0.8),0,0,0,Math.sqrt(0.2)], dtype: dtype)
235
+
236
+ err = case dtype
237
+ when :float32, :complex64
238
+ 1e-5
239
+ when :float64, :complex128
240
+ 1e-14
241
+ end
242
+
243
+ expect(s).to be_within(err).of(s_true)
244
+ expect(u).to be_within(err).of(u_true)
245
+ expect(vt).to be_within(err).of(vt_true)
246
+ end
247
+
248
+ it "calculates eigenvalues and eigenvectors using lapacke_geev" do
249
+ n = 3
250
+ a = NMatrix.new([n,n], [-1,0,0, 0,1,-2, 0,1,-1], dtype: dtype)
251
+ w = NMatrix.new([n], dtype: dtype)
252
+ if a.complex_dtype? #for real dtypes, imaginary parts of eigenvalues are stored in separate vector
253
+ wi = nil
254
+ else
255
+ wi = NMatrix.new([n], dtype: dtype)
256
+ end
257
+ vl = NMatrix.new([n,n], dtype: dtype)
258
+ vr = NMatrix.new([n,n], dtype: dtype)
259
+
260
+ NMatrix::LAPACK.lapacke_geev(:row, :t, :t, n, a, n, w, wi, vl, n, vr, n)
261
+
262
+ if !a.complex_dtype?
263
+ w = w + wi*Complex(0,1)
264
+ end
265
+
266
+ w_true = NMatrix.new([n], [Complex(0,1), -Complex(0,1), -1], dtype: NMatrix.upcast(dtype, :complex64))
267
+ if a.complex_dtype?
268
+ #For complex types the right/left eigenvectors are stored as columns
269
+ #of vr/vl.
270
+ vr_true = NMatrix.new([n,n],[0,0,1,
271
+ 2/Math.sqrt(6),2/Math.sqrt(6),0,
272
+ Complex(1,-1)/Math.sqrt(6),Complex(1,1)/Math.sqrt(6),0], dtype: dtype)
273
+ vl_true = NMatrix.new([n,n],[0,0,1,
274
+ Complex(-1,1)/Math.sqrt(6),Complex(-1,-1)/Math.sqrt(6),0,
275
+ 2/Math.sqrt(6),2/Math.sqrt(6),0], dtype: dtype)
276
+ else
277
+ #For real types, the real part of the first and second eigenvectors is
278
+ #stored in the first column, the imaginary part of the first (= the
279
+ #negative of the imaginary part of the second) eigenvector is stored
280
+ #in the second column, and the third eigenvector (purely real) is the
281
+ #third column.
282
+ vr_true = NMatrix.new([n,n],[0,0,1,
283
+ 2/Math.sqrt(6),0,0,
284
+ 1/Math.sqrt(6),-1/Math.sqrt(6),0], dtype: dtype)
285
+ vl_true = NMatrix.new([n,n],[0,0,1,
286
+ -1/Math.sqrt(6),1/Math.sqrt(6),0,
287
+ 2/Math.sqrt(6),0,0], dtype: dtype)
288
+ end
289
+
290
+ err = case dtype
291
+ when :float32, :complex64
292
+ 1e-6
293
+ when :float64, :complex128
294
+ 1e-15
295
+ end
296
+
297
+ expect(w).to be_within(err).of(w_true)
298
+ expect(vr).to be_within(err).of(vr_true)
299
+ expect(vl).to be_within(err).of(vl_true)
300
+ end
301
+ end
302
+ end
303
+ end