Package evaluation of OnlinePCA on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T19:08:54.516 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.35s ################################################################################ # Installation # Installing OnlinePCA... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [975b03d1] + OnlinePCA v0.3.9 Updating `~/.julia/environments/v1.10/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [4d4711f2] + MatrixMarket v0.5.2 [e1d29d7a] + Missings v1.2.0 [975b03d1] + OnlinePCA v0.3.9 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [b718987f] + TextWrap v1.0.2 [3bb67fe8] + TranscodingStreams v0.11.3 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.1+0 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.7+2 [458c3c95] + OpenSSL_jll v3.5.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [477f73a3] + libaec_jll v1.1.3+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 13.79s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 122.91s ################################################################################ # Testing # Testing OnlinePCA Status `/tmp/jl_GlrkuR/Project.toml` [c7e460c6] ArgParse v1.2.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [1a297f60] FillArrays v1.13.0 [4d4711f2] MatrixMarket v0.5.2 [975b03d1] OnlinePCA v0.3.9 [37e2e46d] LinearAlgebra [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_GlrkuR/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.6 [34da2185] Compat v4.16.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.4 [1a297f60] FillArrays v1.13.0 [38e38edf] GLM v1.9.0 [f67ccb44] HDF5 v0.17.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [3da0fdf6] MPIPreferences v0.1.11 [4d4711f2] MatrixMarket v0.5.2 [e1d29d7a] Missings v1.2.0 [975b03d1] OnlinePCA v0.3.9 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.4 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [b718987f] TextWrap v1.0.2 [3bb67fe8] TranscodingStreams v0.11.3 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.1+0 [7cb0a576] MPICH_jll v4.3.0+1 [f1f71cc9] MPItrampoline_jll v5.5.3+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.7+2 [458c3c95] OpenSSL_jll v3.5.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [3161d3a3] Zstd_jll v1.5.7+1 [477f73a3] libaec_jll v1.1.3+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... /tmp/jl_DVYub4 Running all tests... ####### Binarization of CSV (Julia API) ####### 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 ####### Binarization of CSV (Command line) ####### Parsed args: binfile => /tmp/jl_DVYub4/Data.zst csvfile => /tmp/jl_DVYub4/Data.csv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 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####### Parsed args: pseudocount => 1.0 binfile => /tmp/jl_DVYub4/Data.zst mode => dense outdir => /tmp/jl_wSqtuD 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Julia API) ####### 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Command line) ####### Parsed args: pseudocount => 1.0 binfile => /tmp/jl_DVYub4/Data.mtx.zst mode => sparse_mm outdir => /tmp/jl_LjS1nw 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### HVG (Julia API) ####### Highly Variable Genes are calculated... ####### HVG (Command line) ####### Parsed args: rowmeanlist => /tmp/jl_wSqtuD/Feature_Means.csv binfile => /tmp/jl_DVYub4/Data.zst rowcv2list => /tmp/jl_wSqtuD/Feature_CV2s.csv rowvarlist => /tmp/jl_wSqtuD/Feature_Vars.csv outdir => /tmp/jl_wSqtuD Highly Variable Genes are calculated... ####### Filtering (Julia API) ####### ####### Filtering (Command line) ####### Parsed args: samplelist => /tmp/jl_wSqtuD/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_wSqtuD input => /tmp/jl_DVYub4/Data.zst featurelist => /tmp/jl_wSqtuD/Feature_Means.csv Parsed args: samplelist => thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_wSqtuD input => /tmp/jl_DVYub4/Data.zst featurelist => /tmp/jl_wSqtuD/Feature_Means.csv Parsed args: samplelist => /tmp/jl_wSqtuD/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_wSqtuD input => /tmp/jl_DVYub4/Data.zst featurelist => ####### GD (Julia API) ####### ####### GD (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => "/tmp/jl_wSqtuD/Eigen_vectors.csv" colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => "/tmp/jl_wSqtuD/Loadings.csv" cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false ####### Oja (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:01:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:01:08 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:01:11 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### Oja (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:05:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:06:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:08:36 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:08:16 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### SGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:25 Progress: 1%|▍ | ETA: 0:03:03 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:01:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:02:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### SGD (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:06:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:07:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:08:06 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:09:03 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### CCIPCA (Julia API) ####### Progress: 1%|▎ | ETA: 0:01:26 Progress: 1%|▍ | ETA: 0:01:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### CCIPCA (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 offsetStoch => 1.0f-15 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:11:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 ####### RSGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:24:15 Progress: 1%|▍ | ETA: 0:17:41 Progress: 100%|█████████████████████████████████████████| Time: 0:00:10 Progress: 1%|▎ | ETA: 0:02:55 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:03:36 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:04:14 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### RSGD (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:17:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:17:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:18:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:09 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:20:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:09 ####### SVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:04:20 Progress: 1%|▍ | ETA: 0:05:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:04:41 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:05:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:06:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### SVRG (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:17:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:17:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:19:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:17:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 ####### RSVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:04:19 Progress: 1%|▍ | ETA: 0:05:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:04:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:05:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:06:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### RSVRG (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:27:52 Progress: 100%|█████████████████████████████████████████| Time: 0:00:13 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:28:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:12 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:29:21 Progress: 100%|█████████████████████████████████████████| Time: 0:00:12 Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:27:59 Progress: 100%|█████████████████████████████████████████| Time: 0:00:12 ####### Orthogonal Iteration (Julia API) ####### Progress: 0%|▏ | ETA: 0:06:27 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### Orthogonal Iteration (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" upper => 1.0f38 scale => "ftt" outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 0%|▏ | ETA: 0:30:34 Progress: 33%|█████████████▊ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 ####### Randomized Block Krylov Iteration (Julia API) ####### Progress: 33%|█████████████▊ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Q' A Q' A' A svd(Q' A' A) Q*U ####### Randomized Block Krylov Iteration (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" upper => 1.0f38 scale => "ftt" outdir => "/tmp/jl_wSqtuD" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 0%|▏ | ETA: 0:28:30 Progress: 33%|█████████████▊ | ETA: 0:00:11 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 Q' A Q' A' A svd(Q' A' A) Q*U ####### ARNOLDI (Julia API) ####### Progress: 20%|████████▎ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### ARNOLDI (Command line) ####### Parsed args: scale => "ftt" outdir => "/tmp/jl_wSqtuD" rowvarlist => "" cper => 1.0f0 pseudocount => 1.0f0 colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### LANCZOS (Julia API) ####### ####### LANCZOS (Command line) ####### Parsed args: scale => "ftt" outdir => "/tmp/jl_wSqtuD" rowvarlist => "" cper => 1.0f0 pseudocount => 1.0f0 colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### HALKO (Julia API) ####### Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:00:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 QR factorization : Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### HALKO (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:06:18 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 QR factorization : Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) Progress: 1%|▎ | ETA: 0:01:14 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### ALGORITHM971 (Julia API) ####### Random Projection : Y = A Ω LU factorization : L = lu(Y) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) QR factorization (3/3) : Q = qr(A lu(A' L)) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### ALGORITHM971 (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:06:23 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 LU factorization : L = lu(Y) Normalized power iterations (1/3) : A' L Progress: 1%|▎ | ETA: 0:01:16 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) QR factorization (3/3) : Q = qr(A lu(A' L)) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### SINGLEPASS (Julia API) ####### Random Projection : Y = A Ω, Ytilde = A' Ωtilde QR factorization : Q = qr(Y), Qtilde = qr(Ytilde) Solve linear equation : Ωtilde' Q B = Ytilde' Qtilde for B SVD with small matrix : svd(B) ####### SINGLEPASS (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω, Ytilde = A' Ωtilde Progress: 1%|▎ | ETA: 0:02:58 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 QR factorization : Q = qr(Y), Qtilde = qr(Ytilde) Solve linear equation : Ωtilde' Q B = Ytilde' Qtilde for B SVD with small matrix : svd(B) ####### SINGLEPASS2 (Julia API) ####### Random Projection : G = A Ω, H = A' A Ω Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) SVD with small matrix : svd(B) ####### SINGLEPASS2 (Command line) ####### Parsed args: logdir => "/tmp/jl_wSqtuD" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_wSqtuD" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.zst" rowmeanlist => "/tmp/jl_wSqtuD/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : G = A Ω, H = A' A Ω Progress: 1%|▎ | ETA: 0:02:36 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) SVD with small matrix : svd(B) ####### Sparse Randomized SVD (Julia API) ####### Initial Setting... Progress: 40%|████████████████▍ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Random Projection : Y = A Ω Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 LU factorization : L = lu(Y) ##### Iteration 1 / 3 ##### Normalized power iterations (1/3) : A' L Progress: 40%|████████████████▍ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 2 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 3 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L QR decomposition (3/3) : Q = qr(A A' L) Small matrix computation : B = Q' A Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 SVD : B = U Σ V' ####### Sparse Randomized SVD (Command line) ####### Parsed args: logdir => "/tmp/jl_LjS1nw" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_LjS1nw" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 initW => nothing colsumlist => "" input => "/tmp/jl_DVYub4/Data.mtx.zst" rowmeanlist => "/tmp/jl_LjS1nw/Feature_FTTMeans.csv" dim => "3" perm => false chunksize => "51" Initial Setting... Progress: 40%|████████████████▍ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Random Projection : Y = A Ω Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 LU factorization : L = lu(Y) ##### Iteration 1 / 3 ##### Normalized power iterations (1/3) : A' L Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 2 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 3 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L QR decomposition (3/3) : Q = qr(A A' L) Small matrix computation : B = Q' A Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 SVD : B = U Σ V' ####### Exact Out-of-Core PCA (Dense, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:04 Progress: 6 Time: 0:00:04 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:02 Progress: 6 Time: 0:00:02 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (Dense, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "dense" dim => "3" outdir => "/tmp/jl_wSqtuD" input => "/tmp/jl_DVYub4/Data.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:02 Progress: 6 Time: 0:00:02 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (MM-Sparse, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (MM-Sparse, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "sparse_mm" dim => "3" outdir => "/tmp/jl_LjS1nw" input => "/tmp/jl_DVYub4/Data.mtx.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (BinCOO-Sparse, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (BinCOO-Sparse, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "sparse_bincoo" dim => "3" outdir => "/tmp/jl_LjS1nw" input => "/tmp/jl_DVYub4/Data.bincoo.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues Inner product (Dense): 0.9710151732309676 Inner product (Sparse MM): 0.9999999872997415 Inner product (Sparse BinCOO): 0.9999999872997415 All tests completed. Testing OnlinePCA tests passed Testing completed after 1562.09s PkgEval succeeded after 1727.97s