Package evaluation of OnlinePCA on Julia 1.13.0-DEV.759 (3bb7518b04*) started at 2025-06-19T20:43:02.817 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.53s ################################################################################ # Installation # Installing OnlinePCA... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [975b03d1] + OnlinePCA v0.3.9 Updating `~/.julia/environments/v1.13/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 v0.9.5 [1a297f60] + FillArrays v1.13.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.4 [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 v1.3.2 [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 [10745b16] + Statistics v1.11.1 [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 v5.0.8+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [477f73a3] + libaec_jll v1.1.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 8.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 287.25s ################################################################################ # Testing # Testing OnlinePCA Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_a8zd9B/Project.toml` [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.120 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.13.0 [975b03d1] + OnlinePCA v0.3.9 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.12.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_a8zd9B/Manifest.toml` [944b1d66] ↑ CodecZlib v0.7.6 ⇒ v0.7.8 [6b39b394] + CodecZstd v0.8.6 [a8cc5b0e] + Crayons v4.1.1 [a93c6f00] + DataFrames v1.7.0 [864edb3b] ↑ DataStructures v0.18.20 ⇒ v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.120 [ffbed154] ↑ DocStringExtensions v0.9.3 ⇒ v0.9.5 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.13.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [34004b35] ↑ HypergeometricFunctions v0.3.24 ⇒ v0.3.28 [842dd82b] + InlineStrings v1.4.4 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] ↑ IrrationalConstants v0.2.2 ⇒ v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] ↑ JLLWrappers v1.5.0 ⇒ v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] ↑ LogExpFunctions v0.3.28 ⇒ v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [975b03d1] + OnlinePCA v0.3.9 [bac558e1] ↑ OrderedCollections v1.6.3 ⇒ v1.8.1 [90014a1f] ↑ PDMats v0.11.31 ⇒ v0.11.35 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] ↑ PtrArrays v1.2.0 ⇒ v1.3.0 [1fd47b50] ↑ QuadGK v2.10.1 ⇒ v2.11.2 [ae029012] + Requires v1.3.1 [79098fc4] ↑ Rmath v0.7.1 ⇒ v0.8.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [276daf66] ↑ SpecialFunctions v2.4.0 ⇒ v2.5.1 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [82ae8749] ↑ StatsAPI v1.7.0 ⇒ v1.7.1 [2913bbd2] ↑ StatsBase v0.34.3 ⇒ v0.34.5 [4c63d2b9] ↑ StatsFuns v1.3.1 ⇒ v1.5.0 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] ↑ TranscodingStreams v0.11.2 ⇒ 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 [c8ffd9c3] - MbedTLS_jll v2.28.2+1 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+0 [efe28fd5] ↑ OpenSpecFun_jll v0.5.5+0 ⇒ v0.5.6+0 [f50d1b31] ↑ Rmath_jll v0.4.3+0 ⇒ v0.5.1+0 [477f73a3] + libaec_jll v1.1.3+0 [0dad84c5] ↑ ArgTools v1.1.1 ⇒ v1.1.2 [56f22d72] ~ Artifacts ⇒ v1.11.0 [2a0f44e3] ~ Base64 ⇒ v1.11.0 [ade2ca70] ~ Dates ⇒ v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] ↑ Downloads v1.6.0 ⇒ v1.7.0 [7b1f6079] ~ FileWatching ⇒ v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] ~ InteractiveUtils ⇒ v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [76f85450] ~ LibGit2 ⇒ v1.11.0 [8f399da3] ~ Libdl ⇒ v1.11.0 [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0 [56ddb016] ~ Logging ⇒ v1.11.0 [d6f4376e] ~ Markdown ⇒ v1.11.0 [a63ad114] ~ Mmap ⇒ v1.11.0 [ca575930] ↑ NetworkOptions v1.2.0 ⇒ v1.3.0 [44cfe95a] ↑ Pkg v1.10.0 ⇒ v1.13.0 [de0858da] ~ Printf ⇒ v1.11.0 [3fa0cd96] ~ REPL ⇒ v1.11.0 [9a3f8284] ~ Random ⇒ v1.11.0 [9e88b42a] ~ Serialization ⇒ v1.11.0 [6462fe0b] ~ Sockets ⇒ v1.11.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.12.0 [f489334b] + StyledStrings v1.11.0 [8dfed614] ~ Test ⇒ v1.11.0 [cf7118a7] ~ UUIDs ⇒ v1.11.0 [4ec0a83e] ~ Unicode ⇒ v1.11.0 [e66e0078] ↑ CompilerSupportLibraries_jll v1.1.1+0 ⇒ v1.3.0+1 [deac9b47] ↑ LibCURL_jll v8.4.0+0 ⇒ v8.14.1+1 [e37daf67] ↑ LibGit2_jll v1.6.4+0 ⇒ v1.9.0+0 [29816b5a] ↑ LibSSH2_jll v1.11.0+1 ⇒ v1.11.3+1 [14a3606d] ↑ MozillaCACerts_jll v2023.1.10 ⇒ v2025.5.20 [4536629a] ↑ OpenBLAS_jll v0.3.23+4 ⇒ v0.3.29+0 [05823500] ↑ OpenLibm_jll v0.8.1+2 ⇒ v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] ↑ SuiteSparse_jll v7.2.1+1 ⇒ v7.10.1+0 [83775a58] ↑ Zlib_jll v1.2.13+1 ⇒ v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] ↑ libblastrampoline_jll v5.8.0+1 ⇒ v5.12.0+0 [8e850ede] ↑ nghttp2_jll v1.52.0+1 ⇒ v1.65.0+0 [3f19e933] ↑ p7zip_jll v17.4.0+2 ⇒ v17.5.0+2 Test Successfully re-resolved Status `/tmp/jl_a8zd9B/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 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.12.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_a8zd9B/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 v0.9.5 [1a297f60] FillArrays v1.13.0 [38e38edf] GLM v1.9.0 [f67ccb44] HDF5 v0.17.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.4 [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 v1.3.2 [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 [10745b16] Statistics v1.11.1 [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 v5.0.8+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [477f73a3] libaec_jll v1.1.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.14.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... Precompiling packages... 9037.7 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 11 seconds. 49 already precompiled. /tmp/jl_FJW4qf 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) ####### Precompiling packages... 1514.5 ms ✓ ShiftedArrays 1273.2 ms ✓ TextWrap 4357.1 ms ✓ Crayons 1756.7 ms ✓ InlineStrings 2250.2 ms ✓ CodecZstd 954.9 ms ✓ InvertedIndices 1067.3 ms ✓ DelimitedFiles 1121.9 ms ✓ PooledArrays 1413.0 ms ✓ MatrixMarket 6675.2 ms ✓ SentinelArrays 6887.4 ms ✓ StringManipulation 6274.6 ms ✓ StatsModels 2353.2 ms ✓ ArgParse 65672.9 ms ✓ PrettyTables 7396.4 ms ✓ GLM 207584.1 ms ✓ DataFrames 21368.2 ms ✓ OnlinePCA 17 dependencies successfully precompiled in 344 seconds. 91 already precompiled. Parsed args: csvfile => /tmp/jl_FJW4qf/Data.csv binfile => /tmp/jl_FJW4qf/Data.zst 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 MM (Julia API) ####### ####### Binarization of MM (Command line) ####### Parsed args: binfile => /tmp/jl_FJW4qf/Data.mtx.zst mmfile => /tmp/jl_FJW4qf/Data.mtx ####### Binarization of Binary COO (Julia API) ####### ####### Binarization of Binary COO (Command line) ####### Parsed args: binfile => /tmp/jl_FJW4qf/Data.bincoo.zst bincoofile => /tmp/jl_FJW4qf/Data.bincoo ####### Summarization (Julia API) ####### 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Command line) ####### Parsed args: outdir => /tmp/jl_eTSJi5 binfile => /tmp/jl_FJW4qf/Data.zst pseudocount => 1.0 mode => dense 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: outdir => /tmp/jl_BT6uR4 binfile => /tmp/jl_FJW4qf/Data.mtx.zst pseudocount => 1.0 mode => sparse_mm 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: rowcv2list => /tmp/jl_eTSJi5/Feature_CV2s.csv outdir => /tmp/jl_eTSJi5 binfile => /tmp/jl_FJW4qf/Data.zst rowvarlist => /tmp/jl_eTSJi5/Feature_Vars.csv rowmeanlist => /tmp/jl_eTSJi5/Feature_Means.csv Highly Variable Genes are calculated... ####### Filtering (Julia API) ####### ####### Filtering (Command line) ####### Parsed args: input => /tmp/jl_FJW4qf/Data.zst direct1 => + outdir => /tmp/jl_eTSJi5 direct2 => + thr2 => 10 samplelist => /tmp/jl_eTSJi5/Sample_NoCounts.csv featurelist => /tmp/jl_eTSJi5/Feature_Means.csv thr1 => 10 Parsed args: input => /tmp/jl_FJW4qf/Data.zst direct1 => + outdir => /tmp/jl_eTSJi5 direct2 => + thr2 => 10 samplelist => featurelist => /tmp/jl_eTSJi5/Feature_Means.csv thr1 => 10 Parsed args: input => /tmp/jl_FJW4qf/Data.zst direct1 => + outdir => /tmp/jl_eTSJi5 direct2 => + thr2 => 10 samplelist => /tmp/jl_eTSJi5/Sample_NoCounts.csv featurelist => thr1 => 10 ####### GD (Julia API) ####### ####### GD (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => "/tmp/jl_eTSJi5/Eigen_vectors.csv" lower => 0 offsetStoch => 1.0f-6 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => "/tmp/jl_eTSJi5/Loadings.csv" initW => nothing lower => 0 offsetStoch => 1.0f-6 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 ####### Oja (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:53 Progress: 1%|▍ | ETA: 0:03:15 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:49 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:54 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:03:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### Oja (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:06:04 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:06:57 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:08:54 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:08:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### SGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:03:10 Progress: 1%|▍ | ETA: 0:03:58 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:04:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:04:34 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:04:40 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### SGD (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:06:34 Progress: 1%|▍ | ETA: 0:05:22 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:07:18 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:09:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:08:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### CCIPCA (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:09 Progress: 1%|▍ | ETA: 0:02:43 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### CCIPCA (Command line) ####### Parsed args: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" numepoch => "1" expvar => 0.1f0 perm => false evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-15 Progress: 1%|▎ | ETA: 0:07:31 Progress: 1%|▍ | ETA: 0:06:21 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### RSGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:15:58 Progress: 1%|▍ | ETA: 0:12:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Progress: 1%|▎ | ETA: 0:04:03 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:05:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:04:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### RSGD (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:12:26 Progress: 1%|▍ | ETA: 0:09:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:14:47 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:13:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:14:31 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 ####### SVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:05:04 Progress: 1%|▍ | ETA: 0:05:44 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:06:11 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:09:22 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:07:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### SVRG (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:16:18 Progress: 1%|▍ | ETA: 0:12:49 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:16:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:18:22 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:18:05 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 ####### RSVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:04:26 Progress: 1%|▍ | ETA: 0:05:31 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:06:13 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:08:51 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Progress: 1%|▎ | ETA: 0:07:33 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### RSVRG (Command line) ####### Parsed args: scheduling => "robbins-monro" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:21:02 Progress: 1%|▍ | ETA: 0:15:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:09 Parsed args: scheduling => "momentum" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:22:23 Progress: 100%|█████████████████████████████████████████| Time: 0:00:09 Parsed args: scheduling => "nag" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:23:31 Progress: 100%|█████████████████████████████████████████| Time: 0:00:09 Parsed args: scheduling => "adagrad" rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" epsilon => 1.0f-8 pseudocount => 1.0f0 rowvarlist => "" offsetFull => 1.0f-20 colsumlist => "" stepsize => "1.0e-15" upper => 1.0f38 cper => 1.0f0 scale => "ftt" g => 0.9f0 numepoch => "1" expvar => 0.1f0 perm => false numbatch => 100 evalfreq => 5000 initV => nothing initW => nothing lower => 0 offsetStoch => 1.0f-6 Progress: 1%|▎ | ETA: 0:24:16 Progress: 100%|█████████████████████████████████████████| Time: 0:00:10 ####### Orthogonal Iteration (Julia API) ####### Progress: 0%|▏ | ETA: 0:06:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### Orthogonal Iteration (Command line) ####### Parsed args: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" upper => 1.0f38 cper => 1.0f0 scale => "ftt" numepoch => "3" expvar => 0.1f0 perm => false initV => nothing initW => nothing lower => 0 Progress: 0%|▏ | ETA: 0:21:26 Progress: 33%|█████████████▊ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 ####### Randomized Block Krylov Iteration (Julia API) ####### Progress: 0%|▏ | ETA: 0:00:46 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: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" upper => 1.0f38 cper => 1.0f0 scale => "ftt" numepoch => "3" expvar => 0.1f0 perm => false initV => nothing initW => nothing lower => 0 Progress: 0%|▏ | ETA: 0:20:40 Progress: 33%|█████████████▊ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 Q' A Q' A' A svd(Q' A' A) Q*U ####### ARNOLDI (Julia API) ####### Progress: 20%|████████▎ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### ARNOLDI (Command line) ####### Parsed args: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" cper => 1.0f0 scale => "ftt" numepoch => "3" expvar => 0.1f0 perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### LANCZOS (Julia API) ####### Progress: 20%|████████▎ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### LANCZOS (Command line) ####### Parsed args: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" cper => 1.0f0 scale => "ftt" numepoch => "3" expvar => 0.1f0 perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### HALKO (Julia API) ####### Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:01:11 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: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" noversamples => 5 cper => 1.0f0 niter => 3 scale => "ftt" perm => false initV => nothing initW => nothing Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:06:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 QR factorization : Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) Progress: 1%|▎ | ETA: 0:01:52 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: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" noversamples => 5 cper => 1.0f0 niter => 3 scale => "ftt" perm => false initV => nothing initW => nothing Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:06:11 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 LU factorization : L = lu(Y) Normalized power iterations (1/3) : A' L Progress: 1%|▎ | ETA: 0:01:54 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: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" noversamples => 5 cper => 1.0f0 niter => 3 scale => "ftt" perm => false initV => nothing initW => nothing Random Projection : Y = A Ω, Ytilde = A' Ωtilde Progress: 1%|▎ | ETA: 0:02:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 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: rowmeanlist => "/tmp/jl_eTSJi5/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_eTSJi5" input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 rowvarlist => "" colsumlist => "" noversamples => 5 cper => 1.0f0 niter => 3 scale => "ftt" perm => false initV => nothing initW => nothing Random Projection : G = A Ω, H = A' A Ω Progress: 1%|▎ | ETA: 0:02:25 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 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: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 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' ####### Sparse Randomized SVD (Command line) ####### Parsed args: rowmeanlist => "/tmp/jl_BT6uR4/Feature_FTTMeans.csv" dim => "3" logdir => "/tmp/jl_BT6uR4" input => "/tmp/jl_FJW4qf/Data.mtx.zst" outdir => "/tmp/jl_BT6uR4" rowvarlist => "" colsumlist => "" noversamples => 5 cper => 1.0f0 niter => 3 scale => "ftt" chunksize => "51" perm => false initV => nothing initW => nothing Initial Setting... Progress: 40%|████████████████▍ | ETA: 0:00:06 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: 0:00:00 Progress: 6 Time: 0:00:00 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (Dense, Command line) ####### Parsed args: input => "/tmp/jl_FJW4qf/Data.zst" outdir => "/tmp/jl_eTSJi5" pseudocount => 1.0f0 mode => "dense" dim => "3" chunksize => "51" scale => "raw" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 3. PC Score (Z = XV) is being calculated. ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 470 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x7a6ee2fa224f) at /lib/x86_64-linux-gnu/libc.so.6 __libc_free at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) _ZN4llvm15ScalarEvolution24computeExitLimitFromCondEPKNS_4LoopEPNS_5ValueEbbb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15ScalarEvolution16computeExitLimitEPKNS_4LoopEPNS_10BasicBlockEbb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15ScalarEvolution25computeBackedgeTakenCountEPKNS_4LoopEb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15ScalarEvolution20getBackedgeTakenInfoEPKNS_4LoopE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15ScalarEvolution21getBackedgeTakenCountEPKNS_4LoopENS0_13ExitCountKindE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16LoopDeletionPass3runERNS_4LoopERNS_15AnalysisManagerIS1_JRNS_27LoopStandardAnalysisResultsEEEES5_RNS_10LPMUpdaterE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_4LoopENS_15AnalysisManagerIS1_JRNS_27LoopStandardAnalysisResultsEEEEJS4_RNS_10LPMUpdaterEEE13runSinglePassIS1_St10unique_ptrINS_6detail11PassConceptIS1_S5_JS4_S7_EEESt14default_deleteISD_EEEESt8optionalINS_17PreservedAnalysesEERT_RT0_RS5_S4_S7_RNS_19PassInstrumentationE.isra.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm11PassManagerINS_4LoopENS_15AnalysisManagerIS1_JRNS_27LoopStandardAnalysisResultsEEEEJS4_RNS_10LPMUpdaterEEE24runWithoutLoopNestPassesERS1_RS5_S4_S7_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm11PassManagerINS_4LoopENS_15AnalysisManagerIS1_JRNS_27LoopStandardAnalysisResultsEEEEJS4_RNS_10LPMUpdaterEEE3runERS1_RS5_S4_S7_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm25FunctionToLoopPassAdaptor3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_8FunctionENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/src/pipeline.cpp:791 operator() at /source/src/jitlayers.cpp:1518 withModuleDo<(anonymous namespace)::sizedOptimizerT::operator()(llvm::orc::ThreadSafeModule) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1479 [inlined] operator() at /source/src/jitlayers.cpp:1631 [inlined] addModule at /source/src/jitlayers.cpp:2088 jl_compile_codeinst_now at /source/src/jitlayers.cpp:683 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:883 jl_compile_method_internal at /source/src/gf.c:3212 _jl_invoke at /source/src/gf.c:3684 [inlined] ijl_apply_generic at /source/src/gf.c:3892 #exact_ooc_pca#118 at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:43 exact_ooc_pca at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:25 unknown function (ip: 0x7a6ee1b4f37d) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 main at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/bin/exact_ooc_pca:33 unknown function (ip: 0x7a6ee1b14d9f) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:309 exec_options at ./client.jl:324 _start at ./client.jl:557 jfptr__start_68643.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] true_main at /source/src/jlapi.c:964 jl_repl_entrypoint at /source/src/jlapi.c:1132 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7a6ee2f33249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== # 4. Out-of-Core PC Score Calculation # 5. Delayed Centering Correction ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 # 6. Normalize W and Calculate EigenvaluesOverhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007a6ec8e00010 Total snapshots: 1. Utilization: 100% ####### Exact Out-of-Core PCA (MM-Sparse, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 171 running 1 of 1 signal (10): User defined signal 1 jl_specializations_get_linfo_ at /source/src/gf.c:237 cache_method at /source/src/gf.c:1576 ml_matches at /source/src/gf.c:4772 ml_matches at /source/src/gf.c:4426 [inlined] ijl_matching_methods at /source/src/gf.c:2820 [inlined] ijl_matching_methods at /source/src/gf.c:2807 _methods_by_ftype at ./runtime_internals.jl:1470 [inlined] _findall at ./../usr/share/julia/Compiler/src/methodtable.jl:97 [inlined] #findall#5 at ./../usr/share/julia/Compiler/src/methodtable.jl:70 [inlined] findall at ./../usr/share/julia/Compiler/src/methodtable.jl:70 [inlined] #findall#7 at ./../usr/share/julia/Compiler/src/methodtable.jl:105 findall at ./../usr/share/julia/Compiler/src/methodtable.jl:102 [inlined] find_simple_method_matches at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:386 #find_method_matches#134 at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:348 jfptr_YY.find_method_matchesYY.134_79335.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_invoke at /source/src/gf.c:3699 tojlinvoke87385.1 at /opt/julia/lib/julia/sys.so (unknown line) j_YY.find_method_matchesYY.134_79333.1 at /opt/julia/lib/julia/sys.so (unknown line) find_method_matches at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:342 abstract_call_gf_by_type at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:120 abstract_call_known at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2796 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2903 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2896 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3056 abstract_eval_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3074 abstract_eval_statement_expr at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3430 Progress: 2 Time: 0:00:03 Progress: 6 Time: 0:00:03 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3819 [inlined] abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3776 [inlined] typeinf_local at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4325 jfptr_typeinf_local_84251.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4483 typeinf_ext at ./../usr/share/julia/Compiler/src/typeinfer.jl:1391 typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1560 typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1568 jfptr_typeinf_ext_toplevel_84209.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] jl_type_infer at /source/src/gf.c:461 jl_compile_method_internal at /source/src/gf.c:3199 _jl_invoke at /source/src/gf.c:3684 [inlined] ijl_apply_generic at /source/src/gf.c:3892 #ooc_cov##0 at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:0 #open#330 at ./io.jl:420 open at ./io.jl:417 [inlined] ooc_cov at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:70 #exact_ooc_pca#118 at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:33 exact_ooc_pca at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/src/exact_ooc_pca.jl:25 unknown function (ip: 0x70d6f761a7eb) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_30481.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_30481.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:290 _start at ./client.jl:557 jfptr__start_68643.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] true_main at /source/src/jlapi.c:964 jl_repl_entrypoint at /source/src/jlapi.c:1132 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x70d715910249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_36099.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Progress: 2 Time: 0:00:02 ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000070d6fb800010 Total snapshots: 1. Utilization: 100% Progress: 6 Time: 0:00:13 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (MM-Sparse, Command line) ####### ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000722869690970 Total snapshots: 464. Utilization: 0% ╎464 @Base/task.jl:1150 wait_forever() 463╎ 464 @Base/task.jl:1213 wait() [171] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/test/test_exact_ooc_pca.jl:40 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 [474] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/UhOUu/bin/exact_ooc_pca:1 obvious_subtype at /source/src/subtype.c:1938 obvious_subtype at /source/src/subtype.c:2155 obvious_subtype at /source/src/subtype.c:1938 [inlined] obvious_subtype at /source/src/subtype.c:1944 obvious_subtype at /source/src/subtype.c:2155 ijl_subtype_env at /source/src/subtype.c:2269 intersect at /source/src/subtype.c:4150 intersect_tuple at /source/src/subtype.c:3694 wait at ./task.jl:1213 intersect at /source/src/subtype.c:4215 wait at ./task.jl:1213 intersect_all at /source/src/subtype.c:4357 jl_type_intersection_env_s at /source/src/subtype.c:4605 jl_typemap_intersection_node_visitor at /source/src/typemap.c:543 jl_typemap_intersection_visitor at /source/src/typemap.c:805 jl_typemap_intersection_visitor at /source/src/typemap.c:768 ml_mtable_visitor at /source/src/gf.c:4137 [inlined] ml_matches at /source/src/gf.c:4513 ml_matches at /source/src/gf.c:4426 [inlined] ijl_matching_methods at /source/src/gf.c:2820 [inlined] ijl_matching_methods at /source/src/gf.c:2807 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_36099.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jfptr_wait_forever_36099.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 21843901 (Pool: 21843383; Big: 518); GC: 22 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 126560153 (Pool: 126558582; Big: 1571); GC: 73 _methods_by_ftype at ./runtime_internals.jl:1470 [inlined] verify_call at ./staticdata.jl:310 [inlined] verify_method at ./staticdata.jl:169 verify_method at ./staticdata.jl:234 verify_method at ./staticdata.jl:234 verify_method at ./staticdata.jl:234 verify_method at ./staticdata.jl:234 verify_method at ./staticdata.jl:234 verify_method_graph at ./staticdata.jl:59 _insert_backedges at ./staticdata.jl:33 _insert_backedges at ./staticdata.jl:30 [inlined] insert_backedges at ./staticdata.jl:23 [inlined] #_include_from_serialized#868 at ./loading.jl:1290 _include_from_serialized at ./loading.jl:1246 [inlined] #_require_search_from_serialized#884 at ./loading.jl:2075 _require_search_from_serialized at ./loading.jl:1982 jfptr__require_search_from_serialized_33694.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 __require_prelocked at ./loading.jl:2600 _require_prelocked at ./loading.jl:2466 macro expansion at ./loading.jl:2394 [inlined] macro expansion at ./lock.jl:376 [inlined] __require at ./loading.jl:2359 jfptr___require_61742.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] jl_f_invoke_in_world at /source/src/builtins.c:896 require at ./loading.jl:2335 [inlined] eval_import_path at ./module.jl:36 [inlined] eval_import_path_all at ./module.jl:60 _eval_using at ./module.jl:137 PkgEval terminated after 2741.54s: test duration exceeded the time limit