Package evaluation of PALEOsediment on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:06:47.435 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.55s ################################################################################ # Installation # Installing PALEOsediment... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [e0a37952] + PALEOsediment v0.3.4 Updating `~/.julia/environments/v1.11/Manifest.toml` [79e6a3ab] + Adapt v4.3.0 [ec485272] + ArnoldiMethod v0.4.0 [a9b6321e] + Atomix v1.1.1 [13072b0f] + AxisAlgorithms v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.0 [e1450e63] + BufferedStreams v1.2.2 ⌅ [179af706] + CFTime v0.1.4 [d360d2e6] + ChainRulesCore v1.25.1 [da1fd8a2] + CodeTracking v1.3.9 [944b1d66] + CodecZlib v0.7.8 [1fbeeb36] + CommonDataModel v0.3.8 [34da2185] + Compat v4.16.0 [187b0558] + ConstructionBase v1.5.8 [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 [3c3547ce] + DiskArrays v0.4.12 [ffbed154] + DocStringExtensions v0.9.4 [e2ba6199] + ExprTools v0.1.10 [86223c79] + Graphs v1.12.1 [f67ccb44] + HDF5 v0.17.2 [5903a43b] + Infiltrator v1.8.7 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [a98d9a8b] + Interpolations v0.15.1 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [aa1ae85d] + JuliaInterpreter v0.9.42 [8ac3fa9e] + LRUCache v1.6.2 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [6f1432cf] + LoweredCodeUtils v3.1.0 [23992714] + MAT v0.10.7 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.15 [e1d29d7a] + Missings v1.2.0 [85f8d34a] + NCDatasets v0.14.7 [6fe1bfb0] + OffsetArrays v1.16.0 [bac558e1] + OrderedCollections v1.8.0 [673cec3b] + PALEOaqchem v0.3.19 [804b410e] + PALEOboxes v0.22.4 [e0a37952] + PALEOsediment v0.3.4 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [295af30f] + Revise v3.7.3 [fdea26ae] + SIMD v3.7.1 [91c51154] + SentinelArrays v1.4.8 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [09ab397b] + StructArrays v0.7.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [1e6cf692] + TestEnv v1.102.0 [a759f4b9] + TimerOutputs v0.5.28 [3bb67fe8] + TranscodingStreams v0.11.3 [013be700] + UnsafeAtomics v0.3.0 [efce3f68] + WoodburyMatrices v1.0.0 ⌅ [ddb6d928] + YAML v0.4.12 [0b7ba130] + Blosc_jll v1.21.7+0 [6e34b625] + Bzip2_jll v1.0.9+0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [7243133f] + NetCDF_jll v401.900.300+0 [fe0851c0] + OpenMPI_jll v5.0.7+2 [458c3c95] + OpenSSL_jll v3.0.16+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [63e82ce6] + SLEEF_jll v3.7.0+0 [02c8fc9c] + XML2_jll v2.13.6+1 [ffd25f8a] + XZ_jll v5.8.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [477f73a3] + libaec_jll v1.1.3+0 [337d8026] + libzip_jll v1.11.3+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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [781609d7] + GMP_jll v6.3.0+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [3a97d323] + MPFR_jll v4.2.1+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [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 7.75s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 476.83s ################################################################################ # Testing # Testing PALEOsediment Status `/tmp/jl_Jo8SME/Project.toml` [a93c6f00] DataFrames v1.7.0 [e30172f5] Documenter v1.10.1 [5903a43b] Infiltrator v1.8.7 [d3d80556] LineSearches v7.3.0 [2774e3e8] NLsolve v4.5.1 [673cec3b] PALEOaqchem v0.3.19 [804b410e] PALEOboxes v0.22.4 [bf7b4fbe] PALEOmodel v0.16.5 [e0a37952] PALEOsediment v0.3.4 [91a5bcdd] Plots v1.40.11 [276daf66] SpecialFunctions v2.5.0 [c3572dad] Sundials v4.27.0 [1e6cf692] TestEnv v1.102.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Jo8SME/Manifest.toml` [47edcb42] ADTypes v1.14.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.18.0 [a9b6321e] Atomix v1.1.1 [13072b0f] AxisAlgorithms v1.1.0 [6e4b80f9] BenchmarkTools v1.6.0 [d1d4a3ce] BitFlags v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [fa961155] CEnum v0.5.0 ⌅ [179af706] CFTime v0.1.4 [2a0fbf3d] CPUSummary v0.2.6 [d360d2e6] ChainRulesCore v1.25.1 [fb6a15b2] CloseOpenIntervals v0.1.13 [da1fd8a2] CodeTracking v1.3.9 [944b1d66] CodecZlib v0.7.8 [35d6a980] ColorSchemes v3.29.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.0 [1fbeeb36] CommonDataModel v0.3.8 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 [2569d6c7] ConcreteStructs v0.2.3 [f0e56b4a] ConcurrentUtilities v2.5.0 [187b0558] ConstructionBase v1.5.8 [d38c429a] Contour v0.6.3 [adafc99b] CpuId v0.3.1 [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 [2b5f629d] DiffEqBase v6.167.2 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.6.50 [3c3547ce] DiskArrays v0.4.12 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [4e289a0a] EnumX v1.0.5 [f151be2c] EnzymeCore v0.8.8 [460bff9d] ExceptionUnwrapping v0.1.11 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [c87230d0] FFMPEG v0.4.2 [7034ab61] FastBroadcast v0.3.5 [9aa1b823] FastClosures v0.3.2 [a4df4552] FastPower v1.1.2 [5789e2e9] FileIO v1.17.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.38 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [28b8d3ca] GR v0.73.13 [d7ba0133] Git v1.3.1 [86223c79] Graphs v1.12.1 [42e2da0e] Grisu v1.0.2 [f67ccb44] HDF5 v0.17.2 [cd3eb016] HTTP v1.10.15 [b5f81e59] IOCapture v0.2.5 [615f187c] IfElse v0.1.1 [5903a43b] Infiltrator v1.8.7 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [a98d9a8b] Interpolations v0.15.1 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [1019f520] JLFzf v0.1.10 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [ae98c720] Jieko v0.2.1 [aa1ae85d] JuliaInterpreter v0.9.42 [8ac3fa9e] LRUCache v1.6.2 [b964fa9f] LaTeXStrings v1.4.0 [23fbe1c1] Latexify v0.16.7 [10f19ff3] LayoutPointers v0.1.17 [0e77f7df] LazilyInitializedFields v1.3.0 [d3d80556] LineSearches v7.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.1.0 [6f1432cf] LoweredCodeUtils v3.1.0 [23992714] MAT v0.10.7 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.15 [d125e4d3] ManualMemory v0.1.8 [d0879d2d] MarkdownAST v0.1.2 [739be429] MbedTLS v1.1.9 [442fdcdd] Measures v0.3.2 [e1d29d7a] Missings v1.2.0 [2e0e35c7] Moshi v0.3.5 [46d2c3a1] MuladdMacro v0.2.4 [bdf0d083] MultiFloats v2.3.0 [85f8d34a] NCDatasets v0.14.7 [d41bc354] NLSolversBase v7.9.1 [2774e3e8] NLsolve v4.5.1 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.16.0 [4d8831e6] OpenSSL v1.4.3 [bac558e1] OrderedCollections v1.8.0 [673cec3b] PALEOaqchem v0.3.19 [804b410e] PALEOboxes v0.22.4 [bf7b4fbe] PALEOmodel v0.16.5 [e0a37952] PALEOsediment v0.3.4 [65ce6f38] PackageExtensionCompat v1.0.2 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [ccf2f8ad] PlotThemes v3.3.0 [995b91a9] PlotUtils v1.4.3 [91a5bcdd] Plots v1.40.11 [f517fe37] Polyester v0.7.16 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [c84ed2f1] Ratios v0.4.5 [3cdcf5f2] RecipesBase v1.3.4 [01d81517] RecipesPipeline v0.6.12 [731186ca] RecursiveArrayTools v3.31.2 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v0.3.7 [892a3eda] StringManipulation v0.4.1 [09ab397b] StructArrays v0.7.1 [c3572dad] Sundials v4.27.0 [2efcf032] SymbolicIndexingInterface v0.3.38 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [62fd8b95] TensorCore v0.1.1 [1e6cf692] TestEnv v1.102.0 [8290d209] ThreadingUtilities v0.5.2 [a759f4b9] TimerOutputs v0.5.28 [3bb67fe8] TranscodingStreams v0.11.3 [781d530d] TruncatedStacktraces v1.4.0 [5c2747f8] URIs v1.5.2 [3a884ed6] UnPack v1.0.2 [1cfade01] UnicodeFun v0.4.1 [1986cc42] Unitful v1.22.0 [45397f5d] UnitfulLatexify v1.6.4 [013be700] UnsafeAtomics v0.3.0 [41fe7b60] Unzip v0.2.0 [19fa3120] VertexSafeGraphs v0.2.0 [efce3f68] WoodburyMatrices v1.0.0 ⌅ [ddb6d928] YAML v0.4.12 [0b7ba130] Blosc_jll v1.21.7+0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.4+0 [ee1fde0b] Dbus_jll v1.16.2+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.6.5+0 ⌅ [b22a6f82] FFMPEG_jll v4.4.4+1 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Cloning git-repo `https://github.com/PALEOtoolkit/NLsolve.jl` Updating git-repo `https://github.com/PALEOtoolkit/NLsolve.jl` Resolving package versions... Updating `/tmp/jl_Jo8SME/Project.toml` [2774e3e8] ~ NLsolve v4.5.1 ⇒ v4.5.1 `https://github.com/PALEOtoolkit/NLsolve.jl#project_region` Updating `/tmp/jl_Jo8SME/Manifest.toml` [2774e3e8] ~ NLsolve v4.5.1 ⇒ v4.5.1 `https://github.com/PALEOtoolkit/NLsolve.jl#project_region` Precompiling NLsolve... 3553.0 ms ✓ NLsolve 1 dependency successfully precompiled in 6 seconds. 46 already precompiled. Precompiling PALEOboxes... 2486.7 ms ✓ YAML 8803.0 ms ✓ Graphs 2881.5 ms ✓ BenchmarkTools 7844.3 ms ✓ NCDatasets Info Given PALEOboxes was explicitly requested, output will be shown live  [ Info: PALEOboxes.SIMDutils defining USE_SLEEF = false in LocalPreferences.toml 86786.6 ms ✓ PALEOboxes 5 dependencies successfully precompiled in 112 seconds. 139 already precompiled. 1 dependency had output during precompilation: ┌ PALEOboxes │ [Output was shown above] └ Precompiling FiniteDiffStaticArraysExt... 1355.6 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 1 dependency successfully precompiled in 2 seconds. 21 already precompiled. Precompiling PALEOsediment... 24806.2 ms ✓ PALEOaqchem 24162.2 ms ✓ PALEOsediment 2 dependencies successfully precompiled in 51 seconds. 151 already precompiled. Precompiling PALEOmodel... 4481.6 ms ✓ RecursiveArrayTools 2912.4 ms ✓ StaticArrayInterface 4537.8 ms ✓ SparsityTracing 2884.4 ms ✓ VertexSafeGraphs 1573.6 ms ✓ FastPower → FastPowerForwardDiffExt 1408.7 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStructArraysExt 1795.0 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1861.5 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 23199.9 ms ✓ SciMLBase 1500.8 ms ✓ StaticArrayInterface → StaticArrayInterfaceStaticArraysExt 1035.2 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 950.5 ms ✓ CloseOpenIntervals 1161.2 ms ✓ LayoutPointers 2624.6 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 6163.3 ms ✓ SparseDiffTools 1963.6 ms ✓ StrideArraysCore 1654.1 ms ✓ Polyester 1766.5 ms ✓ FastBroadcast 4681.7 ms ✓ SparseDiffTools → SparseDiffToolsPolyesterExt 1965.3 ms ✓ RecursiveArrayTools → RecursiveArrayToolsFastBroadcastExt 6815.8 ms ✓ DiffEqBase 3697.9 ms ✓ DiffEqBase → DiffEqBaseChainRulesCoreExt 4120.9 ms ✓ DiffEqBase → DiffEqBaseForwardDiffExt 3591.8 ms ✓ DiffEqBase → DiffEqBaseSparseArraysExt 25378.7 ms ✓ Sundials 28808.8 ms ✓ PALEOmodel 26 dependencies successfully precompiled in 146 seconds. 235 already precompiled. ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel sediment_Corg_O2 │ config_file: /home/pkgeval/.julia/packages/PALEOsediment/UyLVX/examples/boudreau1996/PALEO_examples_sediment_cfg.yaml └ ================================================================================ ┌ Info: Model.parameters: │ num_columns = 3 │ CIsotope = ScalarData └ SIsotope = ScalarData ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 54 Reactions ┌ Info: │ ================================================================================ │ creating domain 'global' ID=1 └ ================================================================================ ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=2 └ ================================================================================ ┌ Info: create_reaction_from_config: oceanfloor.floorstubphys classname ReactionConst └ set parameters: [config.yaml] constnames =["Afloor", "zfloor", "temp", "sal", "phi", "w_accum", "zbio", "Dbio", "alpha"] ┌ Info: create_reaction_from_config: oceanfloor.grid classname ReactionUnstructuredVectorGrid │ set parameters: [config.yaml] ncells =external%num_columns │ expandvalue: external%num_columns -> 3 └ after substitution ncells=3 ┌ Info: create_reaction_from_config: oceanfloor.transfer_particulatefluxOceanfloor classname ReactionFluxTransfer │ set parameters: [config.yaml] input_fluxes =fluxOceanfloor.particulateflux_$fluxname$ │ set parameters: [config.yaml] output_fluxes =sediment.oceanfloor.$fluxname$_sms │ set parameters: [Default] transfer_multiplier =1.0 └ set parameters: [config.yaml] transfer_matrix =Identity ┌ Info: create_reaction_from_config: oceanfloor.floorstubsoluteconc classname ReactionConst └ set parameters: [config.yaml] constnames =["O2_conc", "P_conc", "SO4_conc::SIsotope", "H2S_conc::SIsotope", "CH4_conc"] ┌ Info: │ ================================================================================ │ creating domain 'sediment' ID=3 └ ================================================================================ ┌ Info: create_reaction_from_config: sediment.redox_CH4_SO4 classname ReactionRedoxCH4_SO4 │ set parameters: [config.yaml] R_CH4_SO4 =10.0 └ set parameters: [config.yaml] CIsotope =ScalarData ┌ Info: create_reaction_from_config: sediment.reservoir_P classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.pocdecay1 classname ReactionParticleDecay │ set parameters: [config.yaml] decay_timescale =1.6393 │ set parameters: [Default] decay_threshold =-Inf │ set parameters: [Default] show_decayrate =false └ set parameters: [Default] field_data =PALEOboxes.ScalarData ┌ Info: create_reaction_from_config: sediment.transportsedsolute classname ReactionSedimentTransportSolute │ set parameters: [config.yaml] zdbl =0.0004 └ set parameters: [Default] solute_burial_flux =false ┌ Info: create_reaction_from_config: sediment.reservoir_Corg2 classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.redox_CH4_O2 classname ReactionRedoxCH4_O2 │ set parameters: [config.yaml] R_CH4_O2 =1.0e7 └ set parameters: [config.yaml] CIsotope =ScalarData ┌ Info: create_reaction_from_config: sediment.reservoir_CH4 classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.pocdecaycomponents classname ReactionFluxToComponents │ set parameters: [config.yaml] outputflux_prefix =remin_ │ set parameters: [config.yaml] outputflux_names =["Corg", "N", "P"] │ set parameters: [config.yaml] outputflux_stoich =[1.0, 0.15094, 0.009434] │ set parameters: [Default] allow_unlinked_outputflux=false └ set parameters: [Default] field_data =PALEOboxes.ScalarData ┌ Info: create_reaction_from_config: sediment.physsed classname ReactionSedimentPhys │ set parameters: [Default] f_porosity =Const │ set parameters: [Default] zpor =0.1 └ set parameters: [Default] w_solute =false ┌ Info: create_reaction_from_config: sediment.reservoir_O2 classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.reminsed classname ReactionReminO2_SO4_CH4 │ set parameters: [Default] oxreminlimit =0.008 │ set parameters: [config.yaml] SO4reminlimit =1.0 │ set parameters: [config.yaml] CIsotope =ScalarData └ set parameters: [config.yaml] SIsotope =ScalarData ┌ Info: create_reaction_from_config: sediment.pocdecay2 classname ReactionParticleDecay │ set parameters: [config.yaml] decay_timescale =100.0 │ set parameters: [Default] decay_threshold =-Inf │ set parameters: [Default] show_decayrate =false └ set parameters: [Default] field_data =PALEOboxes.ScalarData ┌ Info: create_reaction_from_config: sediment.transportsedsolid classname ReactionSedimentTransportSolid └ set parameters: [Default] trspt_sms_ext =_sms ┌ Info: create_reaction_from_config: sediment.redox_H2S_O2 classname ReactionRedoxH2S_O2 │ set parameters: [config.yaml] R_H2S_O2 =300000.0 └ set parameters: [config.yaml] SIsotope =ScalarData ┌ Info: create_reaction_from_config: sediment.gridsed classname ReactionSedimentGridn1D │ set parameters: [config.yaml] L =0.15 │ set parameters: [config.yaml] ncellspercol =100 │ set parameters: [config.yaml] f_grid =quadratic │ set parameters: [config.yaml] grid_eta =0.075 └ set parameters: [Default] rho_ref =1027.0 ┌ Info: create_reaction_from_config: sediment.bioratesed classname ReactionSedimentBioRates │ set parameters: [Default] f_bioTurbRate =Prescribed │ set parameters: [Default] f_bioTurbDepth =ConstCutoff │ set parameters: [Default] f_bioIrrigDepth =ConstCutoff │ set parameters: [Default] f_bioO2 =None │ set parameters: [Default] bioO2halfmax =0.02 │ set parameters: [Default] bioO2decreaserate =0.012 └ set parameters: [Default] separate_zbio =false ┌ Info: create_reaction_from_config: sediment.reservoir_H2S classname ReactionReservoirTotal │ set parameters: [config.yaml] field_data =external%SIsotope │ expandvalue: external%SIsotope -> ScalarData │ after substitution field_data=ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.reservoir_SO4 classname ReactionReservoirTotal │ set parameters: [config.yaml] field_data =external%SIsotope │ expandvalue: external%SIsotope -> ScalarData │ after substitution field_data=ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: sediment.reservoir_Corg1 classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: │ ================================================================================ │ creating domain 'sedimentfloor' ID=4 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'sedimentfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'fluxOceanfloor' ID=5 └ ================================================================================ ┌ Info: create_reaction_from_config: fluxOceanfloor.floorstubparticulateflux classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["Corg1", "Corg2"] │ set parameters: [config.yaml] target_prefix =particulateflux_ │ set parameters: [Default] flux_totals =false └ set parameters: [config.yaml] const_stub =true ┌ Info: create_reaction_from_config: fluxOceanfloor.floorstubsoluteflux classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["O2", "P", "SO4::SIsotope", "H2S::SIsotope", "CH4"] │ set parameters: [config.yaml] target_prefix =soluteflux_ │ set parameters: [Default] flux_totals =false └ set parameters: [Default] const_stub =false ┌ Info: │ ================================================================================ │ creating domain 'fluxOceanBurial' ID=6 └ ================================================================================ ┌ Info: create_reaction_from_config: fluxOceanBurial.transfer classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["Corg1", "Corg2"] │ set parameters: [config.yaml] target_prefix =flux_ │ set parameters: [Default] flux_totals =false └ set parameters: [Default] const_stub =false ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ [ Info: set_model_geometry oceanfloor.grid [ Info: set oceanfloor Domain size=3 grid=UnstructuredVectorGrid(ncells=3, cellnames=Dict{Symbol, Int64}(), subdomains: String[]) [ Info: ReactionSedimentGridn1D set_model_geometry: sediment.gridsed [ Info: Defining 3 sediment columns each 100 cells [ Info: set sediment.sedimentsurface Subdomain size=3 [ Info: set sediment.sedimentfloor Subdomain size=3 [ Info: using existing oceanfloor.grid [ Info: setting fluxOceanfloor grid [ Info: setting fluxOceanBurial size and grid ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ [ Info: register_methods! sediment.redox_CH4_SO4 CIsotopeType=PALEOboxes.ScalarData [ Info: register_methods! sediment.redox_CH4_O2 CIsotopeType=PALEOboxes.ScalarData [ Info: register_methods! sediment.reminsed CIsotopeType=PALEOboxes.ScalarData, SIsotopeType=PALEOboxes.ScalarData [ Info: register_methods! sediment.redox_H2S_O2 SIsotopeType=PALEOboxes.ScalarData ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionConst oceanfloor.floorstubphys variable_attributes: │ set attribute: w_accum :initial_value = [0.0003, 3.0e-5, 3.0e-5] │ set attribute: phi :norm_value = 0.8 │ set attribute: zfloor :initial_value = [-100.0, -1000.0, -1000.0] │ set attribute: zbio :initial_value = 0.1 │ set attribute: temp :initial_value = [278.15, 275.15, 275.15] │ set attribute: phi :initial_value = 0.8 │ set attribute: Afloor :norm_value = 1.0 │ set attribute: sal :initial_value = 35.0 │ set attribute: Afloor :initial_value = 1.0 │ set attribute: Dbio :initial_value = [0.000135, 2.69e-5, 0.0] └ set attribute: alpha :initial_value = 0.0 ┌ Info: _configure_variables: ReactionConst oceanfloor.floorstubsoluteconc variable_attributes: │ set attribute: H2S_conc :initial_value = 0.0 │ set attribute: SO4_conc :initial_value = 28.756 │ set attribute: CH4_conc :initial_value = 0.0 │ set attribute: H2S_conc :initial_delta = 0.0 │ set attribute: O2_conc :initial_value = [0.25, 0.18, 0.18] │ set attribute: SO4_conc :initial_delta = 0.0 └ set attribute: P_conc :initial_value = 0.001 ┌ Info: _configure_variables: ReactionRedoxCH4_SO4 sediment.redox_CH4_SO4 variable_links: └ set variable_links: volume -> volume_solute ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_P variable_links: │ set variable_links: R -> P │ set variable_links: R_sms -> P_sms │ set variable_links: R_total -> P_total │ set variable_links: R_conc -> P_conc │ set variable_links: volume -> volume_solute │ _configure_variables: ReactionReservoir sediment.reservoir_P variable_attributes: │ set attribute: R_conc :vphase = VP_Solute │ set attribute: R_conc :diffusivity_speciesname = PO4 │ set attribute: R :norm_value = 0.002 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionParticleDecay sediment.pocdecay1 variable_links: │ set variable_links: Particle -> Corg1 │ set variable_links: Particle_sms -> Corg1_sms └ set variable_links: decayflux -> POC_decay WARNING: SedimentTransport.parse_number_name is deprecated, use PALEOboxes.parse_number_name instead. likely near /home/pkgeval/.julia/packages/PALEOsediment/UyLVX/examples/boudreau1996/runtests.jl:14 in #find_solute_vars#9 at /home/pkgeval/.julia/packages/PALEOsediment/UyLVX/src/sediment/SedimentTransport.jl ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_Corg2 variable_links: │ set variable_links: R -> Corg2 │ set variable_links: R_sms -> Corg2_sms │ set variable_links: R_total -> Corg2_total │ set variable_links: R_conc -> Corg2_conc │ set variable_links: volume -> volume_solid │ _configure_variables: ReactionReservoir sediment.reservoir_Corg2 variable_attributes: │ set attribute: R_conc :vphase = VP_Solid │ set attribute: R :norm_value = 2083.3 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionRedoxCH4_O2 sediment.redox_CH4_O2 variable_links: └ set variable_links: volume -> volume_solute ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_CH4 variable_links: │ set variable_links: R -> CH4 │ set variable_links: R_sms -> CH4_sms │ set variable_links: R_total -> CH4_total │ set variable_links: R_conc -> CH4_conc │ set variable_links: volume -> volume_solute │ _configure_variables: ReactionReservoir sediment.reservoir_CH4 variable_attributes: │ set attribute: R_conc :vphase = VP_Solute │ set attribute: R_conc :diffusivity_speciesname = CH4 │ set attribute: R :norm_value = 0.2 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionFluxToComponents sediment.pocdecaycomponents variable_links: └ set variable_links: inputflux -> POC_decay ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_O2 variable_links: │ set variable_links: R -> O2 │ set variable_links: R_sms -> O2_sms │ set variable_links: R_total -> O2_total │ set variable_links: R_conc -> O2_conc │ set variable_links: volume -> volume_solute │ _configure_variables: ReactionReservoir sediment.reservoir_O2 variable_attributes: │ set attribute: R_conc :vphase = VP_Solute │ set attribute: R_conc :diffusivity_speciesname = O2 │ set attribute: R :norm_value = 0.2 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionReminO2_SO4_CH4 sediment.reminsed variable_links: │ set variable_links: soluteflux_P -> P_sms │ set variable_links: soluteflux_TNH3 -> TNH3_sms │ set variable_links: soluteflux_DIC -> DIC_sms │ set variable_links: soluteflux_TAlk -> TAlk_sms │ set variable_links: soluteflux_O2 -> O2_sms │ set variable_links: soluteflux_SO4 -> SO4_sms │ set variable_links: soluteflux_H2S -> H2S_sms └ set variable_links: soluteflux_CH4 -> CH4_sms ┌ Info: _configure_variables: ReactionParticleDecay sediment.pocdecay2 variable_links: │ set variable_links: Particle -> Corg2 │ set variable_links: Particle_sms -> Corg2_sms └ set variable_links: decayflux -> POC_decay WARNING: SedimentTransport.parse_number_name is deprecated, use PALEOboxes.parse_number_name instead. likely near /home/pkgeval/.julia/packages/PALEOsediment/UyLVX/examples/boudreau1996/runtests.jl:14 in find_solid_vars at /home/pkgeval/.julia/packages/PALEOsediment/UyLVX/src/sediment/SedimentTransport.jl ┌ Info: _configure_variables: ReactionRedoxH2S_O2 sediment.redox_H2S_O2 variable_links: └ set variable_links: volume -> volume_solute ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_H2S variable_links: │ set variable_links: R -> H2S │ set variable_links: R_sms -> H2S_sms │ set variable_links: R_total -> H2S_total │ set variable_links: R_conc -> H2S_conc │ set variable_links: volume -> volume_solute │ _configure_variables: ReactionReservoir sediment.reservoir_H2S variable_attributes: │ set attribute: R_conc :vphase = VP_Solute │ set attribute: R_conc :diffusivity_speciesname = H2S │ set attribute: R :norm_value = 0.2 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_SO4 variable_links: │ set variable_links: R -> SO4 │ set variable_links: R_sms -> SO4_sms │ set variable_links: R_total -> SO4_total │ set variable_links: R_conc -> SO4_conc │ set variable_links: volume -> volume_solute │ _configure_variables: ReactionReservoir sediment.reservoir_SO4 variable_attributes: │ set attribute: R_conc :vphase = VP_Solute │ set attribute: R_conc :diffusivity_speciesname = SO4 │ set attribute: R :norm_value = 20.0 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionReservoir sediment.reservoir_Corg1 variable_links: │ set variable_links: R -> Corg1 │ set variable_links: R_sms -> Corg1_sms │ set variable_links: R_total -> Corg1_total │ set variable_links: R_conc -> Corg1_conc │ set variable_links: volume -> volume_solid │ _configure_variables: ReactionReservoir sediment.reservoir_Corg1 variable_attributes: │ set attribute: R_conc :vphase = VP_Solid │ set attribute: R :norm_value = 2083.3 └ set attribute: R :initial_value = 1.0e-30 ┌ Info: _configure_variables: ReactionFluxTarget fluxOceanfloor.floorstubparticulateflux variable_attributes: │ set attribute: particulateflux_Corg1 :initial_value = [1.3, 0.0, 0.0] └ set attribute: particulateflux_Corg2 :initial_value = [0.0, 0.185, 0.185] ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: │ ================================================================================ │ optional sediment.redox_CH4_SO4 DIC_sms -| DIC_sms │ optional sediment.redox_CH4_SO4 TAlk_sms -| TAlk_sms │ optional sediment.redox_CH4_O2 DIC_sms -| DIC_sms │ optional sediment.physsed oceanfloor_phimin -| oceanfloor.phimin │ optional sediment.physsed oceanfloor_phimin -| oceanfloor.phimin │ optional sediment.physsed oceanfloor_phimin -| oceanfloor.phimin │ optional sediment.reminsed soluteflux_TNH3 -| TNH3_sms │ optional sediment.reminsed soluteflux_DIC -| DIC_sms │ optional sediment.reminsed soluteflux_TAlk -| TAlk_sms │ optional sediment.reminsed soluteflux_TAlk -| TAlk_sms │ optional sediment.reminsed soluteflux_DIC -| DIC_sms └ optional sediment.redox_H2S_O2 TAlk_sms -| TAlk_sms ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ Add expt: baseline ┌ Info: │ ================================================================================ │ PALEOmodel.initialize! start └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain global data dimensions PALEOboxes.NamedDimension[] allocating 0 variables (hostdep=nothing) [ Info: Domain oceanfloor data dimensions PALEOboxes.NamedDimension[] allocating 14 variables (hostdep=nothing) [ Info: Domain sediment data dimensions PALEOboxes.NamedDimension[] allocating 76 variables (hostdep=nothing) [ Info: Domain sedimentfloor data dimensions PALEOboxes.NamedDimension[] allocating 0 variables (hostdep=nothing) [ Info: Domain fluxOceanfloor data dimensions PALEOboxes.NamedDimension[] allocating 7 variables (hostdep=nothing) [ Info: Domain fluxOceanBurial data dimensions PALEOboxes.NamedDimension[] allocating 2 variables (hostdep=nothing) [ Info: set_default_solver_view: ┌ Info: SolverView: │ host-dependent Variables: │ ------------------------------------------------------------------------------------------------------------------------------------------------ │ Domain operatorID VF_StateExplicit VF_Total VF_Constraint VF_StateTotal VF_State VF_Undefined │ global 0 0 0 0 0 0 0 │ oceanfloor 0 0 0 0 0 0 0 │ sediment 0 7 0 0 0 0 0 │ sedimentfloor 0 0 0 0 0 0 0 │ fluxOceanfloor 0 0 0 0 0 0 0 │ fluxOceanBurial 0 0 0 0 0 0 0 │ ------------------------------------------------------------------------------------------------------------------------------------------------ │ Total - 7 0 0 0 0 0 │ ------------------------------------------------------------------------------------------------------------------------------------------------ │ n_state_vars 7 (stateexplicit 7 + statetotal 0 + state 0) │ n_equations 7 (stateexplicit 7 + total 0 + constraint 0) │ including all host-dependent non-state Variables └ host-dependent non-state Variables (:vfunction PB.VF_Undefined): Any[] ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: prepare_do_transfer: ReactionMethod oceanfloor.transfer_particulatefluxOceanfloor.do_transfer │ active fluxes: │ Corg2 fluxOceanfloor.particulateflux_Corg2 -> sediment.Corg2_sms │ Corg1 fluxOceanfloor.particulateflux_Corg1 -> sediment.Corg1_sms └ using Identity transfer matrix * 1.0 ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: oceanfloor.floorstubphys.setup_initialvalue_vars_default: [ Info: init_values! :initial_value oceanfloor.Afloor = 1.0 [ Info: init_values! :initial_value oceanfloor.zfloor = [-100.0, -1000.0, -1000.0] [ Info: init_values! :initial_value oceanfloor.temp = [278.15, 275.15, 275.15] [ Info: init_values! :initial_value oceanfloor.sal = 35.0 [ Info: init_values! :initial_value oceanfloor.phi = 0.8 [ Info: init_values! :initial_value oceanfloor.w_accum = [0.0003, 3.0e-5, 3.0e-5] [ Info: init_values! :initial_value oceanfloor.zbio = 0.1 [ Info: init_values! :initial_value oceanfloor.Dbio = [0.000135, 2.69e-5, 0.0] [ Info: init_values! :initial_value oceanfloor.alpha = 0.0 [ Info: oceanfloor.floorstubsoluteconc.setup_initialvalue_vars_default: [ Info: init_values! :initial_value oceanfloor.O2_conc = [0.25, 0.18, 0.18] [ Info: init_values! :initial_value oceanfloor.P_conc = 0.001 [ Info: init_values! :initial_value oceanfloor.SO4_conc = 28.756 [ Info: init_values! :initial_value oceanfloor.H2S_conc = 0.0 [ Info: init_values! :initial_value oceanfloor.CH4_conc = 0.0 ┌ Info: setup_sediment_transport sediment.transportsedsolute ReactionSedimentTransportSolute │ │ Solute Variable gamma transport flux │ sediment.H2S_conc 1 ["1.0*sediment.H2S_sms"] │ sediment.O2_conc 1 ["1.0*sediment.O2_sms"] │ sediment.P_conc 1 ["1.0*sediment.P_sms"] │ sediment.SO4_conc 1 ["1.0*sediment.SO4_sms"] └ sediment.CH4_conc 1 ["1.0*sediment.CH4_sms"] ┌ Info: setup_sediment_transport_solid sediment.transportsedsolid ReactionSedimentTransportSolid │ │ Solid Variable transport flux │ sediment.Corg2_conc ["1.0*sediment.Corg2_sms"] └ sediment.Corg1_conc ["1.0*sediment.Corg1_sms"] [ Info: fluxOceanfloor.floorstubparticulateflux.setup_initialvalue_vars_default: [ Info: init_values! :initial_value fluxOceanfloor.particulateflux_Corg1 = [1.3, 0.0, 0.0] [ Info: init_values! :initial_value fluxOceanfloor.particulateflux_Corg2 = [0.0, 0.185, 0.185] [ Info: do_sediment_setup_grid sediment.gridsed: volume_total 0.4500000000000005 m^3 ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ [ Info: sediment.reservoir_P.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.P = 0.002 * volume [ Info: sediment.reservoir_Corg2.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.Corg2 = 2083.3 * volume [ Info: sediment.reservoir_CH4.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.CH4 = 0.2 * volume [ Info: sediment.reservoir_O2.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.O2 = 0.2 * volume [ Info: sediment.reservoir_H2S.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.H2S = 0.2 * volume [ Info: sediment.reservoir_SO4.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.SO4 = 20.0 * volume [ Info: sediment.reservoir_Corg1.setup_initialvalue_vars_default: [ Info: init_values! :norm_value sediment.Corg1 = 2083.3 * volume ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ [ Info: sediment.reservoir_P.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.P = 1.0e-30 * volume [ Info: sediment.reservoir_Corg2.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.Corg2 = 1.0e-30 * volume [ Info: sediment.reservoir_CH4.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.CH4 = 1.0e-30 * volume [ Info: sediment.reservoir_O2.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.O2 = 1.0e-30 * volume [ Info: sediment.reservoir_H2S.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.H2S = 1.0e-30 * volume [ Info: sediment.reservoir_SO4.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.SO4 = 1.0e-30 * volume [ Info: sediment.reservoir_Corg1.setup_initialvalue_vars_default: [ Info: init_values! :initial_value sediment.Corg1 = 1.0e-30 * volume ┌ Info: │ ================================================================================ │ PALEOmodel.initialize! done └ ================================================================================ ┌ Info: │ ================================================================================ │ PALEOmodel.SteadyState.steadystate │ tss=0.0 │ jac_ad=ForwardDiffSparse │ using BLAS with 1 threads" └ ================================================================================ [ Info: 0 algebraic constraints [ Info: steadystate: using Jacobian ForwardDiffSparse [ Info: jac_config_ode: jac_ad=ForwardDiffSparse [ Info: using ForwardDiff sparse Jacobian with sparsity calculated at t=0.0 [ Info: calcJacobianSparsitySparsityTracing! [ Info: add_arrays_data! (arrays_eltype=SparsityTracing.ADval{Float64}, arrays_tagname=sparsity_tracing) [ Info: calcJacobianSparsitySparsityTracing! do_deriv [ Info: calcJacobianSparsitySparsityTracing! initial_jac size=(2100, 2100) nnz=12258 non-zero=11968 at time=0.0 [ Info: fill_sparse_jac: initial_jac nnz 12258 (0.278%) non-zero 11968 [ Info: fill_sparse_jac: after filling diagonal nnz 12258 [ Info: add_arrays_data! (arrays_eltype=ForwardDiff.Dual{Nothing, Float64, 8}, arrays_tagname=jac_ad) [ Info: jac_prototype nnz=12258 num colors=15 chunksize=8) ┌ Info: │ ================================================================================ │ steadystate: calling nlsolve... └ ================================================================================ Iter f(x) inf-norm Step 2-norm ------ -------------- -------------- 0 1.034834e+03 NaN 1 3.131983e+03 2.340105e+01 2 2.184683e+02 4.371833e-04 3 3.231658e+01 2.368169e-05 4 3.075188e+00 1.715797e-06 5 6.047928e-01 5.133440e-08 6 1.022068e-01 2.438465e-07 7 1.640095e-02 5.453053e-08 8 2.647289e-03 6.241591e-09 9 2.274744e-04 2.382029e-10 10 2.481495e-06 1.397821e-12 11 2.821392e-10 1.072574e-16 18.273398 seconds (6.68 M allocations: 371.106 MiB, 0.91% gc time, 99.37% compilation time) ┌ Info: │ ================================================================================ │ * Algorithm: Newton with line-search │ * Inf-norm of residuals: 2.8213918891918795e-10 │ * Iterations: 11 │ * Convergence: true │ * |x - x'| < 0.0: false │ * |f(x)| < 1.0e-8: true │ * Function Calls (f): 12 │ * Jacobian Calls (df/dx): 12 └ ================================================================================ [ Info: check F inf-norm 2.8213918891918795e-10 2-norm 7.550871969307518e-10 conservation checks: check values at end of run: check fluxOceanfloor.soluteflux_O2 [-1.6416397532415026, -0.24070973277232094, -0.23910869776569535] [-1.64229, -0.24071, -0.23907] 0.001 check fluxOceanfloor.soluteflux_H2S [0.02539890944598178, 6.883260250178225e-5, 0.0008664805131996578] [0.025073, 6.8626e-5, 0.00088524] 0.025 ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/utilities/utilities.jl:660 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. ┌ Warning: ReactionSedimentTransport Deprecated monolithic version - replace with `ReactionSedimentGridn1D`, `ReactionSedimentPhys`, `ReactionSedimentTransportSolid`, `ReactionSedimentTransportSolute`] └ @ PALEOsediment.Sediment.SedimentTransportDeprecated ~/.julia/packages/PALEOsediment/UyLVX/src/sediment/SedimentTransportDeprecated.jl:238 [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Total Time PALEOsediment all | 4 4 10m55.5s Testing PALEOsediment tests passed Testing completed after 691.08s PkgEval succeeded after 1201.23s