Package evaluation of PALEOboxes on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T18:27:41.864 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.81s ################################################################################ # Installation # Installing PALEOboxes... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [804b410e] + PALEOboxes v0.22.4 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 [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 [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 [804b410e] + PALEOboxes v0.22.4 [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 [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 [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 [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 7.27s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 141.9s ################################################################################ # Testing # Testing PALEOboxes Status `/tmp/jl_9uFwfI/Project.toml` [a9b6321e] Atomix v1.1.1 [6e4b80f9] BenchmarkTools v1.6.0 [a93c6f00] DataFrames v1.7.0 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [86223c79] Graphs v1.12.1 [5903a43b] Infiltrator v1.8.7 [a98d9a8b] Interpolations v0.15.1 [23992714] MAT v0.10.7 [85f8d34a] NCDatasets v0.14.7 [bac558e1] OrderedCollections v1.8.0 [804b410e] PALEOboxes v0.22.4 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [295af30f] Revise v3.7.3 [fdea26ae] SIMD v3.7.1 [90137ffa] StaticArrays v1.9.13 [09ab397b] StructArrays v0.7.1 [1e6cf692] TestEnv v1.102.0 [a759f4b9] TimerOutputs v0.5.28 ⌅ [ddb6d928] YAML v0.4.12 [63e82ce6] SLEEF_jll v3.7.0+0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [de0858da] Printf v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_9uFwfI/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [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 [e30172f5] Documenter v1.10.1 [e2ba6199] ExprTools v0.1.10 [d7ba0133] Git v1.3.1 [86223c79] Graphs v1.12.1 [f67ccb44] HDF5 v0.17.2 [b5f81e59] IOCapture v0.2.5 [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 [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 [0e77f7df] LazilyInitializedFields v1.3.0 [6f1432cf] LoweredCodeUtils v3.1.0 [23992714] MAT v0.10.7 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.15 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [85f8d34a] NCDatasets v0.14.7 [6fe1bfb0] OffsetArrays v1.16.0 [bac558e1] OrderedCollections v1.8.0 [804b410e] PALEOboxes v0.22.4 [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 [2792f1a3] RegistryInstances v0.1.0 [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 [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 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.49.0+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 [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 [8dfed614] Test v1.11.0 [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 [efcefdf7] PCRE2_jll v10.42.0+1 [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. Testing Running tests... Precompiling PALEOboxes... Info Given PALEOboxes was explicitly requested, output will be shown live  [ Info: PALEOboxes.SIMDutils defining USE_SLEEF = false in LocalPreferences.toml 93326.9 ms ✓ PALEOboxes 1 dependency successfully precompiled in 96 seconds. 143 already precompiled. 1 dependency had output during precompilation: ┌ PALEOboxes │ [Output was shown above] └ Precompiling Documenter... 49471.3 ms ✓ Documenter 1 dependency successfully precompiled in 50 seconds. 50 already precompiled. ┌ 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. [ Info: ReactionForceInterp.register_methods! test.test [ Info: register_methods! test.test [ Info: register_methods! test.test ┌ Info: register_methods: test.test PALEOboxes.VariableStats.ReactionSum │ add 2 * myvar │ add 1 * myothervar └ add -1 * mythirdvar [ Info: ReactionFluxPerturb.register_methods! test.test [ 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). ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ ┌ Info: Model.parameters: └ model_par1 = 0.15 ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock2 classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =external%model_par1 │ expandvalue: external%model_par1 -> 0.15 │ after substitution par1=0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =external%model_par1 │ expandvalue: external%model_par1 -> 0.15 │ after substitution par1=0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock2', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock2 variable_links: │ set variable_links: phy -> mock2_phy └ set variable_links: scalar_dep -> julia_paleo_mock/scalar_prop ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock variable_links: └ set variable_links: phy -> mock_phy ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ All methods_setup: MethodSort All methods_initialize: MethodSort All methods_do: MethodSort group=BitSet([2, 3, 4]) ocean.julia_paleo_mock2.do_react ocean.julia_paleo_mock.do_stateandeqb ocean.julia_paleo_mock.do_react group=BitSet([1]) ocean.julia_paleo_mock2.do_stateandeqb Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 4 variables (hostdep=false) ┌ Error: Domain "ocean" unallocated variables: └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:265 ┌ Error: "scalar_dep" linked by: ["ocean.julia_paleo_mock.do_stateandeqb.scalar_dep"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ VariableAggregatorNamed(modeldata=ModelData(model=Model(config_files='["/home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml"]', name='model1'), domain_data=Tuple{DataType, String}[(Float64, "base")]), arrays_idx=1, ocean.*[:julia_paleo_mock__scalar_prop, :julia_paleo_mock2__scalar_prop, :mock2_phy, :mock_phy, :scalar_dep], ) ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_loop │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock2 classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock1 classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock2', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock1', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock2 variable_links: │ set variable_links: phy -> phy2 └ set variable_links: scalar_dep -> julia_paleo_mock1/scalar_prop ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock1 variable_links: │ set variable_links: phy -> phy1 └ set variable_links: scalar_dep -> julia_paleo_mock2/scalar_prop ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_invalid_parameter │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_empty_parameters │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [Default] par1 =0.0 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock variable_links: └ set variable_links: phy -> mock_phy ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_empty_variable_link │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [Default] par1 =0.0 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Warning: _configure_variables: error setting Variable link for ReactionPaleoMock ocean.julia_paleo_mock phy └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Reaction.jl:479 ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_invalid_variable_attribute │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [Default] par1 =0.0 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Warning: _configure_variables: error setting Variable attribute for ReactionPaleoMock ocean.julia_paleo_mock phy.something └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Reaction.jl:521 ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase_pt1.yaml │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase_pt2.yaml └ ================================================================================ ┌ Info: Model.parameters: └ model_par1 = 0.15 ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock2 classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =external%model_par1 │ expandvalue: external%model_par1 -> 0.15 │ after substitution par1=0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =external%model_par1 │ expandvalue: external%model_par1 -> 0.15 │ after substitution par1=0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock2', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock2 variable_links: │ set variable_links: phy -> mock2_phy └ set variable_links: scalar_dep -> julia_paleo_mock/scalar_prop ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock variable_links: └ set variable_links: phy -> mock_phy ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model_with_unlinked_variable │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configbase.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [Default] par1 =0.0 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ creating domain 'oceansurface' ID=2 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceansurface' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ creating domain 'oceanfloor' ID=3 └ ================================================================================ ┌ Warning: create_domain_from_config Domain 'oceanfloor' empty 'reactions:' key in .yaml file └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:349 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock variable_links: └ set variable_links: scalar_dep -> host_supplied_dep ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Warning: check_variable_links: unexpected host-dependent Variable ocean.host_supplied_dep (usually an unlinked Variable due to eg a missing renaming in the :variable_links sections in the .yaml file, a spelling mistake either in a Variable default name in the code or renaming in the .yaml file, or a missing Reaction) │ PALEOboxes.VariableDomPropDep "ocean.host_supplied_dep" links: │ property: nothing │ dependencies: ["ocean.julia_paleo_mock.do_stateandeqb.scalar_dep"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Model.jl:379 ┌ Error: check_variable_links failed └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Model.jl:386 WARNING: replacing module ReactionPaleoMockModule. ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel cartesiangrid │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configgrids.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.grid classname ReactionCartesianGrid │ set parameters: [config.yaml] dimnames =["z", "lat", "lon"] └ set parameters: [config.yaml] dims =[2, 3, 4] ┌ Info: create_reaction_from_config: ocean.julia_paleo_mock classname ReactionPaleoMock │ set parameters: [config.yaml] par1 =0.15 │ set parameters: [Default] parint =2 │ set parameters: [Default] parbool =true └ set parameters: [Default] parstring =a_string ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ [ Info: set_model_geometry ocean.grid [ Info: set ocean Domain size=24 grid=CartesianArrayGrid(ncells=24, dimensions: PALEOboxes.NamedDimension[(name=z, size=2), (name=lat, size=3), (name=lon, size=4)], dimensions_extra PALEOboxes.NamedDimension[(name=bnds, size=2)], subdomains: String[]) ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ReactionPaleoMock.register_methods! rj=Main.ReactionPaleoMockModule.ReactionPaleoMock(name='julia_paleo_mock', classname='ReactionPaleoMock', domain='ocean, operatorID=[1]) parint=2 parbool=true parstring=a_string ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionPaleoMock ocean.julia_paleo_mock variable_links: └ set variable_links: phy -> mock_phy ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 2 variables (hostdep=false) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ [ Info: allvars: VariableAggregatorNamed(modeldata=ModelData(model=Model(config_files='["/home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configgrids.yaml"]', name='cartesiangrid'), domain_data=Tuple{DataType, String}[(Float64, "base")]), arrays_idx=1, ocean.*[:julia_paleo_mock__scalar_prop, :mock_phy, :scalar_dep], ) ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel cartesianlinear2D │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configgrids.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'surface' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: surface.grid2D classname ReactionGrid2DNetCDF │ set parameters: [config.yaml] grid_type =CartesianLinearGrid │ set parameters: [config.yaml] grid_file =coords.nc │ set parameters: [config.yaml] coordinate_names =["longitude", "latitude"] │ set parameters: [config.yaml] equalspacededges =true │ set parameters: [config.yaml] area_var = └ set parameters: [config.yaml] planet_radius =6.371229e6 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ [ Info: set_model_geometry surface.grid2D [ Info: reading 2D grid from coords.nc [ Info: CartesianGrid creating PALEOboxes.Grids.CartesianLinearGrid{2} from dimnames=["longitude", "latitude"] in netcdf file coords.nc [ Info: read dimension longitude = 144 [ Info: assuming equal spacing 2.5 to calculate coordinate edges longitude_edges [ Info: dim 1 got standard_name=='longitude' [ Info: read dimension latitude = 90 [ Info: assuming equal spacing 2.0 to calculate coordinate edges latitude_edges [ Info: dim 2 got standard_name=='latitude' [ Info: set surface Domain size=12960 grid=CartesianLinearGrid(ncells=12960, dimensions: PALEOboxes.NamedDimension[(name=longitude, size=144), (name=latitude, size=90)], dimensions_extra: PALEOboxes.NamedDimension[(name=bnds, size=2), (name=longitude_edges, size=145), (name=latitude_edges, size=91)], subdomains: String[]) ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ [ Info: register_methods! surface.grid2D ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain surface data dimensions PALEOboxes.NamedDimension[] allocating 6 variables (hostdep=nothing) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: surface.grid2D.setup_grid_2DNetCDF: ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel cartesianarray2D │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configgrids.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 23 Reactions ┌ Info: │ ================================================================================ │ creating domain 'surface' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: surface.grid2D classname ReactionGrid2DNetCDF │ set parameters: [config.yaml] grid_type =CartesianArrayGrid │ set parameters: [config.yaml] grid_file =coords.nc │ set parameters: [config.yaml] coordinate_names =["longitude", "latitude"] │ set parameters: [config.yaml] equalspacededges =true │ set parameters: [config.yaml] area_var = └ set parameters: [config.yaml] planet_radius =6.371229e6 ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ [ Info: set_model_geometry surface.grid2D [ Info: reading 2D grid from coords.nc [ Info: CartesianGrid creating PALEOboxes.Grids.CartesianArrayGrid{2} from dimnames=["longitude", "latitude"] in netcdf file coords.nc [ Info: read dimension longitude = 144 [ Info: assuming equal spacing 2.5 to calculate coordinate edges longitude_edges [ Info: dim 1 got standard_name=='longitude' [ Info: read dimension latitude = 90 [ Info: assuming equal spacing 2.0 to calculate coordinate edges latitude_edges [ Info: dim 2 got standard_name=='latitude' [ Info: set surface Domain size=12960 grid=CartesianArrayGrid(ncells=12960, dimensions: PALEOboxes.NamedDimension[(name=longitude, size=144), (name=latitude, size=90)], dimensions_extra PALEOboxes.NamedDimension[(name=bnds, size=2), (name=longitude_edges, size=145), (name=latitude_edges, size=91)], subdomains: String[]) ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ [ Info: register_methods! surface.grid2D ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain surface data dimensions PALEOboxes.NamedDimension[] allocating 6 variables (hostdep=nothing) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: surface.grid2D.setup_grid_2DNetCDF: ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ NoReaction PALEOboxes.NoReaction ReactionAreaVolumeValInRange PALEOboxes.VariableStats.ReactionAreaVolumeValInRange ReactionCartesianGrid PALEOboxes.GridReactions.ReactionCartesianGrid ReactionConst PALEOboxes.Reservoirs.ReactionConst ReactionFluxPerturb PALEOboxes.FluxPerturb.ReactionFluxPerturb ReactionFluxTarget PALEOboxes.Fluxes.ReactionFluxTarget ReactionFluxTransfer PALEOboxes.Fluxes.ReactionFluxTransfer ReactionForceGrid PALEOboxes.GridForcings.ReactionForceGrid ReactionForceInterp PALEOboxes.Forcings.ReactionForceInterp ReactionGrid2DNetCDF PALEOboxes.GridReactions.ReactionGrid2DNetCDF ReactionPaleoMock Main.ReactionPaleoMockModule.ReactionPaleoMock ReactionReservoir PALEOboxes.Reservoirs.ReactionReservoir ReactionReservoirConst PALEOboxes.Reservoirs.ReactionReservoirConst ReactionReservoirFlux Main.ReactionReservoirFluxModule.ReactionReservoirFlux ReactionReservoirForced PALEOboxes.Reservoirs.ReactionReservoirForced ReactionReservoirScalar PALEOboxes.Reservoirs.ReactionReservoirScalar ReactionReservoirTotal PALEOboxes.Reservoirs.ReactionReservoirTotal ReactionReservoirWellMixed PALEOboxes.Reservoirs.ReactionReservoirWellMixed ReactionRestore PALEOboxes.FluxPerturb.ReactionRestore ReactionScalarConst PALEOboxes.Reservoirs.ReactionScalarConst ReactionSum PALEOboxes.VariableStats.ReactionSum ReactionUnstructuredVectorGrid PALEOboxes.GridReactions.ReactionUnstructuredVectorGrid ReactionVectorSum PALEOboxes.VariableStats.ReactionVectorSum ReactionWeightedMean PALEOboxes.VariableStats.ReactionWeightedMean ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configreservoirs.yaml └ ================================================================================ ┌ Info: Model.parameters: └ CIsotope = IsotopeLinear ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 24 Reactions ┌ Info: │ ================================================================================ │ creating domain 'global' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: global.reservoir_NormS classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] const =false └ set parameters: [config.yaml] state_norm =true ┌ Info: create_reaction_from_config: global.reservoir_A classname ReactionReservoirScalar │ set parameters: [config.yaml] field_data =external%CIsotope │ expandvalue: external%CIsotope -> IsotopeLinear │ after substitution field_data=IsotopeLinear │ set parameters: [Default] const =false └ set parameters: [Default] state_norm =false ┌ Info: create_reaction_from_config: global.reservoir_ConstNormS classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [config.yaml] const =true └ set parameters: [config.yaml] state_norm =true ┌ Info: create_reaction_from_config: global.reservoir_O classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] const =false └ set parameters: [Default] state_norm =false ┌ Info: create_reaction_from_config: global.reservoir_ConstS classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [config.yaml] const =true └ set parameters: [Default] state_norm =false ┌ Info: create_reaction_from_config: global.scalar_sum classname ReactionSum │ set parameters: [config.yaml] vars_to_add =["1e-4*ocean.vectorsum", "ConstS"] │ set parameters: [Default] vars_prefix = │ set parameters: [Default] component_to_add =0 └ set parameters: [Default] vectorsum =false ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=2 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.reservoir_const classname ReactionReservoirConst └ set parameters: [config.yaml] field_data =IsotopeLinear ┌ Info: create_reaction_from_config: ocean.const_volume_total classname ReactionScalarConst └ set parameters: [config.yaml] constnames =["volume_total"] ┌ Info: create_reaction_from_config: ocean.reservoir_tracer 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: ocean.const_volume classname ReactionConst └ set parameters: [config.yaml] constnames =["volume"] ┌ Info: create_reaction_from_config: ocean.grid classname ReactionUnstructuredVectorGrid └ set parameters: [config.yaml] ncells =1000 ┌ Info: create_reaction_from_config: ocean.weightedmean classname ReactionWeightedMean └ set parameters: [config.yaml] field_data =IsotopeLinear ┌ Info: create_reaction_from_config: ocean.volinrange classname ReactionAreaVolumeValInRange │ set parameters: [config.yaml] range_min =0.0 └ set parameters: [config.yaml] range_max =0.2 ┌ Info: create_reaction_from_config: ocean.reservoir_conc_tracer classname ReactionReservoirTotal │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [config.yaml] state_conc =true ┌ Info: create_reaction_from_config: ocean.vector_sum classname ReactionVectorSum │ set parameters: [config.yaml] vars_to_add =["0.5*C", "2*T"] │ set parameters: [Default] vars_prefix = │ set parameters: [Default] component_to_add =0 └ set parameters: [Default] vectorsum =true ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ [ Info: set_model_geometry ocean.grid [ Info: set ocean Domain size=1000 grid=UnstructuredVectorGrid(ncells=1000, cellnames=Dict{Symbol, Int64}(), subdomains: String[]) ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ┌ Info: register_methods: global.scalar_sum PALEOboxes.VariableStats.ReactionSum │ add 0.0001 * ocean.vectorsum └ add 1 * ConstS ┌ Info: register_methods: ocean.vector_sum PALEOboxes.VariableStats.ReactionSum │ add 0.5 * C └ add 2 * T ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_NormS variable_links: │ set variable_links: R -> NormS │ set variable_links: R_solve -> NormS_solve │ set variable_links: R_sms -> NormS_sms │ set variable_links: R_solve_sms -> NormS_solve_sms │ set variable_links: R_norm -> NormS_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_NormS variable_attributes: │ set attribute: R :norm_value = 10.0 └ set attribute: R :initial_value = 1.0 ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_A variable_links: │ set variable_links: R -> A │ set variable_links: R_sms -> A_sms │ set variable_links: R_norm -> A_norm │ set variable_links: R_delta -> A_delta │ _configure_variables: ReactionReservoirScalar global.reservoir_A variable_attributes: │ set attribute: R :norm_value = 3.193e17 │ set attribute: R :initial_value = 3.193e18 └ set attribute: R :initial_delta = 2.0 ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_ConstNormS variable_links: │ set variable_links: R -> ConstNormS │ set variable_links: R_sms -> ConstNormS_sms │ set variable_links: R_norm -> ConstNormS_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_ConstNormS variable_attributes: │ set attribute: R :norm_value = 10.0 └ set attribute: R :initial_value = 1.0 ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_O variable_links: │ set variable_links: R -> O │ set variable_links: R_sms -> O_sms │ set variable_links: R_norm -> O_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_O variable_attributes: │ set attribute: R :norm_value = 3.7e18 └ set attribute: R :initial_value = 3.7e19 ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_ConstS variable_links: │ set variable_links: R -> ConstS │ set variable_links: R_sms -> ConstS_sms │ set variable_links: R_norm -> ConstS_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_ConstS variable_attributes: │ set attribute: R :norm_value = 10.0 └ set attribute: R :initial_value = 1.0 [ Info: Reaction global.scalar_sum Variable global.scalarsum adding data=PALEOboxes.ScalarData ┌ Info: _configure_variables: ReactionSum global.scalar_sum variable_links: │ set variable_links: sum -> scalarsum │ _configure_variables: ReactionSum global.scalar_sum variable_attributes: └ set attribute: sum :units = mol ┌ Info: _configure_variables: ReactionReservoirConst ocean.reservoir_const variable_links: │ set variable_links: R_conc -> const_conc │ _configure_variables: ReactionReservoirConst ocean.reservoir_const variable_attributes: │ set attribute: R_conc :initial_delta = -2.0 └ set attribute: R_conc :initial_value = 0.1 ┌ Info: _configure_variables: ReactionConst ocean.const_volume_total variable_attributes: │ set attribute: volume_total :initial_value = 10000.0 └ set attribute: volume_total :units = m^3 ┌ Info: _configure_variables: ReactionReservoir ocean.reservoir_tracer variable_links: │ set variable_links: R -> T │ set variable_links: R_sms -> T_sms │ set variable_links: R_total -> T_total │ set variable_links: R_conc -> T_conc │ _configure_variables: ReactionReservoir ocean.reservoir_tracer variable_attributes: │ set attribute: R :norm_value = 10.0 └ set attribute: R :initial_value = 1.0 ┌ Info: _configure_variables: ReactionConst ocean.const_volume variable_attributes: │ set attribute: volume :units = m3 └ set attribute: volume :initial_value = 10.0 ┌ Info: _configure_variables: ReactionWeightedMean ocean.weightedmean variable_links: │ set variable_links: measure -> volume │ set variable_links: measure_total -> volume_total │ set variable_links: var_mean -> const_conc_mean └ set variable_links: var -> const_conc ┌ Info: _configure_variables: ReactionAreaVolumeValInRange ocean.volinrange variable_links: │ set variable_links: measure -> volume │ set variable_links: measure_total -> volume_total └ set variable_links: rangevar -> const_conc ┌ Info: _configure_variables: ReactionReservoir ocean.reservoir_conc_tracer variable_links: │ set variable_links: R_conc -> C_conc │ set variable_links: R_conc_sms -> C_conc_sms │ set variable_links: R_sms -> C_sms │ set variable_links: R_total -> C_total │ set variable_links: R -> C │ _configure_variables: ReactionReservoir ocean.reservoir_conc_tracer variable_attributes: │ set attribute: R_conc :norm_value = 10.0 └ set attribute: R_conc :initial_value = 2.0 [ Info: Reaction ocean.vector_sum Variable ocean.vectorsum adding data=PALEOboxes.ScalarData ┌ Info: _configure_variables: ReactionSum ocean.vector_sum variable_links: │ set variable_links: sum -> vectorsum │ _configure_variables: ReactionSum ocean.vector_sum variable_attributes: └ set attribute: sum :units = mol ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain global data dimensions PALEOboxes.NamedDimension[] allocating 13 variables (hostdep=false) [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 12 variables (hostdep=false) ┌ Error: Domain "global" unallocated variables: └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:265 ┌ Error: "NormS_solve_sms" linked by: ["global.reservoir_NormS.do_reactionreservoirscalar_sms.R_solve_sms", "global.reservoir_NormS.initialize_zero_vars_default.R_solve_sms"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Error: "NormS_solve" linked by: ["global.reservoir_NormS.setup_reactionreservoirscalar.R_solve", "global.reservoir_NormS.do_reactionreservoirscalar.R_solve"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Error: "O" linked by: ["global.reservoir_O.setup_reactionreservoirscalar.R", "global.reservoir_O.do_reactionreservoirscalar.R"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Error: "O_sms" linked by: ["global.reservoir_O.methodfn_do_nothing.R_sms", "global.reservoir_O.initialize_zero_vars_default.R_sms"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Error: "A" linked by: ["global.reservoir_A.setup_reactionreservoirscalar.R", "global.reservoir_A.do_reactionreservoirscalar.R"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Error: "A_sms" linked by: ["global.reservoir_A.methodfn_do_nothing.R_sms", "global.reservoir_A.initialize_zero_vars_default.R_sms"] └ @ PALEOboxes ~/.julia/packages/PALEOboxes/k4QWy/src/Domain.jl:268 ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain global data dimensions PALEOboxes.NamedDimension[] allocating 6 variables (hostdep=true) [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 4 variables (hostdep=true) [ Info: all_vars: VariableAggregatorNamed(modeldata=ModelData(model=Model(config_files='["/home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configreservoirs.yaml"]', name='model1'), domain_data=Tuple{DataType, String}[(Float64, "base")]), arrays_idx=1, global.*[:A, :A_delta, :A_norm, :A_sms, :ConstNormS, :ConstNormS_norm, :ConstNormS_sms, :ConstS, :ConstS_norm, :ConstS_sms, :NormS, :NormS_norm, :NormS_sms, :NormS_solve, :NormS_solve_sms, :O, :O_norm, :O_sms, :scalarsum], ocean.*[:C, :C_conc, :C_conc_sms, :C_sms, :C_total, :R_delta, :T, :T_conc, :T_sms, :T_total, :const_conc, :const_conc_mean, :frac, :vectorsum, :volume, :volume_total], ) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ [ Info: dispatch_setup ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: init_values! :initial_value global.ConstNormS = 1.0 [ Info: init_values! :initial_value global.ConstS = 1.0 [ Info: ocean.reservoir_const.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.const_conc = 0.1, delta=-2.0 [ Info: ocean.const_volume_total.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.volume_total = 10000.0 [ Info: ocean.const_volume.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.volume = 10.0 ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ [ Info: init_values! :norm_value global.NormS_solve = 10.0 / 10.0 [from global.NormS] [ Info: init_values! :norm_value global.A = 3.193e17, delta=1.0 (fixed delta value to calculate norm) [ Info: init_values! :norm_value global.O = 3.7e18 [ Info: ocean.reservoir_conc_tracer.setup_initialvalue_vars_default: [ Info: init_values! :norm_value ocean.C_conc = 10.0 [ Info: ocean.reservoir_tracer.setup_initialvalue_vars_default: [ Info: init_values! :norm_value ocean.T = 10.0 * volume ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ [ Info: init_values! :initial_value global.NormS_solve = 1.0 / 10.0 [from global.NormS] [ Info: init_values! :initial_value global.A = 3.193e18, delta=2.0 [ Info: init_values! :initial_value global.O = 3.7e19 [ Info: ocean.reservoir_conc_tracer.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.C_conc = 2.0 [ Info: ocean.reservoir_tracer.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.T = 1.0 * volume [ Info: global stateexplicit variables: [ Info: global const variables: [ Info: ocean host-dependent variable initialisation: [ Info: global model-created variables: [ Info: ocean model-created variables: [ Info: sum variables: [ Info: ocean constant concentrations [ Info: weighted mean [ Info: volume in range [ Info: test complete ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configreservoirsfluxes.yaml └ ================================================================================ [ Info: Model.parameters: ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 24 Reactions ┌ Info: │ ================================================================================ │ creating domain 'global' ID=1 └ ================================================================================ [ Info: create_reaction_from_config: global.flux_O classname ReactionReservoirFlux [ Info: create_reaction_from_config: global.flux_constS classname ReactionReservoirFlux ┌ Info: create_reaction_from_config: global.reservoir_O classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [Default] const =false └ set parameters: [Default] state_norm =false ┌ Info: create_reaction_from_config: global.reservoir_ConstS classname ReactionReservoirScalar │ set parameters: [Default] field_data =PALEOboxes.ScalarData │ set parameters: [config.yaml] const =true └ set parameters: [Default] state_norm =false ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionReservoirFlux global.flux_O variable_links: │ set variable_links: R -> O └ set variable_links: R_sms -> O_sms ┌ Info: _configure_variables: ReactionReservoirFlux global.flux_constS variable_links: │ set variable_links: R -> ConstS └ set variable_links: R_sms -> ConstS_sms ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_O variable_links: │ set variable_links: R -> O │ set variable_links: R_sms -> O_sms │ set variable_links: R_norm -> O_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_O variable_attributes: │ set attribute: R :norm_value = 3.7e18 └ set attribute: R :initial_value = 3.7e19 ┌ Info: _configure_variables: ReactionReservoirScalar global.reservoir_ConstS variable_links: │ set variable_links: R -> ConstS │ set variable_links: R_sms -> ConstS_sms │ set variable_links: R_norm -> ConstS_norm │ _configure_variables: ReactionReservoirScalar global.reservoir_ConstS variable_attributes: │ set attribute: R :norm_value = 10.0 └ set attribute: R :initial_value = 1.0 ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configfluxes.yaml └ ================================================================================ ┌ Info: Model.parameters: └ CIsotope = IsotopeLinear ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 24 Reactions ┌ Info: │ ================================================================================ │ creating domain 'global' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: global.flux_transfer classname ReactionFluxTransfer │ set parameters: [config.yaml] input_fluxes =ocean.flux_$fluxname$ │ set parameters: [config.yaml] output_fluxes =tflux_$fluxname$ │ set parameters: [config.yaml] transfer_multiplier =-1.0 └ set parameters: [config.yaml] transfer_matrix =Distribute ┌ Info: create_reaction_from_config: global.transferred_flux classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["B", "C::CIsotope"] │ set parameters: [config.yaml] target_prefix =tflux_ │ set parameters: [Default] flux_totals =false └ set parameters: [Default] const_stub =false ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=2 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.flux_transfer classname ReactionFluxTransfer │ set parameters: [config.yaml] input_fluxes =flux_$fluxname$ │ set parameters: [config.yaml] output_fluxes =tflux_$fluxname$ │ set parameters: [config.yaml] transfer_multiplier =2.0 └ set parameters: [config.yaml] transfer_matrix =Identity ┌ Info: create_reaction_from_config: ocean.transferred_flux classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["A", "C::CIsotope"] │ set parameters: [config.yaml] target_prefix =tflux_ │ set parameters: [config.yaml] flux_totals =true └ set parameters: [Default] const_stub =false ┌ Info: create_reaction_from_config: ocean.const_flux classname ReactionFluxTarget │ set parameters: [config.yaml] fluxlist =["A", "B", "C::CIsotope"] │ set parameters: [Default] target_prefix =flux_ │ set parameters: [Default] flux_totals =false └ set parameters: [config.yaml] const_stub =true ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionFluxTarget ocean.const_flux variable_attributes: │ set attribute: flux_C :initial_delta = -1.0 │ set attribute: flux_A :initial_value = 10.0 │ set attribute: flux_B :initial_value = 20.0 └ set attribute: flux_C :initial_value = 2.0 ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: │ ================================================================================ │ optional global.flux_transfer output_A -| tflux_A └ optional ocean.flux_transfer output_B -| tflux_B ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain global data dimensions PALEOboxes.NamedDimension[] allocating 2 variables (hostdep=nothing) [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 7 variables (hostdep=nothing) [ Info: all_vars: VariableAggregatorNamed(modeldata=ModelData(model=Model(config_files='["/home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configfluxes.yaml"]', name='model1'), domain_data=Tuple{DataType, String}[(Float64, "base")]), arrays_idx=1, global.*[:tflux_B, :tflux_C], ocean.*[:flux_A, :flux_B, :flux_C, :tflux_A, :tflux_C, :tflux_total_A, :tflux_total_C], ) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: prepare_do_transfer: ReactionMethod global.flux_transfer.do_transfer │ active fluxes: │ B ocean.flux_B -> global.tflux_B │ C ocean.flux_C -> global.tflux_C │ A ocean.flux_A output not linked └ using Distribute transfer matrix size (input, output) (1000, 1) * -1.0 ┌ Info: prepare_do_transfer: ReactionMethod ocean.flux_transfer.do_transfer │ active fluxes: │ B ocean.flux_B output not linked │ C ocean.flux_C -> ocean.tflux_C │ A ocean.flux_A -> ocean.tflux_A └ using Identity transfer matrix * 2.0 [ Info: dispatch_setup ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: ocean.const_flux.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.flux_A = 10.0 [ Info: init_values! :initial_value ocean.flux_B = 20.0 [ Info: init_values! :initial_value ocean.flux_C = 2.0, delta=-1.0 ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ [ Info: const fluxes: [ Info: transferred fluxes [ Info: transferred flux totals [ Info: global transferred fluxes [ Info: test complete ┌ Info: │ ================================================================================ │ create_model_from_config: configmodel model1 │ config_file: /home/pkgeval/.julia/packages/PALEOboxes/k4QWy/test/configratestoich.yaml └ ================================================================================ ┌ Info: Model.parameters: └ Sisotope = IsotopeLinear ┌ Info: │ ================================================================================ │ creating Domains └ ================================================================================ [ Info: generated Reaction catalog with 25 Reactions ┌ Info: │ ================================================================================ │ creating domain 'ocean' ID=1 └ ================================================================================ ┌ Info: create_reaction_from_config: ocean.reservoir_H2S classname ReactionReservoirTotal │ set parameters: [config.yaml] field_data =external%Sisotope │ expandvalue: external%Sisotope -> IsotopeLinear │ after substitution field_data=IsotopeLinear │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: ocean.reservoir_SO4 classname ReactionReservoirTotal │ set parameters: [config.yaml] field_data =external%Sisotope │ expandvalue: external%Sisotope -> IsotopeLinear │ after substitution field_data=IsotopeLinear │ set parameters: [Default] total =true │ set parameters: [Default] limit_delta_conc =0.0 └ set parameters: [Default] state_conc =false ┌ Info: create_reaction_from_config: ocean.const_volume classname ReactionConst └ set parameters: [config.yaml] constnames =["volume"] [ Info: create_reaction_from_config: ocean.redox_H2S_O2 classname ReactionRateStoichMock ┌ Info: │ ================================================================================ │ set_model_geometry └ ================================================================================ ┌ Info: │ ================================================================================ │ register_reaction_methods! └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: first pass └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables: register_reaction_dynamic_methods and configure variables └ ================================================================================ ┌ Info: _configure_variables: ReactionReservoir ocean.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: R_delta -> H2S_delta │ _configure_variables: ReactionReservoir ocean.reservoir_H2S variable_attributes: │ set attribute: R :initial_value = 1.0 └ set attribute: R :initial_delta = -30.0 ┌ Info: _configure_variables: ReactionReservoir ocean.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: R_delta -> SO4_delta │ _configure_variables: ReactionReservoir ocean.reservoir_SO4 variable_attributes: │ set attribute: R :initial_value = 1.0 └ set attribute: R :initial_delta = 0.0 ┌ Info: _configure_variables: ReactionConst ocean.const_volume variable_attributes: │ set attribute: volume :units = m3 └ set attribute: volume :initial_value = 10.0 ┌ Info: │ ================================================================================ │ link_variables: second pass: └ ================================================================================ ┌ Info: │ ================================================================================ │ link_variables! unlinked variables: │ ================================================================================ └ optional ocean.redox_H2S_O2 O2_sms -| O2_sms ┌ Info: │ ================================================================================ │ create_model_from_config: done └ ================================================================================ ┌ Info: │ ================================================================================ │ allocate_variables! (modeldata arrays_idx=1) └ ================================================================================ [ Info: Domain ocean data dimensions PALEOboxes.NamedDimension[] allocating 12 variables (hostdep=nothing) ┌ Info: │ ================================================================================ │ initialize_reactiondata! (modeldata arrays_indices=1:1) └ ================================================================================ ┌ Info: │ ================================================================================ │ dispatch_setup :setup └ ================================================================================ [ Info: ocean.const_volume.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.volume = 10.0 ┌ Info: │ ================================================================================ │ dispatch_setup :norm_value └ ================================================================================ [ Info: ocean.reservoir_H2S.setup_initialvalue_vars_default: [ Info: init_values! :norm_value ocean.H2S = 1.0 * volume, delta=1.0 (fixed delta value to calculate norm) [ Info: ocean.reservoir_SO4.setup_initialvalue_vars_default: [ Info: init_values! :norm_value ocean.SO4 = 1.0 * volume, delta=1.0 (fixed delta value to calculate norm) ┌ Info: │ ================================================================================ │ dispatch_setup :initial_value └ ================================================================================ [ Info: ocean.reservoir_H2S.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.H2S = 1.0 * volume, delta=-30.0 [ Info: ocean.reservoir_SO4.setup_initialvalue_vars_default: [ Info: init_values! :initial_value ocean.SO4 = 1.0 * volume, delta=0.0 [ Info: stoichiometry Test Summary: | Pass Broken Total Time PALEOboxes | 151 1 152 5m13.0s Testing PALEOboxes tests passed Testing completed after 439.09s PkgEval succeeded after 605.33s