Package evaluation to test OceanBioME on Julia 1.12.4 (0f21d93eaa*) started at 2026-01-27T06:14:46.394 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.02s ################################################################################ # Installation # Installing OceanBioME... Resolving package versions... Installed GibbsSeaWater ─ v0.1.4 Updating `~/.julia/environments/v1.12/Project.toml` [a49af516] + OceanBioME v0.16.9 Updating `~/.julia/environments/v1.12/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.4.0 [a9b6321e] + Atomix v1.1.2 [ab4f0b2a] + BFloat16s v0.6.1 [fa961155] + CEnum v0.5.0 [052768ef] + CUDA v5.9.6 [1af6417a] + CUDA_Runtime_Discovery v1.0.0 [0b6fb165] + ChunkCodecCore v1.0.1 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [7445602f] + CubedSphere v0.3.4 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [21656369] + ExpressionExplorer v1.1.3 [7a1cc6ca] + FFTW v1.10.0 [5789e2e9] + FileIO v1.17.1 [0c68f7d7] + GPUArrays v11.3.4 [46192b85] + GPUArraysCore v0.2.0 [61eb1bfa] + GPUCompiler v1.8.1 [096a3bc2] + GPUToolbox v1.0.0 [9a22fb26] + GibbsSeaWater v0.1.4 [c27321d9] + Glob v1.4.0 [076d061b] + HashArrayMappedTries v0.2.0 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.6.3 [692b3bcd] + JLLWrappers v1.7.1 [63c18a36] + KernelAbstractions v0.9.39 [ba0b0d4f] + Krylov v0.10.5 [929cbde3] + LLVM v9.4.4 [8b046642] + LLVMLoopInfo v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [da04e1cc] + MPI v0.20.23 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [46d2c3a1] + MuladdMacro v0.2.4 [5da4648a] + NVTX v1.0.3 [a49af516] + OceanBioME v0.16.9 [9e8cae18] + Oceananigans v0.104.2 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [eebad327] + PkgVersion v0.3.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [94ee1d12] + Quaternions v0.7.7 [74087812] + Random123 v1.7.1 [e6cf234a] + RandomNumbers v1.6.0 [a3311ec8] + ReactantCore v0.1.16 [c1ae055f] + RealDot v0.1.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [6038ab10] + Rotations v1.7.1 [7e506255] + ScopedValues v1.5.0 [6c6a2e73] + Scratch v1.3.0 [d496a93d] + SeawaterPolynomials v0.3.10 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [892a3eda] + StringManipulation v0.4.2 [09ab397b] + StructArrays v0.7.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [6aa5eb33] + TaylorSeries v0.20.10 [e689c965] + Tracy v0.1.6 [013be700] + UnsafeAtomics v0.3.0 [d1e2174e] + CUDA_Compiler_jll v0.4.1+1 [4ee394cb] + CUDA_Driver_jll v13.1.0+2 ⌅ [76a88914] + CUDA_Runtime_jll v0.19.2+0 [f5851436] + FFTW_jll v3.3.11+0 [6727f6b2] + GibbsSeaWater_jll v3.5.2+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [9c1d0b0a] + JuliaNVTXCallbacks_jll v0.2.1+0 [dad2f222] + LLVMExtra_jll v0.0.38+0 [ad6e5548] + LibTracyClient_jll v0.13.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [e98f9f5b] + NVTX_jll v3.2.2+0 [fe0851c0] + OpenMPI_jll v5.0.9+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [1e29f10c] + demumble_jll v1.3.0+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building GibbsSeaWater → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/f4318e7a751703a5db8b57c112e5cd5c218d296b/build.log` Installation completed after 21.65s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 407929.3 ms ✓ OceanBioME 1 dependency successfully precompiled in 414 seconds. 195 already precompiled. Precompilation completed after 456.65s ################################################################################ # Testing # Testing OceanBioME Status `/tmp/jl_CW6Pgc/Project.toml` [79e6a3ab] Adapt v4.4.0 [a9b6321e] Atomix v1.1.2 [052768ef] CUDA v5.9.6 [124859b0] DataDeps v0.7.13 [e30172f5] Documenter v1.16.1 [9a22fb26] GibbsSeaWater v0.1.4 [033835bb] JLD2 v0.6.3 [63c18a36] KernelAbstractions v0.9.39 [a49af516] OceanBioME v0.16.9 [9e8cae18] Oceananigans v0.104.2 [6fe1bfb0] OffsetArrays v1.17.0 [d496a93d] SeawaterPolynomials v0.3.10 [10745b16] Statistics v1.11.1 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_CW6Pgc/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [a9b6321e] Atomix v1.1.2 [ab4f0b2a] BFloat16s v0.6.1 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [052768ef] CUDA v5.9.6 [1af6417a] CUDA_Runtime_Discovery v1.0.0 [0b6fb165] ChunkCodecCore v1.0.1 [4c0bbee4] ChunkCodecLibZlib v1.0.0 [55437552] ChunkCodecLibZstd v1.0.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.0 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [7445602f] CubedSphere v0.3.4 [9a962f9c] DataAPI v1.16.0 [124859b0] DataDeps v0.7.13 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 [460bff9d] ExceptionUnwrapping v0.1.11 [e2ba6199] ExprTools v0.1.10 [21656369] ExpressionExplorer v1.1.3 [7a1cc6ca] FFTW v1.10.0 [5789e2e9] FileIO v1.17.1 [0c68f7d7] GPUArrays v11.3.4 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v1.8.1 [096a3bc2] GPUToolbox v1.0.0 [9a22fb26] GibbsSeaWater v0.1.4 [d7ba0133] Git v1.5.0 [c27321d9] Glob v1.4.0 [cd3eb016] HTTP v1.10.19 [076d061b] HashArrayMappedTries v0.2.0 [b5f81e59] IOCapture v1.0.0 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.6.3 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [63c18a36] KernelAbstractions v0.9.39 [ba0b0d4f] Krylov v0.10.5 [929cbde3] LLVM v9.4.4 [8b046642] LLVMLoopInfo v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [e6f89c97] LoggingExtras v1.2.0 [da04e1cc] MPI v0.20.23 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.2 [739be429] MbedTLS v1.1.9 [e1d29d7a] Missings v1.2.0 [46d2c3a1] MuladdMacro v0.2.4 [5da4648a] NVTX v1.0.3 [a49af516] OceanBioME v0.16.9 [9e8cae18] Oceananigans v0.104.2 [6fe1bfb0] OffsetArrays v1.17.0 [4d8831e6] OpenSSL v1.6.1 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [eebad327] PkgVersion v0.3.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [94ee1d12] Quaternions v0.7.7 [74087812] Random123 v1.7.1 [e6cf234a] RandomNumbers 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[83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 4968.7 ms ✓ StructUtils → StructUtilsTablesExt 1 dependency successfully precompiled in 5 seconds. 11 already precompiled. [ Info: Benchmark times are given for each solver, but should be taken with a pinch of salt as they vary a lot depending on the problem and start point [ Info: Tested NewtonRaphsonSolver with benchmark time: 1053.2ns per solve [ Info: Tested NewtonRaphsonSafeSolver with benchmark time: 874.4ns per solve [ Info: Tested DampedNewtonRaphsonSolver with benchmark time: 1160.2ns per solve [ Info: Tested Bisection with benchmark time: 3312.8ns per solve Test Summary: | Pass Total Time Testing solvers | 20 20 6.8s [ Info: Initializing simulation... [ Info: ... simulation initialization complete (524.394 ms) [ Info: Executing initial time step... [ Info: Simulation is stopping after running for 0 seconds. [ Info: Model iteration 1 equals or exceeds stop iteration 1. [ Info: ... initial time step complete (10.300 seconds). [ Info: Initializing simulation... [ Info: ... simulation initialization complete (285.536 ms) [ Info: Executing initial time step... [ Info: Simulation is stopping after running for 0 seconds. [ Info: Model iteration 1 equals or exceeds stop iteration 1. [ Info: ... initial time step complete (1.148 seconds). Test Summary: | Pass Total Time Test negative tracer handeling | 2 2 2m48.9s Test Summary: | Pass Total Time Test sinking velocity setup | 6 6 2.3s ┌ Info: Testing light with LOBSTER in NonhydrostaticModel on 2×2×2 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 2×2×2 halo │ ├── Periodic x ∈ [0.0, 2.0) regularly spaced with Δx=1.0 │ ├── Periodic y ∈ [0.0, 2.0) regularly spaced with Δy=1.0 └ └── Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... ┌ Info: Testing light with NutrientPhytoplanktonZooplanktonDetritus in NonhydrostaticModel on 2×2×2 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 2×2×2 halo │ ├── Periodic x ∈ [0.0, 2.0) regularly spaced with Δx=1.0 │ ├── Periodic y ∈ [0.0, 2.0) regularly spaced with Δy=1.0 └ └── Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... ┌ Info: Testing light with LOBSTER in HydrostaticFreeSurfaceModel on 2×2×2 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 2×2×2 halo │ ├── Periodic x ∈ [0.0, 2.0) regularly spaced with Δx=1.0 │ ├── Periodic y ∈ [0.0, 2.0) regularly spaced with Δy=1.0 └ └── Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... ┌ Info: Testing light with NutrientPhytoplanktonZooplanktonDetritus in HydrostaticFreeSurfaceModel on 2×2×2 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 2×2×2 halo │ ├── Periodic x ∈ [0.0, 2.0) regularly spaced with Δx=1.0 │ ├── Periodic y ∈ [0.0, 2.0) regularly spaced with Δy=1.0 └ └── Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... ┌ Info: Testing light with LOBSTER in HydrostaticFreeSurfaceModel on 5×5×2 LatitudeLongitudeGrid{Float64, Periodic, Bounded, Bounded} on CPU with 3×3×2 halo │ ├── longitude: Periodic λ ∈ [-180.0, 180.0) regularly spaced with Δλ=72.0 │ ├── latitude: Bounded φ ∈ [-85.0, 85.0] regularly spaced with Δφ=34.0 └ └── z: Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... ┌ Info: Testing light with NutrientPhytoplanktonZooplanktonDetritus in HydrostaticFreeSurfaceModel on 5×5×2 LatitudeLongitudeGrid{Float64, Periodic, Bounded, Bounded} on CPU with 3×3×2 halo │ ├── longitude: Periodic λ ∈ [-180.0, 180.0) regularly spaced with Δλ=72.0 │ ├── latitude: Bounded φ ∈ [-85.0, 85.0] regularly spaced with Δφ=34.0 └ └── z: Bounded z ∈ [-2.0, 0.0] regularly spaced with Δz=1.0... Test Summary: | Pass Total Time Light attenuaiton model | 36 36 19m04.1s Test Summary: | Pass Total Time Float32 TwoBandPhotosyntheticallyActiveRadiation | 8 8 4.0s Test Summary: | Pass Total Time Testing basic particle property integration | 3 3 36.0s WARNING: Method definition required_tracers(Main.SimpleParticleBiogeochemistry) in module Main at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:18 overwritten at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:50. Test Summary: | Pass Total Time Testing particle tracer detection | 2 2 23.7s Test Summary: | Pass Total Time Testing particle lagrangian advection | 2 2 5.7s WARNING: Method definition coupled_tracers(Main.SimpleParticleBiogeochemistry) in module Main at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:19 overwritten at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:90. WARNING: Method definition SimpleParticleBiogeochemistry(Base.Val{:A}, Any, Any, Any) in module Main at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:52 overwritten at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_particles.jl:92. WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in cpu__update_tracer_tendencies!(Any, Base.Val{field_name}, Base.Val{target_name}, Any, Any, Any, Any, Any, Any) where {field_name, target_name} at none Test Summary: | Pass Total Time Testing particle-tracer uptake | 2 2 2.8s Test Summary: | Pass Total Time Testing particle-tracer uptake with scalefactors | 2 2 0.1s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/TwoParticleAndDissolved/false/false | 5 5 39.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/TwoParticleAndDissolved/false/false | 5 5 34.1s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/TwoParticleAndDissolved/false/false | 7 7 37.4s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/TwoParticleAndDissolved/false/false | 7 7 41.5s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Oxygen/TwoParticleAndDissolved/false/false | 5 5 35.0s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Oxygen/TwoParticleAndDissolved/false/false | 5 5 37.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Oxygen/TwoParticleAndDissolved/false/false | 7 7 41.3s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Oxygen/TwoParticleAndDissolved/false/false | 7 7 45.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/VariableRedfieldDetritus/false/false | 5 5 43.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/VariableRedfieldDetritus/false/false | 5 5 44.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/VariableRedfieldDetritus/false/false | 7 7 49.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/VariableRedfieldDetritus/false/false | 7 7 53.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Oxygen/VariableRedfieldDetritus/false/false | 5 5 45.2s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Oxygen/VariableRedfieldDetritus/false/false | 5 5 47.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Oxygen/VariableRedfieldDetritus/false/false | 7 7 53.4s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Oxygen/VariableRedfieldDetritus/false/false | 7 7 55.1s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/TwoParticleAndDissolved/true/false | 5 5 0.5s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/TwoParticleAndDissolved/true/false | 5 5 0.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/TwoParticleAndDissolved/true/false | 7 7 0.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/TwoParticleAndDissolved/true/false | 7 7 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Oxygen/TwoParticleAndDissolved/true/false | 5 5 0.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Oxygen/TwoParticleAndDissolved/true/false | 5 5 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Oxygen/TwoParticleAndDissolved/true/false | 7 7 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Oxygen/TwoParticleAndDissolved/true/false | 7 7 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/VariableRedfieldDetritus/true/false | 5 5 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/VariableRedfieldDetritus/true/false | 5 5 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/VariableRedfieldDetritus/true/false | 7 7 1.0s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/VariableRedfieldDetritus/true/false | 7 7 1.1s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Oxygen/VariableRedfieldDetritus/true/false | 5 5 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Oxygen/VariableRedfieldDetritus/true/false | 5 5 1.0s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Oxygen/VariableRedfieldDetritus/true/false | 7 7 1.1s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Oxygen/VariableRedfieldDetritus/true/false | 7 7 1.2s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/TwoParticleAndDissolved/false/true | 5 5 0.6s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/TwoParticleAndDissolved/false/true | 5 5 0.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/TwoParticleAndDissolved/false/true | 7 7 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/TwoParticleAndDissolved/false/true | 7 7 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Oxygen/TwoParticleAndDissolved/false/true | 5 5 0.7s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Oxygen/TwoParticleAndDissolved/false/true | 5 5 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Oxygen/TwoParticleAndDissolved/false/true | 7 7 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Oxygen/TwoParticleAndDissolved/false/true | 7 7 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/Nothing/Nothing/VariableRedfieldDetritus/false/true | 5 5 0.8s Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/Nothing/Nothing/VariableRedfieldDetritus/false/true | 5 5 0.9s Test Summary: | Pass Total Time LOBSTER (NitrateAmmonia/CarbonateSystem/Nothing/VariableRedfieldDetritus/false/true | 7 7 1.0s ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 424 running 1 of 1 signal (10): User defined signal 1 getindex at ./namedtuple.jl:165 [inlined] #compute_flux_bc_tendencies!##2 at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/Models/NonhydrostaticModels/compute_nonhydrostatic_tendencies.jl:177 foreach at ./abstractarray.jl:3188 unknown function (ip: 0x7f57566e8f7c) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 compute_flux_bc_tendencies! at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/Models/NonhydrostaticModels/compute_nonhydrostatic_tendencies.jl:177 pressure_correction_rk3_substep! at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/Models/NonhydrostaticModels/nonhydrostatic_rk3_substep.jl:35 rk3_substep! at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/Models/NonhydrostaticModels/nonhydrostatic_rk3_substep.jl:11 [inlined] #time_step!#9 at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/TimeSteppers/runge_kutta_3.jl:153 time_step! at /home/pkgeval/.julia/packages/Oceananigans/8uTGc/src/TimeSteppers/runge_kutta_3.jl:104 unknown function (ip: 0x7f57566cf00a) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 test_LOBSTER at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_LOBSTER.jl:99 unknown function (ip: 0x7f5756793e34) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 macro expansion at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_LOBSTER.jl:135 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] top-level scope at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_LOBSTER.jl:135 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_invoke at /source/src/gf.c:4017 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 Test Summary: | Pass Total Time LOBSTER (NitrateAmmoniaIron/CarbonateSystem/Nothing/VariableRedfieldDetritus/false/true | 7 7 1.1s eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_58627.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_58627.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_39366.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7f57c90c5249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Test Summary: | Pass Total ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./process.jl:685 wait at ./process.jl:686 jfptr_wait_37520.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2553 unknown function (ip: 0x7ad8ecd8bdb3) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #205 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2493 withenv at ./env.jl:265 #190 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2308 with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2161 #186 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2275 #mktempdir#21 at ./file.jl:936 unknown function (ip: 0x7ad8ecd82efc) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 mktempdir at ./file.jl:932 mktempdir at ./file.jl:932 #sandbox#182 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2222 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2212 unknown function (ip: 0x7ad8ecd7d829) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #test#193 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2478 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2384 [inlined] #test#170 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:538 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:515 unknown function (ip: 0x7ad8ecd7cd91) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 unknown function (ip: 0x7ad8ecd7c890) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:158 #test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] #test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 unknown function (ip: 0x7ad8ecd72c3f) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2930 include at ./Base.jl:306 exec_options at ./client.jl:317 _start at ./client.jl:550 jfptr__start_39366.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7ad908dfe249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007ad8ee9fc010 Total snapshots: 373. Utilization: 0% ╎373 @Base/client.jl:550 _start() ╎ 373 @Base/client.jl:317 exec_options(opts::Base.JLOptions) ╎ 373 @Base/Base.jl:306 include(mod::Module, _path::String) ╎ 373 @Base/loading.jl:2930 _include(mapexpr::Function, mod::Module, _pat… ╎ 373 @Base/loading.jl:2870 include_string(mapexpr::typeof(identity), mo… ╎ 373 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 373 @Pkg/src/API.jl:156 kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 373 @Pkg/src/API.jl:156 #test#81 ╎ ╎ 373 @Pkg/src/API.jl:157 test ╎ ╎ 373 @Pkg/src/API.jl:157 test(pkgs::Vector{String}; kwargs::Base.P… ╎ ╎ 373 @Pkg/src/API.jl:158 kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 373 @Pkg/src/API.jl:169 test(pkgs::Vector{PackageSpec}; io::IOC… ╎ ╎ ╎ 373 @Pkg/src/API.jl:515 kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 373 @Pkg/src/API.jl:538 test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 373 @Pkg/…erations.jl:2384 test ╎ ╎ ╎ 373 @Pkg/…erations.jl:2478 test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 373 @Pkg/…rations.jl:2212 kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 373 @Pkg/…rations.jl:2222 #sandbox#182 ╎ ╎ ╎ ╎ 373 @Base/file.jl:932 mktempdir(fn::Function) ╎ ╎ ╎ ╎ 373 @Base/file.jl:932 mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 373 @Base/file.jl:936 mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 373 @Pkg/…tions.jl:2275 (::Pkg.Operations.var"#186#18… ╎ ╎ ╎ ╎ ╎ 373 @Pkg/…tions.jl:2161 with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 373 @Pkg/…tions.jl:2308 (::Pkg.Operations.var"#190#… ╎ ╎ ╎ ╎ ╎ 373 @Base/env.jl:265 withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 373 @Pkg/…ions.jl:2493 (::Pkg.Operations.var"#205… ╎ ╎ ╎ ╎ ╎ ╎ 373 @Pkg/…ons.jl:2553 subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 373 @Base/…ss.jl:686 wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 373 @Base/…ss.jl:685 wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 373 @Base/…on.jl:141 wait(c::Base.GenericCond… ╎ ╎ ╎ ╎ ╎ ╎ 373 @Base/…sk.jl:1228 wait() 372╎ ╎ ╎ ╎ ╎ ╎ ╎ 373 @Base/…sk.jl:1216 poptask(W::Base.Intru… [424] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OceanBioME/qC8jE/test/test_LOBSTER.jl:121 append_module_names at /source/src/module.c:1975 ijl_module_names at /source/src/module.c:2004 #unsorted_names#4 at ./runtime_internals.jl:119 [inlined] unsorted_names at ./runtime_internals.jl:119 [inlined] make_typealias at ./show.jl:627 show_typealias at ./show.jl:808 _show_type at ./show.jl:973 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_typeparams at ./show.jl:725 show_typealias at ./show.jl:735 show_typealias at ./show.jl:811 _show_type at ./show.jl:973 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_typeparams at ./show.jl:725 show_datatype at ./show.jl:1219 show_datatype at ./show.jl:1127 [inlined] _show_type at ./show.jl:976 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_typeparams at ./show.jl:725 show_datatype at ./show.jl:1219 show_datatype at ./show.jl:1127 [inlined] _show_type at ./show.jl:976 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_typeparams at ./show.jl:725 show_datatype at ./show.jl:1219 show_datatype at ./show.jl:1127 [inlined] _show_type at ./show.jl:976 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_at_namedtuple at ./show.jl:1232 unknown function (ip: 0x7f57560f3f3d) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_datatype at ./show.jl:1205 show_datatype at ./show.jl:1127 [inlined] _show_type at ./show.jl:976 show at ./show.jl:968 jfptr_show_13287.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 show_typeparams at ./show.jl:725 show_datatype at ./show.jl:1219 show_datatype at ./show.jl:1127 [inlined] _show_type at ./show.jl:976 show at ./show.jl:968 #sprint#437 at ./strings/io.jl:110 sprint at ./strings/io.jl:110 [inlined] #print_type_bicolor#501 at ./show.jl:2751 [inlined] print_type_bicolor at ./show.jl:2750 jfptr_print_type_bicolor_18006.1 at /opt/julia/share/julia/compiled/v1.12/REPL/u0gqU_9HAIE.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #show_tuple_as_call#495 at ./show.jl:2618 show_spec_sig at ./stacktraces.jl:288 show_spec_linfo at ./stacktraces.jl:279 #sprint#437 at ./strings/io.jl:117 sprint at ./strings/io.jl:110 [inlined] tree_format at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1042 print_tree at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1254 tree at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1308 print_group at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:389 #print#5 at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:331 print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 _peek_report at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:91 unknown function (ip: 0x7f57560cbf1f) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2391 [inlined] jl_f_invokelatest at /source/src/builtins.c:881 profile_printing_listener at ./Base.jl:334 #start_profile_listener##0 at ./Base.jl:352 PkgEval terminated after 2723.16s: test duration exceeded the time limit