Package evaluation to test NeighbourLists on Julia 1.12.4 (0f21d93eaa*) started at 2026-01-26T20:05:56.136 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 5.83s ################################################################################ # Installation # Installing NeighbourLists... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [2fcf5ba9] + NeighbourLists v0.6.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [6a4ca0a5] + AcceleratedKernels v0.4.3 [79e6a3ab] + Adapt v4.4.0 [dce04be8] + ArgCheck v2.5.0 [a9b6321e] + Atomix v1.1.2 [6e4b80f9] + BenchmarkTools v1.6.3 [34da2185] + Compat v4.18.1 [46192b85] + GPUArraysCore v0.2.0 [682c06a0] + JSON v1.4.0 [63c18a36] + KernelAbstractions v0.9.39 [1914dd2f] + MacroTools v0.5.16 [2fcf5ba9] + NeighbourLists v0.6.0 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [ae029012] + Requires v1.3.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [ec057cc2] + StructUtils v2.6.2 [013be700] + UnsafeAtomics v0.3.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 3.64s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 13217.4 ms ✓ NeighbourLists 83844.3 ms ✓ NeighbourLists → NeighbourListsCUDAExt 8294.6 ms ✓ NeighbourLists → NeighbourListsAtomsBaseExt 3 dependencies successfully precompiled in 108 seconds. 173 already precompiled. Precompilation completed after 126.12s ################################################################################ # Testing # Testing NeighbourLists Status `/tmp/jl_9NAEKI/Project.toml` [a963bdd2] AtomsBase v0.5.2 [f5cc8831] AtomsBuilder v0.2.3 [052768ef] CUDA v5.9.6 [992eb4ea] CondaPkg v0.2.33 [b4f34e82] Distances v0.10.12 [f6369f11] ForwardDiff v1.3.1 [b8a86587] NearestNeighbors v0.4.26 [2fcf5ba9] NeighbourLists v0.6.0 `~/.julia/packages/NeighbourLists/wX4iR` [6099a3de] PythonCall v0.9.31 [90137ffa] StaticArrays v1.9.16 [1986cc42] Unitful v1.27.0 [37e2e46d] LinearAlgebra v1.12.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_9NAEKI/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [6a4ca0a5] AcceleratedKernels v0.4.3 [79e6a3ab] Adapt v4.4.0 [dce04be8] ArgCheck v2.5.0 [a9b6321e] Atomix v1.1.2 [a963bdd2] AtomsBase v0.5.2 [f5cc8831] AtomsBuilder v0.2.3 [1692102d] AtomsIO v0.3.0 [ab4f0b2a] BFloat16s v0.6.1 [6e4b80f9] BenchmarkTools v1.6.3 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [052768ef] CUDA v5.9.6 [1af6417a] CUDA_Runtime_Discovery v1.0.0 [46823bd8] Chemfiles v0.10.43 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.0 [992eb4ea] CondaPkg v0.2.33 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [e2ba6199] ExprTools v0.1.10 [352459e4] ExtXYZ v0.2.2 [f6369f11] ForwardDiff v1.3.1 [0c68f7d7] GPUArrays v11.3.4 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v1.8.1 [096a3bc2] GPUToolbox v1.0.0 [cd3eb016] HTTP v1.10.19 [076d061b] HashArrayMappedTries v0.2.0 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [0f8b85d8] JSON3 v1.14.3 [63c18a36] KernelAbstractions v0.9.39 [929cbde3] LLVM v9.4.4 [8b046642] LLVMLoopInfo v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [9c8b4983] LightXML v0.9.3 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [739be429] MbedTLS v1.1.9 [0b3b1443] MicroMamba v0.1.14 [e1d29d7a] Missings v1.2.0 [5da4648a] NVTX v1.0.3 [77ba4419] NaNMath v1.1.3 [b8a86587] NearestNeighbors v0.4.26 [2fcf5ba9] NeighbourLists v0.6.0 `~/.julia/packages/NeighbourLists/wX4iR` [4d8831e6] OpenSSL v1.6.1 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 [fa939f87] Pidfile v1.3.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [30e472fa] PubChemCrawler v1.4.0 [6099a3de] PythonCall v0.9.31 [74087812] Random123 v1.7.1 [e6cf234a] RandomNumbers v1.6.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [7e506255] ScopedValues v1.5.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.9 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [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 [856f2bd8] StructTypes v1.11.0 [ec057cc2] StructUtils v2.6.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [e689c965] Tracy v0.1.6 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [1986cc42] Unitful v1.27.0 [a7773ee8] UnitfulAtomic v1.0.0 [013be700] UnsafeAtomics v0.3.0 [e17b2a0c] UnsafePointers v1.0.0 [d1e2174e] CUDA_Compiler_jll v0.4.1+1 [4ee394cb] CUDA_Driver_jll v13.1.0+2 ⌅ [76a88914] CUDA_Runtime_jll v0.19.2+0 [78a364fa] Chemfiles_jll v0.10.4+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 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [e98f9f5b] NVTX_jll v3.2.2+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [02c8fc9c] XML2_jll v2.15.1+0 [1e29f10c] demumble_jll v1.3.0+0 [6ecdc6fc] extxyz_jll v0.1.3+0 [cdc7adba] libcleri_jll v0.12.1+3 ⌅ [f8abcde7] micromamba_jll v1.5.12+0 [4d7b5844] pixi_jll v0.41.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [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 [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 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.44.0+1 [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. Testing Running tests... Precompiling packages... 18807.1 ms ✓ Atomix → AtomixCUDAExt 1 dependency successfully precompiled in 21 seconds. 102 already precompiled. [ Info: CUDA loaded but not functional ┌ Info: AMDGPU not available │ exception = │ ArgumentError: Package AMDGPU not found in current path. └ - Run `import Pkg; Pkg.add("AMDGPU")` to install the AMDGPU package. ┌ Info: Metal not available │ exception = │ ArgumentError: Package Metal not found in current path. └ - Run `import Pkg; Pkg.add("Metal")` to install the Metal package. [ Info: No GPU backend available, using CPU # threads = 1 # GPU backend = none Precompiling packages... 18026.9 ms ✓ CUDA → SpecialFunctionsExt 1 dependency successfully precompiled in 19 seconds. 109 already precompiled. Checking that `fnbody` is correct... [ Info: Testing PairList Correctness: ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = top-level scope at test_celllist.jl:18 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_celllist.jl:18 typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed typeof(nlist) = PairList{Float64, Int32, Vector{SVector{3, Float64}}, Vector{Int32}, Vector{SVector{3, Int32}}} Test Passed sorted: Test Passed neigs: Test Passed ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = test_legacy_vs_sortbased(; N::Int64, density::Float64, cutoff_frac::Float64, pbc::SVector{3, Bool}) at test_utils.jl:315 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_utils.jl:315 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = test_all_pbc_legacy_vs_sortbased(; N::Int64, density::Float64, cutoff_frac::Float64) at test_utils.jl:333 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_utils.jl:333 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = (::var"#47#48")(X::Vector{SVector{3, Float64}}, C::SMatrix{3, 3, Float64, 9}, cutoff::Float64, pbc::SVector{3, Bool}) at test_sortbased.jl:30 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_sortbased.jl:30 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = top-level scope at test_sortbased.jl:9 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_sortbased.jl:9 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = top-level scope at test_sortbased.jl:9 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_sortbased.jl:9 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = (::var"#53#54")(X::Vector{SVector{3, Float64}}, C::SMatrix{3, 3, Float64, 9}, L::Float64, cutoff::Float64) at test_sortbased.jl:68 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_sortbased.jl:68 ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = macro expansion at test_unified_api.jl:62 [inlined] └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_unified_api.jl:62 Precompiling packages... 1646.5 ms ✓ Unitful → ForwardDiffExt 1 dependency successfully precompiled in 2 seconds. 23 already precompiled. Precompiling packages... 4643.6 ms ✓ Chemfiles 5170.9 ms ✓ ExtXYZ 2661.2 ms ✓ PubChemCrawler 2852.4 ms ✓ AtomsIO 9220.2 ms ✓ AtomsBuilder 5 dependencies successfully precompiled in 25 seconds. 64 already precompiled. Precompiling packages... 6181.1 ms ✓ micromamba_jll 3738.6 ms ✓ pixi_jll 3241.9 ms ✓ MicroMamba 6090.5 ms ✓ CondaPkg 4 dependencies successfully precompiled in 20 seconds. 39 already precompiled. Precompiling packages... 26466.0 ms ✓ PythonCall 1 dependency successfully precompiled in 27 seconds. 51 already precompiled. CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/83z4q/CondaPkg.toml CondaPkg Found dev dependencies: /home/pkgeval/.julia/packages/NeighbourLists/wX4iR/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml CondaPkg Resolving changes + libstdcxx + libstdcxx-ng + matscipy + numpy + openssl + python CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ init │ --format pixi └ /tmp/jl_9NAEKI/.CondaPkg ✔ Created /tmp/jl_9NAEKI/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_9NAEKI/.CondaPkg/pixi.toml │ [dependencies] │ openssl = ">=3, <3.6" │ libstdcxx = ">=3.4,<15.0" │ libstdcxx-ng = ">=3.4,<15.0" │ matscipy = "*" │ numpy = "*" │ │ [dependencies.python] │ channel = "conda-forge" │ build = "*cp*" │ version = ">=3.10,!=3.14.0,!=3.14.1,<4" │ │ [project] │ name = ".CondaPkg" │ platforms = ["linux-64"] │ channels = ["conda-forge"] │ channel-priority = "strict" └ description = "automatically generated by CondaPkg.jl" CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ install └ --manifest-path /tmp/jl_9NAEKI/.CondaPkg/pixi.toml ✔ The default environment has been installed. [ Info: matscipy available, running comparison tests ┌ Warning: PairList(X::Vector{SVec}, ...) uses the legacy linked-list algorithm. Use `neighbour_list(X, cutoff, cell, pbc)` for the sort-based implementation with multi-threading and GPU support. │ caller = top-level scope at test_matscipy.jl:63 └ @ Core ~/.julia/packages/NeighbourLists/wX4iR/test/test_matscipy.jl:63 Test Summary: | Pass Broken Total Time NeighbourLists | 649 3 652 4m12.1s Testing NeighbourLists tests passed Testing completed after 302.58s PkgEval succeeded after 463.97s