Package evaluation to test Molly on Julia 1.12.6 (15346901f00) started at 2026-06-29T12:11:07.638 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 6.19s ################################################################################ # Installation # Installing Molly... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [aa0f7f06] + Molly v0.23.3 Updating `~/.julia/environments/v1.12/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [6a4ca0a5] + AcceleratedKernels v0.4.3 [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [ec485272] + ArnoldiMethod v0.4.0 [a9b6321e] + Atomix v1.1.3 [a963bdd2] + AtomsBase v0.5.2 [a3e0e189] + AtomsCalculators v0.2.3 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.1 [3c28c6f8] + BioSymbols v5.2.0 [fa961155] + CEnum v0.5.0 ⌅ [69e1c6dd] + CellListMap v0.9.17 [46823bd8] + Chemfiles v0.10.43 [ae650224] + ChunkSplitters v3.2.0 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.129 [ffbed154] + DocStringExtensions v0.9.5 [8f5d6c58] + EzXML v1.2.3 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.16.0 [1fa38f19] + Format v1.3.7 [0c68f7d7] + GPUArrays v11.5.8 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.14.0 [076d061b] + HashArrayMappedTries v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [63c18a36] + KernelAbstractions v0.9.41 [929cbde3] + LLVM v9.10.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [aa0f7f06] + Molly v0.23.3 [b8a86587] + NearestNeighbors v0.4.27 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.40 ⌅ [d96e819e] + Parameters v0.12.3 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.0 [7e506255] + ScopedValues v1.6.2 [efcf1570] + Setfield v1.1.2 [64031d72] + SimpleCrystals v0.4.5 [699a6c99] + SimpleTraits v0.9.6 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [09ab397b] + StructArrays v0.7.3 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.13.0 [1c621080] + TestItems v1.0.0 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.28.0 [a7773ee8] + UnitfulAtomic v1.0.0 [013be700] + UnsafeAtomics v0.3.1 [78a364fa] + Chemfiles_jll v0.10.4+0 [f5851436] + FFTW_jll v3.3.12+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [dad2f222] + LLVMExtra_jll v0.0.43+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [02c8fc9c] + XML2_jll v2.15.3+0 [1317d2d5] + oneTBB_jll v2022.3.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+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 [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` Installation completed after 7.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 1044.8 ms ✓ CUDA_Driver_jll 1 dependency successfully precompiled in 1 seconds. 28 already precompiled. Precompiling packages... 2928.1 ms ✓ LLVMLoopInfo 826.9 ms ✓ GPUToolbox 793.0 ms ✓ PolygonOps 3787.8 ms ✓ ModernGL 937.9 ms ✓ Contour 904.7 ms ✓ TriplotBase 1904.2 ms ✓ CUDA_Runtime_Discovery 881.3 ms ✓ ChunkSplitters 1470.8 ms ✓ SignedDistanceFields 1791.3 ms ✓ Random123 3521.9 ms ✓ BioGenerics 759.9 ms ✓ EnzymeCore → AdaptExt 3567.3 ms ✓ BFloat16s 1250.7 ms ✓ WoodburyMatrices 6762.8 ms ✓ UnitfulAtomic 4372.5 ms ✓ PeriodicTable 1155.0 ms ✓ Animations 11958.8 ms ✓ ObjectiveC 4022.7 ms ✓ ComputePipeline 1064.4 ms ✓ Roots → RootsChainRulesCoreExt 1262.8 ms ✓ gmmlib_jll 1052.3 ms ✓ EpollShim_jll 1424.4 ms ✓ Chemfiles_jll 1263.6 ms ✓ oneAPI_Level_Zero_Headers_jll 1490.3 ms ✓ ROCmDeviceLibs_jll 1319.1 ms ✓ Hwloc_jll 1402.3 ms ✓ SPIRV_Tools_jll 1272.2 ms ✓ demumble_jll 1222.4 ms ✓ OpenCL_jll 2709.9 ms ✓ SPIRV_LLVM_Translator_jll 1295.1 ms ✓ LLVM_jll 1239.5 ms ✓ isoband_jll 1585.7 ms ✓ MuladdMacro 2229.6 ms ✓ BioSymbols 26197.8 ms ✓ PrettyTables 5282.0 ms ✓ CUDA_Runtime_jll 1208.5 ms ✓ Dbus_jll 1143.2 ms ✓ Measurements → MeasurementsRecipesBaseExt 23002.2 ms ✓ PlotUtils 1553.5 ms ✓ FilePaths 2368.9 ms ✓ libigc_jll 2643.6 ms ✓ LLVMDowngrader_jll 8416.5 ms ✓ MeshIO 11094.2 ms ✓ GridLayoutBase 1952.5 ms ✓ Packing 4184.5 ms ✓ ShaderAbstractions 63302.6 ms ✓ TiffImages 7970.6 ms ✓ Xorg_libxkbfile_jll 1270.7 ms ✓ NVTX → NVTXColorsExt 1003.8 ms ✓ Measurements → MeasurementsSpecialFunctionsExt 1143.1 ms ✓ ColorVectorSpace → SpecialFunctionsExt 7553.3 ms ✓ NearestNeighbors 3222.7 ms ✓ ColorBrewer 1316.9 ms ✓ IntervalArithmetic → IntervalArithmeticSparseArraysExt 905.9 ms ✓ IntervalArithmetic → IntervalArithmeticIntervalSetsExt 1105.3 ms ✓ IntervalArithmetic → IntervalArithmeticIrrationalConstantsExt 1343.0 ms ✓ IntervalArithmetic → IntervalArithmeticRecipesBaseExt 4045.4 ms ✓ Xorg_libXi_jll 1281.1 ms ✓ Xorg_libXinerama_jll 2755.7 ms ✓ Xorg_libXrandr_jll 1281.3 ms ✓ Xorg_libXcursor_jll 2803.8 ms ✓ Graphs → GraphsSharedArraysExt 2268.0 ms ✓ KernelAbstractions → EnzymeExt 18950.8 ms ✓ AcceleratedKernels 1857.0 ms ✓ StructArrays → StructArraysGPUArraysCoreExt 3306.9 ms ✓ UnsafeAtomics → UnsafeAtomicsLLVM 44401.3 ms ✓ GPUCompiler 22483.0 ms ✓ MathTeXEngine 7008.6 ms ✓ ExactPredicates 3272.1 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 6413.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 8848.3 ms ✓ SPIRVIntrinsics 23113.8 ms ✓ CellListMap 2508.1 ms ✓ LLVM → BFloat16sExt 1212.1 ms ✓ AxisAlgorithms 4541.0 ms ✓ AtomsBase 2667.4 ms ✓ Wayland_jll 1254.3 ms ✓ oneAPI_Level_Zero_Loader_jll 846.3 ms ✓ Isoband 2240.9 ms ✓ FFTA 14775.1 ms ✓ BioStructures 104471.2 ms ✓ DataFrames 2681.9 ms ✓ NEO_jll 1305.5 ms ✓ Xorg_xkbcomp_jll 17872.5 ms ✓ GPUArrays 114061.7 ms ✓ Enzyme 11364.8 ms ✓ DelaunayTriangulation 10773.7 ms ✓ SPIRVIntrinsics → SPIRVIntrinsicsSIMDExt 11035.7 ms ✓ Interpolations 4696.4 ms ✓ SimpleCrystals 9482.8 ms ✓ Chemfiles 4178.6 ms ✓ AtomsCalculators 3473.1 ms ✓ AtomsBaseTesting 1240.4 ms ✓ oneAPI_Support_jll 100464.6 ms ✓ BioStructures → BioStructuresDataFramesExt 1150.4 ms ✓ Xorg_xkeyboard_config_jll 51148.6 ms ✓ Metal 31756.0 ms ✓ AMDGPU 69187.4 ms ✓ CUDA 19539.7 ms ✓ Enzyme → EnzymeSpecialFunctionsExt 19238.4 ms ✓ Enzyme → EnzymeStaticArraysExt 18963.3 ms ✓ Enzyme → EnzymeChainRulesCoreExt 18246.4 ms ✓ Enzyme → EnzymeLogExpFunctionsExt 18308.5 ms ✓ Enzyme → EnzymeBFloat16sExt 18341.1 ms ✓ Enzyme → EnzymeGPUArraysCoreExt 19647.0 ms ✓ QuadGK → QuadGKEnzymeExt 2447.8 ms ✓ Interpolations → InterpolationsUnitfulExt 41063.8 ms ✓ KernelDensity 155502.9 ms ✓ Molly 28047.0 ms ✓ oneAPI 1212.9 ms ✓ xkbcommon_jll 48399.9 ms ✓ Atomix → AtomixMetalExt 6495.1 ms ✓ Metal → SpecialFunctionsExt 69304.6 ms ✓ AMDGPU → AMDGPUEnzymeCoreExt 8298.3 ms ✓ AMDGPU → AMDGPUChainRulesCoreExt 152905.0 ms ✓ CUDA → SpecialFunctionsExt 12805.8 ms ✓ Atomix → AtomixCUDAExt 12663.9 ms ✓ CUDA → ChainRulesCoreExt 12477.6 ms ✓ CUDA → EnzymeCoreExt 554600.9 ms ✓ Makie 410491.2 ms ✓ Molly → MollyEnzymeExt ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 15 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #634 at ./asyncevent.jl:359 jfptr_YY.634_15147.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1252 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 0x000070478f6a4790 Total snapshots: 399. Utilization: 0% ╎399 @Base/asyncevent.jl:359 (::Base.var"#634#635"{FileWatching.Pidfile.var… ╎ 399 @Base/asyncevent.jl:185 _trywait(t::Timer) ╎ 399 @Base/condition.jl:136 wait ╎ 399 @Base/condition.jl:141 wait(c::Base.GenericCondition{Base.Threads.S… ╎ 399 @Base/task.jl:1228 wait() 398╎ 399 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronize… ====================================================================================== 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 task_done_hook at ./task.jl:868 jfptr_task_done_hook_59905.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] jl_finish_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:341 start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1263 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 0x0000708c58eaafe0 Total snapshots: 416. Utilization: 0% ╎416 @Base/task.jl:868 task_done_hook(t::Task) ╎ 416 @Base/task.jl:1228 wait() 415╎ 416 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronized{T… [15] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #634 at ./asyncevent.jl:359 jfptr_YY.634_15147.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1252 unknown function (ip: (nil)) at (unknown file) Allocations: 18138932 (Pool: 18137870; Big: 1062); GC: 16 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:156 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 profile_printing_listener at ./Base.jl:332 #start_profile_listener##0 at ./Base.jl:352 jfptr_YY.start_profile_listenerYY.YY.0_16003.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1252 unknown function (ip: (nil)) at (unknown file) Allocations: 11588824 (Pool: 11588190; Big: 634); GC: 11 PkgEval terminated after 2744.2s: test duration exceeded the time limit