Package evaluation to test Molly on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T02:12:13.954 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.11s ################################################################################ # 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 [79e6a3ab] + Adapt v4.6.1 [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 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.127 [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 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [63c18a36] + KernelAbstractions v0.9.41 [929cbde3] + LLVM v9.9.0 [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 v0.11.37 ⌅ [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 [7e506255] + ScopedValues v1.6.2 [efcf1570] + Setfield v1.1.2 [64031d72] + SimpleCrystals v0.4.5 [699a6c99] + SimpleTraits v0.9.6 [a2af1166] + SortingAlgorithms v1.2.2 [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 v1.12.1 [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 v3.5.6+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 7.55s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/RUPmD/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 99350.0 ms ✓ BioStructures → BioStructuresDataFramesExt 13610.5 ms ✓ SPIRVIntrinsics 130589.2 ms ✓ Metal 186394.5 ms ✓ CUDA 106320.2 ms ? Molly 50841.8 ms ✓ AMDGPU 33969.9 ms ✓ Enzyme → EnzymeSpecialFunctionsExt 30249.4 ms ✓ Enzyme → EnzymeLogExpFunctionsExt 30788.6 ms ✓ Enzyme → EnzymeBFloat16sExt 32393.5 ms ✓ QuadGK → QuadGKEnzymeExt ✗ GLMakie 16724.0 ms ✓ SPIRVIntrinsics → SPIRVIntrinsicsSIMDExt 53295.2 ms ✓ oneAPI 73177.0 ms ✓ Atomix → AtomixMetalExt 12407.2 ms ✓ Metal → SpecialFunctionsExt 25338.7 ms ✓ CUDA → SpecialFunctionsExt 211179.5 ms ✓ Atomix → AtomixCUDAExt 23896.9 ms ✓ CUDA → ChainRulesCoreExt 24803.1 ms ✓ CUDA → EnzymeCoreExt 444676.5 ms ✓ Molly → MollyEnzymeExt 47682.9 ms ✓ Molly → MollyKernelDensityExt 239200.0 ms ✓ Molly → MollyCUDAExt 63589.7 ms ✓ AMDGPU → AMDGPUEnzymeCoreExt 15259.6 ms ✓ AMDGPU → AMDGPUChainRulesCoreExt ====================================================================================== 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 /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:693 wait at ./process.jl:686 [inlined] success at ./process.jl:555 jfptr_success_6905.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #compilecache#914 at ./loading.jl:3236 compilecache at ./loading.jl:3192 [inlined] #_precompilepkgs##36 at ./precompilation.jl:1075 with_logstate at ./logging/logging.jl:542 with_logger at ./logging/logging.jl:653 [inlined] #_precompilepkgs##34 at ./precompilation.jl:1069 [inlined] #mkpidlock#8 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96 jfptr_YY.mkpidlockYY.8_49511.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 mkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93 #mkpidlock#7 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined] mkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 jfptr_mkpidlock_68876.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f__apply_iterate at /source/src/builtins.c:868 #trymkpidlock#13 at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f__apply_iterate at /source/src/builtins.c:868 trymkpidlock at /source/usr/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:115 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_f_invoke_in_world at /source/src/builtins.c:900 #invokelatest_gr#239 at ./reflection.jl:1297 [inlined] invokelatest_gr at ./reflection.jl:1289 [inlined] precompile_pkgs_maybe_cachefile_lock at ./precompilation.jl:1310 macro expansion at ./timing.jl:461 [inlined] #_precompilepkgs##30 at ./precompilation.jl:1068 jfptr_YY._precompilepkgsYY.YY.30_3976.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 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 0x000070520ace9b40 Total snapshots: 329. Utilization: 0% ╎329 @Base/precompilation.jl:1068 (::Base.Precompilation.var"#_precompilepk… ╎ 329 @Base/timing.jl:461 macro expansion ╎ 329 @Base/…ecompilation.jl:1310 precompile_pkgs_maybe_cachefile_lock(f::… ╎ 329 @Base/reflection.jl:1289 invokelatest_gr ╎ 329 @Base/reflection.jl:1297 #invokelatest_gr#239 ╎ 329 @FileWatching/…ile.jl:115 kwcall(::@NamedTuple{stale_age::Int64},… ╎ ╎ 329 @FileWatching/…ile.jl:117 trymkpidlock(::Function, ::Vararg{Any}… ╎ ╎ 329 @FileWatching/…ile.jl:91 kwcall(::@NamedTuple{stale_age::Int64,… ╎ ╎ 329 @FileWatching/…le.jl:91 #mkpidlock#7 ╎ ╎ 329 @FileWatching/…le.jl:93 kwcall(::@NamedTuple{stale_age::Int64… ╎ ╎ 329 @FileWatching/…le.jl:96 mkpidlock(f::Base.Precompilation.var… ╎ ╎ ╎ 329 @Base/…pilation.jl:1069 #_precompilepkgs##34 ╎ ╎ ╎ 329 @Base/…/logging.jl:653 with_logger ╎ ╎ ╎ 329 @Base/…/logging.jl:542 with_logstate(f::Base.Precompilati… ╎ ╎ ╎ 329 @Base/…ilation.jl:1075 (::Base.Precompilation.var"#_prec… ╎ ╎ ╎ 329 @Base/loading.jl:3192 compilecache ╎ ╎ ╎ ╎ 329 @Base/loading.jl:3236 compilecache(pkg::Base.PkgId, pa… ╎ ╎ ╎ ╎ 329 @Base/process.jl:555 success(x::Base.Process) ╎ ╎ ╎ ╎ 329 @Base/process.jl:686 wait ╎ ╎ ╎ ╎ 329 @Base/process.jl:693 wait(x::Base.Process, syncd::B… ╎ ╎ ╎ ╎ 329 @Base/…ition.jl:136 wait ╎ ╎ ╎ ╎ ╎ 329 @Base/…ition.jl:141 wait(c::Base.GenericCondition… ╎ ╎ ╎ ╎ ╎ 329 @Base/task.jl:1228 wait() 328╎ ╎ ╎ ╎ ╎ 329 @Base/task.jl:1216 poptask(W::Base.IntrusiveLin… ====================================================================================== 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 task_done_hook at ./task.jl:868 jfptr_task_done_hook_43684.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] jl_finish_task at /source/src/task.c:342 start_task at /source/src/task.c:1264 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 0x000077bafc4b3df0 Total snapshots: 366. Utilization: 0% ╎366 @Base/task.jl:868 task_done_hook(t::Task) ╎ 366 @Base/task.jl:1228 wait() 365╎ 366 @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 /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #653 at ./asyncevent.jl:359 jfptr_YY.653_3180.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 42843282 (Pool: 42842290; Big: 992); GC: 33 [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 /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 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_10036.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 15206786 (Pool: 15206121; Big: 665); GC: 12 PkgEval terminated after 2752.0s: test duration exceeded the time limit