Package evaluation of DPFEHM on Julia 1.13.0-DEV.427 (855bef3b06*) started at 2025-04-24T05:49:03.567 ################################################################################ # Set-up # Set-up completed after 0.28s ################################################################################ # Installation # Installing DPFEHM... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [8c3ed914] + DPFEHM v0.1.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [621f4979] + AbstractFFTs v1.5.0 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 ⌅ [2169fc97] + AlgebraicMultigrid v0.5.1 [66dad0bd] + AliasTables v1.1.3 [a95523ee] + AlmostBlockDiagonals v0.1.10 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 [4c555306] + ArrayLayouts v1.11.1 [a9b6321e] + Atomix v1.1.1 ⌃ [13072b0f] + AxisAlgorithms v1.0.1 [aae01518] + BandedMatrices v1.9.4 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [764a87c0] + BoundaryValueDiffEq v5.16.0 [7227322d] + BoundaryValueDiffEqAscher v1.5.0 [56b672f2] + BoundaryValueDiffEqCore v1.8.0 [85d9eb09] + BoundaryValueDiffEqFIRK v1.6.0 [1a22d4ce] + BoundaryValueDiffEqMIRK v1.6.0 [9255f1d6] + BoundaryValueDiffEqMIRKN v1.5.0 [ed55bfe0] + BoundaryValueDiffEqShooting v1.6.0 [70df07ce] + BracketingNonlinearSolve v1.2.0 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 [082447d4] + ChainRules v1.72.3 [d360d2e6] + ChainRulesCore v1.25.1 [fb6a15b2] + CloseOpenIntervals v0.1.13 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [2569d6c7] + ConcreteStructs v0.2.3 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [8c3ed914] + DPFEHM v0.1.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [bcd4f6db] + DelayDiffEq v5.53.0 [8bb1440f] + DelimitedFiles v1.9.1 [2b5f629d] + DiffEqBase v6.169.0 [459566f4] + DiffEqCallbacks v4.4.1 [77a26b50] + DiffEqNoiseProcess v5.24.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [f6d13b3e] + DifferentiableBackwardEuler v0.1.0 [0c46a032] + DifferentialEquations v7.16.1 [a0c0ee7d] + DifferentiationInterface v0.6.52 [b4f34e82] + Distances v0.10.12 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 10.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 21263.9 ms ✓ SparseDiffTools ✗ Zygote 26871.5 ms ✓ SparseDiffTools → SparseDiffToolsPolyesterExt ✗ Zygote → ZygoteDistancesExt ✗ DifferentiationInterface → DifferentiationInterfaceZygoteExt ✗ RecursiveArrayTools → RecursiveArrayToolsZygoteExt ✗ SciMLBase → SciMLBaseZygoteExt ✗ SparseDiffTools → SparseDiffToolsZygoteExt 76730.2 ms ✓ StochasticDiffEq 879671.9 ms ✓ DifferentialEquations 103028.7 ms ✓ DifferentiableBackwardEuler ✗ DPFEHM 5 dependencies successfully precompiled in 1446 seconds. 353 already precompiled. 1 dependency had output during precompilation: ┌ DifferentialEquations │ WARNING: Constructor for type "BandedMatrixIndex" was extended in `ArrayInterfaceBandedMatricesExt` without explicit qualification or import. │ NOTE: Assumed "BandedMatrixIndex" refers to `ArrayInterface.BandedMatrixIndex`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function BandedMatrixIndex end`. │ Hint: To silence the warning, qualify `BandedMatrixIndex` as `ArrayInterface.BandedMatrixIndex` in the method signature or explicitly `import ArrayInterface: BandedMatrixIndex`. │ WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.RadauIIa5` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIa5` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIb5` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqFIRK.LobattoIIIc5` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK2` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK4` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. │ WARNING: Detected access to binding `BoundaryValueDiffEqMIRK.MIRK6` in a world prior to its definition world. │ Julia 1.12 has introduced more strict world age semantics for global bindings. │ !!! This code may malfunction under Revise. │ !!! This code will error in future versions of Julia. │ Hint: Add an appropriate `invokelatest` around the access to this binding. └ ERROR: LoadError: The following 1 direct dependency failed to precompile: DPFEHM Failed to precompile DPFEHM [8c3ed914-120a-47bd-8d72-56c743732853] to "/home/pkgeval/.julia/compiled/v1.13/DPFEHM/jl_ilpulz" (ProcessExited(1)). WARNING: method definition for checkbounds at /home/pkgeval/.julia/packages/Interpolations/y4lLj/src/Interpolations.jl:454 declares type variable N but does not use it. WARNING: method definition for checkbounds at /home/pkgeval/.julia/packages/Interpolations/y4lLj/src/Interpolations.jl:457 declares type variable N but does not use it. WARNING: method definition for GriddedInterpolation at /home/pkgeval/.julia/packages/Interpolations/y4lLj/src/gridded/gridded.jl:37 declares type variable pad but does not use it. WARNING: method definition for GriddedInterpolation at /home/pkgeval/.julia/packages/Interpolations/y4lLj/src/gridded/gridded.jl:60 declares type variable pad but does not use it. WARNING: method definition for interpolate! at /home/pkgeval/.julia/packages/Interpolations/y4lLj/src/deprecations.jl:30 declares type variable TWeights but does not use it. WARNING: Constructor for type "Variable" was extended in `Zygote` without explicit qualification or import. NOTE: Assumed "Variable" refers to `IRTools.Variable`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function Variable end`. Hint: To silence the warning, qualify `Variable` as `IRTools.Variable` in the method signature or explicitly `import IRTools: Variable`. WARNING: Imported binding InteractiveUtils.typesof was undeclared at import time during import to Zygote. ERROR: LoadError: UndefVarError: `typesof` not defined in `Zygote` Suggestion: this global was defined as `InteractiveUtils.typesof` but not assigned a value. Stacktrace: [1] top-level scope @ ~/.julia/packages/Zygote/1GK3J/src/precompile.jl:13 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [3] IncludeInto @ ./Base.jl:305 [inlined] [4] macro expansion @ ~/.julia/packages/Requires/1eCOK/src/Requires.jl:40 [inlined] [5] precompile() @ Zygote ~/.julia/packages/Zygote/1GK3J/src/Zygote.jl:63 [6] top-level scope @ ~/.julia/packages/Zygote/1GK3J/src/Zygote.jl:84 [7] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [8] include(mod::Module, _path::String) @ Base ./Base.jl:303 [9] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:2978 [10] top-level scope @ stdin:5 [11] eval(m::Module, e::Any) @ Core ./boot.jl:489 [12] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2824 [13] include_string @ ./loading.jl:2834 [inlined] [14] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [15] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/Zygote/1GK3J/src/precompile.jl:13 in expression starting at /home/pkgeval/.julia/packages/Zygote/1GK3J/src/Zygote.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile Zygote [e88e6eb3-aa80-5325-afca-941959d7151f] to "/home/pkgeval/.julia/compiled/v1.13/Zygote/jl_NpRjI8" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3265 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2651 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:93 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:114 [7] apply_gr_kw(::NamedTuple, ::GlobalRef, ::Any, ::Vararg{Any}) @ Base ./reflection.jl:1279 [8] #invokelatest_gr#234 @ ./reflection.jl:1287 [inlined] [9] invokelatest_gr @ ./reflection.jl:1281 [inlined] [10] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3836 [11] maybe_cachefile_lock @ ./loading.jl:3833 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2637 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2465 [14] macro expansion @ ./loading.jl:2393 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2358 [17] require(into::Module, mod::Symbol) @ Base ./loading.jl:2334 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [19] top-level scope @ ~/.julia/packages/DPFEHM/N7RUq/src/DPFEHM.jl:19 [20] include(mod::Module, _path::String) @ Base ./Base.jl:303 [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:2978 [22] top-level scope @ stdin:5 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2824 [25] include_string @ ./loading.jl:2834 [inlined] [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [27] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/DPFEHM/N7RUq/src/wave.jl:1 in expression starting at /home/pkgeval/.julia/packages/DPFEHM/N7RUq/src/DPFEHM.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 1453.37s ################################################################################ # Loading # Loading DPFEHM... Precompiling packages... ✗ Zygote ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 256 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x7c01ee7ccf14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) 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:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x00007c01e2750010 Total snapshots: 232. Utilization: 0% ╎232 @Base/task.jl:1150 wait_forever() 231╎ 232 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007c01e45fc100 Total snapshots: 232. Utilization: 0% ╎232 @Base/task.jl:1150 wait_forever() 231╎ 232 @Base/task.jl:1216 wait() ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x7a5b2c43ff14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) 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:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x00007a5aff99e770 Total snapshots: 239. Utilization: 0% ╎239 @Base/task.jl:1150 wait_forever() 238╎ 239 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007a5b223fc100 Total snapshots: 239. Utilization: 0% ╎239 @Base/task.jl:1150 wait_forever() 238╎ 239 @Base/task.jl:1216 wait() [256] signal 15: Terminated in expression starting at none:1 unknown function (ip: 0x7c01ee7ccf14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 unknown function (ip: 0x7a5b2c43ff14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) 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:454 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:454 wait at ./task.jl:1216 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 15196192 (Pool: 15195985; Big: 207); GC: 33 start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 17936638 (Pool: 17936104; Big: 534); GC: 12 PkgEval terminated after 2756.73s: test duration exceeded the time limit