GC Corruption from Measurements.jl usage
ChrisRackauckas opened this issue · comments
https://gitlab.com/PumasAI/Pumas-jl/-/jobs/264465532 was found in https://github.com/PumasAI/Pumas.jl/pull/605 .
GC error (probable corruption) :
Allocations: 288350199 (Pool: 288312654; Big: 37545); GC: 705
<?#0x7f11e5e9f8c0::Measurements.Measurement{Float64}(val=512.784, err=1.52101, tag=0x0000000000000000, der=Measurements.Derivatives{Float64}(parent=Measurements.Derivatives{Float64}(parent=#<null>, key=(2.37152e-322, 6.90283e-310, 0x00007f11e654f490), value=6.91692e-323), key=(2.268, 0.2, 0x0000000000000002), value=-7.60506))>
0x7f124b99b010: Queued root: 0x7f11e7601c10 :: 0x7f125d721c10 (bits: 3)
of type Core.MethodInstance
0x7f124b99b028: Queued root: 0x7f11e7673c90 :: 0x7f125d721c10 (bits: 3)
of type Core.MethodInstance
0x7f124b99b040: Queued root: 0x7f11e5e32810 :: 0x7f125d721ba0 (bits: 3)
of type Method
0x7f124b99b058: Queued root: 0x7f11e39932b0 :: 0x7f125d721ba0 (bits: 3)
of type Method
0x7f124b99b070: Queued root: 0x7f1266cedb70 :: 0x7f125d721040 (bits: 3)
of type Array{Any, 1}
0x7f124b99b088: r-- Stack frame 0x7ffd33f2d7e0 -- 13 of 16 (direct)
signal (6): Aborted
in expression starting at /builds/PumasAI/Pumas-jl/test/features/measurement_tests.jl:7
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
gc_assert_datatype_fail at /buildworker/worker/package_linux64/build/src/gc.c:1522
gc_mark_loop at /buildworker/worker/package_linux64/build/src/gc.c:2402
_jl_gc_collect at /buildworker/worker/package_linux64/build/src/gc.c:2703
jl_gc_collect at /buildworker/worker/package_linux64/build/src/gc.c:2874
jl_gc_pool_alloc at /buildworker/worker/package_linux64/build/src/gc.c:1102
* at /builds/PumasAI/Pumas-jl/.julia/packages/Measurements/VjRMd/src/math.jl:192
##369 at /builds/PumasAI/Pumas-jl/.julia/packages/ModelingToolkit/3e5pc/src/utils.jl:59
unknown function (ip: 0x7f11e34c93ed)
macro expansion at /builds/PumasAI/Pumas-jl/.julia/packages/ModelingToolkit/3e5pc/src/utils.jl:102 [inlined]
macro expansion at ./none:0 [inlined]
fast_invokelatest at ./none:0 [inlined]
out_f_safe at /builds/PumasAI/Pumas-jl/.julia/packages/ModelingToolkit/3e5pc/src/systems/diffeqs/diffeqsystem.jl:217 [inlined]
DiffEqWrapper at /builds/PumasAI/Pumas-jl/src/simulate_methods/diffeqs.jl:425 [inlined]
ODEFunction at /builds/PumasAI/Pumas-jl/.julia/packages/DiffEqBase/aPwRz/src/diffeqfunction.jl:193 [inlined]
perform_step! at /builds/PumasAI/Pumas-jl/.julia/packages/OrdinaryDiffEq/BhP0W/src/perform_step/low_order_rk_perform_step.jl:589
solve! at /builds/PumasAI/Pumas-jl/.julia/packages/OrdinaryDiffEq/BhP0W/src/perform_step/composite_perform_step.jl:43
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
#__solve#345 at /builds/PumasAI/Pumas-jl/.julia/packages/OrdinaryDiffEq/BhP0W/src/solve.jl:5
jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2332
#__solve at ./none:0 [inlined]
#solve#381 at /builds/PumasAI/Pumas-jl/.julia/packages/DiffEqBase/aPwRz/src/solve.jl:39 [inlined]
#solve at ./none:0 [inlined]
#_solve_diffeq#388 at /builds/PumasAI/Pumas-jl/src/simulate_methods/diffeqs.jl:31
#_solve_diffeq at ./none:0 [inlined]
#_solve#84 at /builds/PumasAI/Pumas-jl/src/models/model_api.jl:138 [inlined]
#_solve at ./none:0 [inlined]
#simobs#87 at /builds/PumasAI/Pumas-jl/src/models/model_api.jl:174
unknown function (ip: 0x7f11e3301d87)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1842
jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2348
#simobs at ./none:0
unknown function (ip: 0x7f11e330167d)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1842
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:625
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f11e64ec7df)
unknown function (ip: 0x14d)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29 [inlined]
include at /builds/PumasAI/Pumas-jl/.julia/packages/SafeTestsets/A83XK/src/SafeTestsets.jl:23
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1842
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f11e675177f)
unknown function (ip: 0x27)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:179
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:614
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:793
eval at ./boot.jl:328
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f11e67440af)
unknown function (ip: 0x3)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1842
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
include at ./client.jl:403
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f12525a97cf)
unknown function (ip: 0x28)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
include at ./client.jl:403
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1842
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7f125d89793f)
unknown function (ip: 0xffffffffffffffff)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:713
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:793
eval at ./boot.jl:328
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
exec_options at ./client.jl:243
_start at ./client.jl:436
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1571 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:96
main at /buildworker/worker/package_linux64/build/ui/repl.c:217
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /usr/local/julia/bin/julia (unknown line)
Allocations: 288350199 (Pool: 288312654; Big: 37545); GC: 705
ERROR: Package Pumas errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Types.jl:120
[2] #test#66(::Bool, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Operations.jl:1329
[3] #test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:0 [inlined]
[4] #test#46(::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:198
[5] #test at ./none:0 [inlined]
[6] #test#45 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:180 [inlined]
[7] #test at ./none:0 [inlined]
[8] #test#44 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:179 [inlined]
[9] #test at ./none:0 [inlined]
[10] #test#43(::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:coverage,),Tuple{Bool}}}, ::Function, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:178
[11] (::getfield(Pkg.API, Symbol("#kw##test")))(::NamedTuple{(:coverage,),Tuple{Bool}}, ::typeof(Pkg.API.test), ::String) at ./none:0
[12] top-level scope at none:0The test that was being run is https://github.com/PumasAI/Pumas.jl/blob/master/test/features/measurement_tests.jl which is sending a Measurement through an ODE.
Thanks for the report, however I cannot reproduce the error by just including the measurement_tests.jl file:
julia> include("measurement_tests.jl")
warnings for Measurements are suppressed.
Test Summary: | Pass Total
Static Vector | 2 2
Test Summary: | Pass Total
Non-static vector | 2 2
Test Summary: | Pass Total
Magic argument | 2 2
Test Summary: | Pass Total
Analytic solution | 2 2
Test.DefaultTestSet("Analytic solution", Any[], 2, false)Information about my environment:
(Pumas) pkg> status
Project Pumas v0.1.0
Status `~/.julia/dev/Pumas/Project.toml`
[0bf59076] + AdvancedHMC v0.2.2
[336ed68f] + CSV v0.5.9
[a93c6f00] + DataFrames v0.18.4
[82cc6244] + DataInterpolations v0.2.0
[864edb3b] + DataStructures v0.17.0
[bcd4f6db] + DelayDiffEq v5.11.0
[2b5f629d] + DiffEqBase v5.17.0
[01453d9d] + DiffEqDiffTools v0.14.0
[c894b116] + DiffEqJump v6.2.0
[163ba53b] + DiffResults v0.0.4
[31c24e10] + Distributions v0.21.1
[f6369f11] + ForwardDiff v0.10.3
[38e38edf] + GLM v1.1.1
[19dc6840] + HCubature v1.4.0
[2ee39098] + LabelledArrays v0.7.1
[c7f686f2] + MCMCChains v0.3.11
[1914dd2f] + MacroTools v0.5.1
[e1d29d7a] + Missings v0.4.1
[961ee093] + ModelingToolkit v0.5.0
[429524aa] + Optim v0.19.2
[1dea7af3] + OrdinaryDiffEq v5.13.0
[90014a1f] + PDMats v0.9.7
[3cdcf5f2] + RecipesBase v0.7.0
[731186ca] + RecursiveArrayTools v1.0.0
[189a3867] + Reexport v0.2.0
[90137ffa] + StaticArrays v0.11.0
[2913bbd2] + StatsBase v0.32.0
[f3b207a7] + StatsPlots v0.10.2
[09ab397b] + StructArrays v0.4.0
[bd369af6] + Tables v0.2.10
[84d833dd] + TransformVariables v0.3.3
[a2a6695c] + TreeViews v0.3.0
[1986cc42] + Unitful v0.16.0
[ade2ca70] + Dates
[8ba89e20] + Distributed
[37e2e46d] + LinearAlgebra
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
Status `~/.julia/dev/Pumas/Manifest.toml`
[0bf59076] + AdvancedHMC v0.2.2
[336ed68f] + CSV v0.5.9
[a93c6f00] + DataFrames v0.18.4
[82cc6244] + DataInterpolations v0.2.0
[864edb3b] + DataStructures v0.17.0
[bcd4f6db] + DelayDiffEq v5.11.0
[2b5f629d] + DiffEqBase v5.17.0
[01453d9d] + DiffEqDiffTools v0.14.0
[c894b116] + DiffEqJump v6.2.0
[163ba53b] + DiffResults v0.0.4
[31c24e10] + Distributions v0.21.1
[f6369f11] + ForwardDiff v0.10.3
[38e38edf] + GLM v1.1.1
[19dc6840] + HCubature v1.4.0
[2ee39098] + LabelledArrays v0.7.1
[c7f686f2] + MCMCChains v0.3.11
[1914dd2f] + MacroTools v0.5.1
[e1d29d7a] + Missings v0.4.1
[961ee093] + ModelingToolkit v0.5.0
[429524aa] + Optim v0.19.2
[1dea7af3] + OrdinaryDiffEq v5.13.0
[90014a1f] + PDMats v0.9.7
[3cdcf5f2] + RecipesBase v0.7.0
[731186ca] + RecursiveArrayTools v1.0.0
[189a3867] + Reexport v0.2.0
[90137ffa] + StaticArrays v0.11.0
[2913bbd2] + StatsBase v0.32.0
[f3b207a7] + StatsPlots v0.10.2
[09ab397b] + StructArrays v0.4.0
[bd369af6] + Tables v0.2.10
[84d833dd] + TransformVariables v0.3.3
[a2a6695c] + TreeViews v0.3.0
[1986cc42] + Unitful v0.16.0
[ade2ca70] + Dates
[8ba89e20] + Distributed
[37e2e46d] + LinearAlgebra
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
julia> versioninfo()
Julia Version 1.1.1
Commit 55e36cc308 (2019-05-16 04:10 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Core(TM) i7-4870HQ CPU @ 2.50GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-6.0.1 (ORCJIT, haswell)
@giordano @ChrisRackauckas this may be related to MakieOrg/Makie.jl#374, which was reported at JuliaLang/julia#32751 and fixed in JuliaLang/julia#32773. I've tested to check that this was fixed on the latest nightlies. If so, you may want to request a backport?
Well, retesting worked 🤷♂