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Segmentation fault on 1.10.3 during precompilation of StructuralIdentifiability.jl #54356

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sumiya11 opened this issue May 4, 2024 · 0 comments · Fixed by #54363
Closed

Segmentation fault on 1.10.3 during precompilation of StructuralIdentifiability.jl #54356

sumiya11 opened this issue May 4, 2024 · 0 comments · Fixed by #54363
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@N5N3
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types and dispatch Types, subtyping and method dispatch

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@sumiya11
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sumiya11 commented May 4, 2024

CI in StructuralIdentifiability.jl started to fail around the release of 1.10.3: SciML/StructuralIdentifiability.jl@82ba1e8. It turns out that StructuralIdentifiability.jl precompiles successfully on 1.10.2, but does not precompile on 1.10.3.

I do not know if there is anything wrong with StructuralIdentifiability.jl code or if this is a bug in Julia, so I am opening this issue to see if anyone would have an idea.

MnWE:

import Pkg; Pkg.activate(temp=true)
Pkg.add(url="https://github.com/SciML/StructuralIdentifiability.jl")

Output:

    Updating git-repo `https://github.com/SciML/StructuralIdentifiability.jl`
   Resolving package versions...
    Updating `/tmp/jl_bgmZSF/Project.toml`
  [220ca800] + StructuralIdentifiability v0.5.7 `https://github.com/SciML/StructuralIdentifiability.jl#master`
    Updating `/tmp/jl_bgmZSF/Manifest.toml`
⌅ [c3fe647b] + AbstractAlgebra v0.40.9
  [a9b6321e] + Atomix v0.1.0
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.5
  [d360d2e6] + ChainRulesCore v1.23.0
  [861a8166] + Combinatorics v1.0.2
  [34da2185] + Compat v4.14.0
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.18.20
  [e2d170a0] + DataValueInterfaces v1.0.0
  [e2ba6199] + ExprTools v0.1.10
  [0b43b601] + Groebner v0.7.4
  [3e5b6fbb] + HostCPUFeatures v0.1.16
  [615f187c] + IfElse v0.1.1
  [18e54dd8] + IntegerMathUtils v0.1.2
  [c8e1da08] + IterTools v1.10.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.5.0
  [b964fa9f] + LaTeXStrings v1.3.1
  [1914dd2f] + MacroTools v0.5.13
  [102ac46a] + MultivariatePolynomials v0.5.4
  [d8a4904e] + MutableArithmetics v1.4.4
⌅ [2edaba10] + Nemo v0.43.3
  [bac558e1] + OrderedCollections v1.6.3
  [3e851597] + ParamPunPam v0.4.0
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.3.1
  [27ebfcd6] + Primes v0.5.6
  [92933f4c] + ProgressMeter v1.10.0
  [fb686558] + RandomExtensions v0.4.4
  [189a3867] + Reexport v1.2.2
  [aedffcd0] + Static v0.8.10
  [892a3eda] + StringManipulation v0.3.4
  [220ca800] + StructuralIdentifiability v0.5.7 `https://github.com/SciML/StructuralIdentifiability.jl#master`
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.11.1
  [a759f4b9] + TimerOutputs v0.5.23
  [013be700] + UnsafeAtomics v0.2.1
  [e21ec000] + Antic_jll v0.201.500+0
  [d9960996] + Arb_jll v200.2300.0+0
  [fcfa6d1b] + Calcium_jll v0.401.100+0
⌅ [e134572f] + FLINT_jll v200.900.9+0
⌅ [656ef2d0] + OpenBLAS32_jll v0.3.24+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [8ba89e20] + Distributed
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b77e0a4c] + InteractiveUtils
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [781609d7] + GMP_jll v6.2.1+6
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [3a97d323] + MPFR_jll v4.2.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Precompiling project...
  ✗ StructuralIdentifiability
  0 dependencies successfully precompiled in 212 seconds. 53 already precompiled.
  1 dependency errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

The output of err is 70k+ lines long and here is the top of it:

ERROR: The following 1 direct dependency failed to precompile:

StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544]

Failed to precompile StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544] to "/home/runner/.julia/compiled/v1.10/StructuralIdentifiability/jl_HKeS4k".
[2257] signal (11.1): Segmentation fault
in expression starting at none:0
local_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1537
forall_exists_equal at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1616
subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1449
exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1634 [inlined]
_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1665
local_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1553
forall_exists_equal at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1619
subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1449
exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1634 [inlined]
_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1665
local_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1553
forall_exists_equal at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1619
subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1449
exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1634 [inlined]
_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1665
local_forall_exists_subtype at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1553
forall_exists_equal at /cache/build/builder-amdci4-2/julialang/julia-release-1-dot-10/src/subtype.c:1619

for the rest I refer to the CI run https://github.com/SciML/StructuralIdentifiability.jl/actions/runs/8907573090/job/24461681774 (will take time to load).
@giordano giordano added types and dispatch Types, subtyping and method dispatch bisect wanted labels May 4, 2024
@N5N3 N5N3 removed the bisect wanted label May 5, 2024
@N5N3 N5N3 self-assigned this May 5, 2024
@N5N3 N5N3 mentioned this issue May 5, 2024
Merged
oscardssmith pushed a commit that referenced this issue May 7, 2024
@N5N3
typeintersect: fix another stack overflow caused by circular constrai…
e47fedd 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356
KristofferC pushed a commit that referenced this issue May 8, 2024
@N5N3 @KristofferC
typeintersect: fix another stack overflow caused by circular constrai…
496d822 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356

(cherry picked from commit e47fedd)
@sumiya11 sumiya11 mentioned this issue May 9, 2024
Closed
@pogudingleb pogudingleb mentioned this issue May 19, 2024
Merged
KristofferC pushed a commit that referenced this issue May 20, 2024
@N5N3
typeintersect: fix another stack overflow caused by circular constrai…
b03de8b 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356

(cherry picked from commit e47fedd)
KristofferC pushed a commit that referenced this issue May 23, 2024
@N5N3
typeintersect: fix another stack overflow caused by circular constrai…
ad785dd 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356

(cherry picked from commit e47fedd)
KristofferC pushed a commit that referenced this issue May 25, 2024
@N5N3 @KristofferC
typeintersect: fix another stack overflow caused by circular constrai…
24de7d7 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356

(cherry picked from commit e47fedd)
KristofferC pushed a commit that referenced this issue May 25, 2024
@N5N3 @KristofferC
typeintersect: fix another stack overflow caused by circular constrai…
1b21830 
…nts (#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close #54356

(cherry picked from commit e47fedd)
@sumiya11 sumiya11 mentioned this issue May 30, 2024
Merged
23 tasks
lazarusA pushed a commit to lazarusA/julia that referenced this issue Jul 12, 2024
@N5N3 @lazarusA
typeintersect: fix another stack overflow caused by circular constrai…
07f92b3 
…nts (JuliaLang#54363)

The added MWE has been broken since 1.8.
The intersect result still looks quite unsoundness, but at least stack
overflow get fixed.

close JuliaLang#54356
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typeintersect: fix another stack overflow caused by circular constraints N5N3/julia
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@giordano @N5N3 @sumiya11