Segmentation fault on 1.10.3 during precompilation of StructuralIdentifiability.jl #54356
Closed
Description
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:1619for the rest I refer to the CI run https://github.com/SciML/StructuralIdentifiability.jl/actions/runs/8907573090/job/24461681774 (will take time to load).
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