Unreachable reached in AtomicStructures.jl on Julia 1.8.1, but not 1.8.0 #46735

jagot · 2022-09-13T06:44:42Z

https://github.com/JuliaAtoms/AtomicStructure.jl/actions/runs/3042781441/jobs/4901317463#step:6:200

Steps to reproduce:

julia> versioninfo()
Julia Version 1.8.1
Commit afb6c60d69a (2022-09-06 15:09 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × AMD Ryzen 9 3950X 16-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, znver2)
  Threads: 1 on 32 virtual cores

(v1.8) pkg> activate .
  Activating new project at `/export/stefanos/work/projects/test-code/test-atomic-structure`

(test-atomic-structure) pkg> add AtomicStructure
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
    Updating `/export/stefanos/work/projects/test-code/test-atomic-structure/Project.toml`
  [e24b7630] + AtomicStructure v0.1.2
    Updating `/export/stefanos/work/projects/test-code/test-atomic-structure/Manifest.toml`
  ⋮

(test-atomic-structure) pkg> test AtomicStructure

The same test suite works fine on 1.6 and 1.8.0. Will endeavour to produce MWE.

jagot · 2022-09-13T07:22:13Z

Smaller working example:

julia> versioninfo()
Julia Version 1.8.1
Commit afb6c60d69a (2022-09-06 15:09 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × AMD Ryzen 9 3950X 16-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, znver2)
  Threads: 1 on 32 virtual cores

(v1.8) pkg> activate .
  Activating new project at `/export/stefanos/work/projects/test-code/test-atomic-structure`

(test-atomic-structure) pkg> add AtomicStructure AtomicLevels CompactBases
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
    Updating `/export/stefanos/work/projects/test-code/test-atomic-structure/Project.toml`
  [10933b4c] + AtomicLevels v0.1.8
  [e24b7630] + AtomicStructure v0.1.2
  [2c0377a8] + CompactBases v0.3.8
  ⋮

julia> using AtomicStructure, AtomicLevels, CompactBases

julia> R = StaggeredFiniteDifferences(0.15, 0.6, 0.002, 50)
Staggered finite differences basis {Float64} on 0.0..7.7452155051783524 with 50 points with spacing varying from 0.15006749493775312 to 0.15663927831901248

julia> atom = Atom(R, csfs([c"1s", c"2s", c"2p", c"3s", c"3p", c"3d"]),
                   pc"H", verbosity=4)

TOMLs attached: unreachable-atoms.zip

DilumAluthge · 2022-09-13T07:30:53Z

Since you're on Linux, an rr trace could be helpful. Just start Julia with julia --bug-report=rr.

jagot · 2022-09-13T08:59:52Z

Here is the crash report: https://s3.amazonaws.com/julialang-dumps/reports/2022-09-13T08-57-03-jagot.tar.zst

I had to manually create a symlink sudo ln -s /usr/lib/libcrypt.so.2 /usr/lib/libcrypt.so.1, otherwise GDB_jll and/or Python_jll would not build. Where do I report this?

N5N3 · 2022-09-13T11:20:31Z

Reduced to

julia> using AtomicStructure: RadialOperator

julia> S = RadialOperator{T,B} where {T,B}
LazyArrays.Applied{<:Any, typeof(*), <:Tuple{var"#s128", M, var"#s127"} where {var"#s128"<:(Union{B, var"#s5"} where var"#s5"<:(QuasiArrays.SubQuasiArray{<:Any, <:Any, <:B})), var"#s127"<:(Union{var"#s7", var"#s6"} where {var"#s7"<:(QuasiArrays.QuasiAdjoint{<:Any, B}), var"#s6"<:(QuasiArrays.QuasiAdjoint{var"#s4", <:QuasiArrays.SubQuasiArray{var"#s4", var"#s8", var"#s9"}} where {var"#s4", var"#s8", var"#s9"<:B})})}} where {T, B, M<:AbstractMatrix{T}}

julia> typeintersect(S, RadialOperator)
LazyArrays.Applied{<:Any, typeof(*), <:Tuple{var"#s128", M, var"#s127"} where {B<:ContinuumArrays.Basis, M<:AbstractMatrix{T}, var"#s128"<:(QuasiArrays.SubQuasiArray{<:Any, <:Any, Union{}}), var"#s127"<:(Union{QuasiArrays.QuasiAdjoint{<:Any, B}, QuasiArrays.QuasiAdjoint{<:Any, B1}, QuasiArrays.QuasiAdjoint{var"#s4", <:QuasiArrays.SubQuasiArray{var"#s4", var"#s8", Union{}}} where {var"#s4", var"#s8"}} where B1<:ContinuumArrays.Basis)}} where T # Union{} after 9b3a2bba31fe4d18d9fa06fac6aaecc2e242d84b

KristofferC · 2022-09-13T15:59:31Z

Could be worth checking if this is also due to 5d03fcd.

vtjnash · 2022-09-13T17:36:43Z

while working to reduce that more, I encountered this mildly interesting additional case:

julia> const RO27{B<:AtomicStructure.Basis,M<:AbstractMatrix} =
           Val{<:Tuple{
           <:Union{B, <:Val{B}},
           M,
           <:(Union{<:AtomicStructure.QuasiArrays.QuasiAdjoint{<:Any, B}, <:AtomicStructure.QuasiArrays.QuasiAdjoint{<:Any, <:Vector{<:B}}})}}
Val{<:Tuple{var"#s23", M, var"#s11"} where {var"#s23"<:(Union{B, var"#s10"} where var"#s10"<:Val{B}), var"#s11"<:(Union{var"#s9", var"#s8"} where {var"#s9"<:(QuasiArrays.QuasiAdjoint{<:Any, B}), var"#s8"<:(QuasiArrays.QuasiAdjoint{<:Any, <:Vector{<:B}})})}} where {B<:ContinuumArrays.Basis, M<:(AbstractMatrix)}

julia> typeintersect(RO27{T,S} where {T,S}, RO27)

ERROR: StackOverflowError:
Stacktrace:
 [1] typeintersect(a::Any, b::Any)
   @ Base ./reflection.jl:683
 [2] top-level scope
   @ REPL[136]:1

(it fails almost instantly, but formatting the stacktrace then takes a minute)

smaller MWEs that doesn't involve any packages:

julia> const RO36{B<:Val, M<:AbstractMatrix} =
           Tuple{
           <:Union{B, <:Val{<:B}},
           M,
           <:(Union{<:AbstractMatrix{B}, <:AbstractMatrix{<:Vector{<:B}}})}
Tuple{var"#s1", M, var"#s2"} where {B<:Val, M<:(AbstractMatrix), var"#s1"<:(Union{B, var"#s3"} where var"#s3"<:(Val{<:B})), var"#s2"<:(Union{var"#s5", var"#s6"} where {var"#s5"<:AbstractMatrix{B}, var"#s6"<:(AbstractMatrix{<:Vector{<:B}})})}

julia> typeintersect(RO36{T,S} where {T,S}, RO36)
Tuple{var"#s1", S, var"#s2"} where {S<:(AbstractMatrix), var"#s1"<:(Val{<:B} where B<:Val), var"#s2"<:(Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{Union{}}}} where B<:Val)}
# Union{}

julia> const RO37{B<:Val, M<:AbstractMatrix} =
           Tuple{
           <:Union{B, <:Val{<:B}},
           M,
           <:(Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{<:B}}})}
Tuple{var"#s1", M, var"#s2"} where {B<:Val, M<:(AbstractMatrix), var"#s1"<:(Union{B, var"#s3"} where var"#s3"<:(Val{<:B})), var"#s2"<:Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{<:B}}}}

julia> typeintersect(RO37{T,S} where {T,S}, RO37)
Tuple{var"#s1", S, var"#s2"} where {S<:(AbstractMatrix), var"#s1"<:(Val{<:B} where B<:Val), var"#s2"<:(Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{<:B}}} where B<:Val)}
# Union{}

also ran into this additional issue too:

julia> const RO38{B<:Val, M<:AbstractMatrix} =
           Tuple{
           <:Union{B, <:Val{<:B}},
           M,
           Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{<:B}}}}
Tuple{var"#s1", M, Union{AbstractMatrix{B}, AbstractMatrix{<:Vector{<:B}}}} where {B<:Val, M<:(AbstractMatrix), var"#s1"<:(Union{B, var"#s2"} where var"#s2"<:(Val{<:B}))}

julia> typeintersect(RO38{T,S} where {T,S}, RO38)
Tuple{Union{var"#s1", var"#s11"}, 
[3247358] signal (11): Segmentation fault
in expression starting at none:0
ijl_isa at /data/vtjnash/julia/src/subtype.c:2075
sig_match_simple at /data/vtjnash/julia/src/typemap.c:239 [inlined]
...
Segmentation fault

with additional MWEs:

julia> Tuple{ccall(:jl_new_structv, Any, (Any, Ptr{Cvoid}, UInt32), Union, [S, S], 2)} where S<:AbstractMatrix
Segmentation fault

julia> (ti, env) = ccall(:jl_type_intersection_with_env, Any, (Any, Any), T, AbstractMatrix); env
svec(#undef)

julia> identity(env...)
Segmentation fault

JeffBezanson · 2022-09-13T20:59:22Z

# Union{} after 9b3a2bba31fe4d18d9fa06fac6aaecc2e242d84b

For reference, 9aabb4c on master.

JeffBezanson · 2022-09-13T21:13:49Z

It might be possible to work around this by simplifying some type constraints a bit, e.g. in

const RadialOperator{T,B<:Basis,M<:AbstractMatrix{T}}

remove the {T} on AbstractMatrix. I haven't tried that specifically but in the past those kinds of changes tend to avoid these issues.

vtjnash · 2022-09-13T22:09:34Z

FWIW, it looks like they already worked around it by removing some of the extraneous <: in their type

jagot · 2022-09-14T05:17:38Z

FWIW, it looks like they already worked around it by removing some of the extraneous <: in their type

Yes, but that caused an interesting StackOverflowError on Julia < 1.8 instead: https://github.com/JuliaAtoms/AtomicStructure.jl/actions/runs/3044747652/jobs/4905539689#step:6:201

I fixed this by removing some overloads which I erroneously thought were not needed anymore, and then broke another package of mine 😱 This I have to fix today. I know that my code is rather type-heavy, because it takes ages to compile and run (for the first time). This is probably compounded by my overloading methods like Base.diff etc.

maleadt · 2022-09-14T06:06:18Z

I had to manually create a symlink sudo ln -s /usr/lib/libcrypt.so.2 /usr/lib/libcrypt.so.1, otherwise GDB_jll and/or Python_jll would not build. Where do I report this?

Please report this on BugReporting.jl

N5N3 added bug Indicates an unexpected problem or unintended behavior types and dispatch Types, subtyping and method dispatch labels Sep 13, 2022

KristofferC added priority This should be addressed urgently regression Regression in behavior compared to a previous version labels Sep 13, 2022

N5N3 mentioned this issue Sep 14, 2022

Also merge var with unchanged bounds. #46757

Merged

N5N3 closed this as completed in #46757 Sep 15, 2022

vtjnash mentioned this issue Sep 15, 2022

Core._apply segfaults on svec(#undef) #46784

Closed

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Unreachable reached in AtomicStructures.jl on Julia 1.8.1, but not 1.8.0 #46735

Unreachable reached in AtomicStructures.jl on Julia 1.8.1, but not 1.8.0 #46735

jagot commented Sep 13, 2022

jagot commented Sep 13, 2022

DilumAluthge commented Sep 13, 2022

jagot commented Sep 13, 2022

N5N3 commented Sep 13, 2022

KristofferC commented Sep 13, 2022

vtjnash commented Sep 13, 2022 •

edited

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JeffBezanson commented Sep 13, 2022

JeffBezanson commented Sep 13, 2022

vtjnash commented Sep 13, 2022

jagot commented Sep 14, 2022

maleadt commented Sep 14, 2022

Unreachable reached in AtomicStructures.jl on Julia 1.8.1, but not 1.8.0 #46735

Unreachable reached in AtomicStructures.jl on Julia 1.8.1, but not 1.8.0 #46735

Comments

jagot commented Sep 13, 2022

jagot commented Sep 13, 2022

DilumAluthge commented Sep 13, 2022

jagot commented Sep 13, 2022

N5N3 commented Sep 13, 2022

KristofferC commented Sep 13, 2022

vtjnash commented Sep 13, 2022 • edited Loading

JeffBezanson commented Sep 13, 2022

JeffBezanson commented Sep 13, 2022

vtjnash commented Sep 13, 2022

jagot commented Sep 14, 2022

maleadt commented Sep 14, 2022

vtjnash commented Sep 13, 2022 •

edited

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