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BUG: Illegal inttoptr error, crashing julia #414

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0x0f0f0f opened this issue Apr 25, 2021 · 9 comments
Closed

BUG: Illegal inttoptr error, crashing julia #414

0x0f0f0f opened this issue Apr 25, 2021 · 9 comments
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@0x0f0f0f
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julia> Pkg.status("Catlab")
      Status `~/.julia/environments/v1.6/Project.toml`
  [134e5e36] Catlab v0.12.1
julia> using Catlab

julia> using Catlab.Programs

julia> using Catlab.Theories

julia> @present TrigFunctions(FreeCartesianCategory) begin
       R::Ob
       sin::Hom(R,R)
       (+)::Hom(otimes(R,R),R)
       end
Presentation{CartesianCategory, Symbol}(Catlab.Theories.FreeCartesianCategory, (Ob = Catlab.Theories.FreeCartesianCategory.Ob{:generator}[R], Hom = Catlab.Theories.FreeCartesianCategory.Hom{:generator}[sin, +]), Dict(:+ => (:Hom => 2), :R => (:Ob => 1), :sin => (:Hom => 1)), Pair[])

julia> @program(TrigFunctions, (x::R) -> sin(x) + sin(x))
Illegal inttoptr
	 %226 = ptrtoint {} addrspace(10)* addrspace(13)* %225 to i64, !dbg !23
Illegal inttoptr
	 %227 = inttoptr i64 %226 to {} addrspace(10)*, !dbg !23

signal (6): Aborted
in expression starting at REPL[5]:1
raise at /builddir/glibc-2.32/signal/../sysdeps/unix/sysv/linux/raise.c:50
abort at /builddir/glibc-2.32/stdlib/abort.c:79
unknown function (ip: 0x7f7556d14680)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f7556e1d7a0)
_ZN4llvm3orc14IRCompileLayer4emitENS0_29MaterializationResponsibilityENS0_16ThreadSafeModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeENS0_29MaterializationResponsibilityE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f75538a4d6f)
_ZNSt17_Function_handlerIFvSt10unique_ptrIN4llvm3orc19MaterializationUnitESt14default_deleteIS3_EENS2_29MaterializationResponsibilityEEPS8_E9_M_invokeERKSt9_Any_dataOS6_OS7_ at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession17runOutstandingMUsEv at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_EENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_EENSN_IS6_SV_EEEEEE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EERKNS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISK_EEEENSL_IS5_EENS_6detail12DenseMapPairIS5_SN_EEEEEE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS_9StringRefENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f7556e211ea)
unknown function (ip: 0x7f7556e22e89)
unknown function (ip: 0x7f7556e2422a)
unknown function (ip: 0x7f7556e256b0)
unknown function (ip: 0x7f7556d9e9fe)
jl_apply_generic at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
parse_wiring_diagram at /home/sea/.julia/packages/Catlab/kQLWB/src/programs/ParseJuliaPrograms.jl:56
unknown function (ip: 0x7f74f6c15845)
unknown function (ip: 0x7f7556db800b)
unknown function (ip: 0x7f7556db7b4d)
unknown function (ip: 0x7f7556db8847)
unknown function (ip: 0x7f7556db93bc)
unknown function (ip: 0x7f7556dd3e96)
unknown function (ip: 0x7f7556dd4b07)
jl_toplevel_eval_in at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f7546d54930)
unknown function (ip: 0x7f7546d5507b)
unknown function (ip: 0x7f7546d558fd)
unknown function (ip: 0x7f7546d81446)
unknown function (ip: 0x7f7546d81508)
unknown function (ip: 0x7f7546fe52c8)
unknown function (ip: 0x7f7546fe5368)
jl_f__call_latest at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f7546f61a38)
unknown function (ip: 0x7f7546f826c0)
unknown function (ip: 0x7f7546f8604c)
unknown function (ip: 0x7f7546f861b5)
unknown function (ip: 0x7f7556df6d45)
repl_entrypoint at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
main at julia (unknown line)
__libc_start_main at /builddir/glibc-2.32/csu/../csu/libc-start.c:314
_start at julia (unknown line)
Allocations: 18173555 (Pool: 18170566; Big: 2989); GC: 19
Aborted
@0x0f0f0f 0x0f0f0f changed the title Illegal inttoptr error, crashing julia BUG: Illegal inttoptr error, crashing julia Apr 25, 2021
@epatters epatters added the bug label Apr 25, 2021
@epatters
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epatters commented Apr 25, 2021

I cannot reproduce on Catlab v0.12.1 using Julia v1.6.1 and a Mac:

julia> using Catlab, Catlab.Theories, Catlab.Programs

julia> @present TrigFunctions(FreeCartesianCategory) begin
              R::Ob
              sin::Hom(R,R)
              (+)::Hom(otimes(R,R),R)
              end
Presentation{CartesianCategory, Symbol}(Catlab.Theories.FreeCartesianCategory, (Ob = Catlab.Theories.FreeCartesianCategory.Ob{:generator}[R], Hom = Catlab.Theories.FreeCartesianCategory.Hom{:generator}[sin, +]), Dict(:+ => (:Hom => 2), :R => (:Ob => 1), :sin => (:Hom => 1)), Pair[])

julia> @program(TrigFunctions, (x::R) -> sin(x) + sin(x))
WiringDiagram{CartesianCategory}([:R], [:R],
[ -2 => {inputs},
  -1 => {outputs},
  1 => Box(:sin, [:R], [:R]),
  2 => Box(:sin, [:R], [:R]),
  3 => Box(:+, [:R,:R], [:R]) ],
[ Wire((-2,1) => (1,1)),
  Wire((-2,1) => (2,1)),
  Wire((2,1) => (3,2)),
  Wire((1,1) => (3,1)),
  Wire((3,1) => (-1,1)) ])

Are you on Julia v1.6.0 or the new patch release Julia v1.6.1?

@0x0f0f0f
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I'm on 1.6.0 and void linux

@epatters
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Would you mind giving v1.6.1 a shot? That the Julia runtime is crashing suggests that at least part of the problem is in Julia itself.

@0x0f0f0f
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Works with 1.6.1. Can close?

@epatters
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Thanks for confirming. We'll chalk this up to a Julia bug.

@Christovis
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Hi, I was just running into the same bug. I use
OS: Manjaro Linux 21.0.5
Julia: 1.6.1
Catlab: v0.13.2

I found the error by simply running the test:
julia --color=yes .julia/packages/Catlab/ESMGn/test/runtests.jl

Running the test using the command above results in the following message:

Test Summary: | Pass  Total
Core          |  148    148
Test Summary: | Pass  Total
Theories      |  251    251
Test Summary:      | Pass  Total
CategoricalAlgebra |  866    866
Test Summary: | Pass  Total
Graphs        |  162    162
Test Summary:  | Pass  Total
WiringDiagrams |  424    424
Test Summary: | Pass  Total
Graphics      |  195    195

Illegal inttoptr
	 %226 = ptrtoint {} addrspace(10)* addrspace(13)* %225 to i64, !dbg !23
Illegal inttoptr
	 %227 = inttoptr i64 %226 to {} addrspace(10)*, !dbg !23

signal (6): Aborted
in expression starting at /.julia/packages/Catlab/ESMGn/test/programs/ParseJuliaPrograms.jl:30
gsignal at /usr/bin/../lib/libc.so.6 (unknown line)
abort at /usr/bin/../lib/libc.so.6 (unknown line)
unknown function (ip: 0x7f204ac03333)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f204ad0ea2c)
_ZN4llvm3orc14IRCompileLayer4emitENS0_29MaterializationResponsibilityENS0_16ThreadSafeModuleE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeENS0_29MaterializationResponsibilityE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f2047723aff)
unknown function (ip: 0x7f2047723c5d)
_ZN4llvm3orc16ExecutionSession17runOutstandingMUsEv at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_EENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_EENSN_IS6_SV_EEEEEE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EERKNS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISK_EEEENSL_IS5_EENS_6detail12DenseMapPairIS5_SN_EEEEEE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS_9StringRefENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-11.so (unknown line)
unknown function (ip: 0x7f204ad12544)
unknown function (ip: 0x7f204ad1422b)
unknown function (ip: 0x7f204ad155f2)
unknown function (ip: 0x7f204ad16ab0)
unknown function (ip: 0x7f204ac8f70f)
jl_apply_generic at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
parse_wiring_diagram at /home/christovis/.julia/packages/Catlab/ESMGn/src/programs/ParseJuliaPrograms.jl:56
unknown function (ip: 0x7f1ff0daef45)
unknown function (ip: 0x7f204aca9115)
unknown function (ip: 0x7f204aca8cd5)
unknown function (ip: 0x7f204aca98d0)
unknown function (ip: 0x7f204acaa3d0)
unknown function (ip: 0x7f204acc55c7)
unknown function (ip: 0x7f204acc5ee3)
unknown function (ip: 0x7f204acc6257)
jl_toplevel_eval_in at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f2039b51487)
unknown function (ip: 0x7f2039b476eb)
include at ./client.jl:444
unknown function (ip: 0x7f204aca9115)
unknown function (ip: 0x7f204aca8cd5)
unknown function (ip: 0x7f204aca98d0)
unknown function (ip: 0x7f204aca9c1e)
unknown function (ip: 0x7f204aca9c1e)
unknown function (ip: 0x7f204acaa3d0)
unknown function (ip: 0x7f204acc55c7)
unknown function (ip: 0x7f204acc6257)
jl_toplevel_eval_in at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f2039b51487)
unknown function (ip: 0x7f2039b476eb)
include at ./client.jl:444
unknown function (ip: 0x7f204aca9115)
unknown function (ip: 0x7f204aca8cd5)
unknown function (ip: 0x7f204aca98d0)
unknown function (ip: 0x7f204aca9c1e)
unknown function (ip: 0x7f204aca9c1e)
unknown function (ip: 0x7f204acaa3d0)
unknown function (ip: 0x7f204acc55c7)
unknown function (ip: 0x7f204acc6257)
jl_toplevel_eval_in at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f2039b51487)
unknown function (ip: 0x7f2039b476eb)
unknown function (ip: 0x7f2039b471a2)
unknown function (ip: 0x7f2039852269)
unknown function (ip: 0x7f203985d9ec)
unknown function (ip: 0x7f203985db55)
unknown function (ip: 0x7f204ace872e)
repl_entrypoint at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
main at julia (unknown line)
__libc_start_main at /usr/bin/../lib/libc.so.6 (unknown line)
_start at julia (unknown line)
Allocations: 792743546 (Pool: 792541862; Big: 201684); GC: 595
zsh: abort (core dumped)  julia --color=yes test/runtests.jl

@epatters epatters reopened this Oct 27, 2021
@epatters
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Oh no, not this again. Can you try on Julia v1.6.2 and see if you get the same result?

@Christovis
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Hehe, yep that worked, phew I used Julia v1.6.3 and that solved it.

@epatters
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Great. It makes me nervous that this bug seems to crop up from time to time, but I'm not sure what to do about it, so I guess I'll close this issue again.

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