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[BUG] Segfault triggered in IJuliaExt when running Pkg.update() #5041

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ajinkya-k opened this issue Jan 20, 2025 · 12 comments
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[BUG] Segfault triggered in IJuliaExt when running Pkg.update() #5041

ajinkya-k opened this issue Jan 20, 2025 · 12 comments
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@ajinkya-k
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I am getting a segfault when I ran Pkg.update() and it tried to precompile Plots.jl

Precompiling project...
  ✗ Plots
  ✗ Plots → FileIOExt
  ✗ Plots → IJuliaExt
  ✗ Plots → GeometryBasicsExt
  ✗ Plots → UnitfulExt
  83 dependencies successfully precompiled in 168 seconds. 361 already precompiled.
  5 dependencies errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

julia> err
PkgPrecompileError: The following 5 direct dependencies failed to precompile:

IJuliaExt

Failed to precompile IJuliaExt [2f4121a4-3b3a-5ce6-9c5e-1f2673ce168a] to "/Users/ajinkya/.julia/compiled/v1.11/IJuliaExt/jl_A6c0Fe".
[41155] signal 11 (2): Segmentation fault: 11
in expression starting at none:0
gks_exit_handler at /Users/ajinkya/.julia/artifacts/3eeeb2e4ac7317a5dd5d1cbbf5fa2cf244e8833b/lib/libGR.dylib (unknown line)
__cxa_finalize_ranges at /usr/lib/system/libsystem_c.dylib (unknown line)
Allocations: 115729633 (Pool: 115725874; Big: 3759); GC: 45
ERROR: LoadError: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/Users/ajinkya/.julia/compiled/v1.11/Plots/jl_KLCerz".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3174
  [3] (::Base.var"#1110#1111"{Base.PkgId})()
    @ Base ./loading.jl:2579
  [4] mkpidlock(f::Base.var"#1110#1111"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1110#1111"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3698
 [10] maybe_cachefile_lock
    @ ./loading.jl:3695 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2565
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2388
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2375
 [16] macro expansion
    @ ./loading.jl:2314 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2271
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2260
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2881
 [24] top-level scope
    @ stdin:6
in expression starting at /Users/ajinkya/.julia/packages/Plots/Ec1L1/ext/IJuliaExt.jl:1
in expression starting at stdin:6
FileIOExt

Failed to precompile FileIOExt [f5f51d8f-5827-5d2e-939b-192fcd6ec70c] to "/Users/ajinkya/.julia/compiled/v1.11/FileIOExt/jl_vk4NEl".
[41199] signal 11 (2): Segmentation fault: 11
in expression starting at none:0
gks_exit_handler at /Users/ajinkya/.julia/artifacts/3eeeb2e4ac7317a5dd5d1cbbf5fa2cf244e8833b/lib/libGR.dylib (unknown line)
__cxa_finalize_ranges at /usr/lib/system/libsystem_c.dylib (unknown line)
Allocations: 115728449 (Pool: 115724687; Big: 3762); GC: 46
ERROR: LoadError: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/Users/ajinkya/.julia/compiled/v1.11/Plots/jl_P1XWl4".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3174
  [3] (::Base.var"#1110#1111"{Base.PkgId})()
    @ Base ./loading.jl:2579
  [4] mkpidlock(f::Base.var"#1110#1111"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1110#1111"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3698
 [10] maybe_cachefile_lock
    @ ./loading.jl:3695 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2565
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2388
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2375
 [16] macro expansion
    @ ./loading.jl:2314 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2271
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2260
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2881
 [24] top-level scope
    @ stdin:6
in expression starting at /Users/ajinkya/.julia/packages/Plots/Ec1L1/ext/FileIOExt.jl:1
in expression starting at stdin:6
@ajinkya-k ajinkya-k added the bug label Jan 20, 2025
@VictorVanthilt
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When installing Plots in an empty (new) project I also get this error.

Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/REDACTED/.julia/compiled/v1.11/Plots/jl_uUKrFo".
[1693062] signal 11 (1): Segmentation fault
in expression starting at none:0
gks_exit_handler at /REDACTED/.julia/artifacts/f528001ccfd4e85b331e6d0150d1aff89a7eab65/lib/libGR.so (unknown line)
unknown function (ip: 0x730157e47a65)
exit at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/cli/loader_exe.c:61
unknown function (ip: 0x730157e2a1c9)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 115787482 (Pool: 115783648; Big: 3834); GC: 42

[1693062] signal 11 (1): Segmentation fault
in expression starting at none:0
gks_exit_handler at /REDACTED/.julia/artifacts/f528001ccfd4e85b331e6d0150d1aff89a7eab65/lib/libGR.so (unknown line)
unknown function (ip: 0x730157e47a65)
exit at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/cli/loader_exe.c:61
unknown function (ip: 0x730157e2a1c9)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 115787482 (Pool: 115783648; Big: 3834); GC: 42

@hurak
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hurak commented Jan 20, 2025

Pretty much the same here:

julia> versioninfo()
Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin24.0.0)
  CPU: 8 × Apple M2
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m2)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Environment:
  DYLD_LIBRARY_PATH = /Library/knitro/lib
(tmp_plots) pkg> st
Status `~/Documents/julia/tmp_plots/Project.toml`
  [91a5bcdd] Plots v1.40.9
julia> err
PkgPrecompileError: The following 2 direct dependencies failed to precompile:

UnitfulExt 

Failed to precompile UnitfulExt [0e51ec96-f580-5f12-a625-1297083d7970] to "/Users/hurak/.julia/compiled/v1.11/UnitfulExt/jl_zNQXSv".
[2330] signal 11 (2): Segmentation fault: 11
in expression starting at none:0
gks_exit_handler at /Users/hurak/.julia/artifacts/3eeeb2e4ac7317a5dd5d1cbbf5fa2cf244e8833b/lib/libGR.dylib (unknown line)
__cxa_finalize_ranges at /usr/lib/system/libsystem_c.dylib (unknown line)
Allocations: 115810254 (Pool: 115806467; Big: 3787); GC: 45
ERROR: LoadError: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/Users/hurak/.julia/compiled/v1.11/Plots/jl_nXUSOR".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3174
  [3] (::Base.var"#1110#1111"{Base.PkgId})()
    @ Base ./loading.jl:2579
  [4] mkpidlock(f::Base.var"#1110#1111"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1110#1111"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3698
 [10] maybe_cachefile_lock
    @ ./loading.jl:3695 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2565
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2388
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2375
 [16] macro expansion
    @ ./loading.jl:2314 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2271
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2260
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2881
 [24] top-level scope
    @ stdin:6
in expression starting at /Users/hurak/.julia/packages/Plots/Ec1L1/ext/UnitfulExt.jl:4
in expression starting at stdin:6
Plots 

Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/Users/hurak/.julia/compiled/v1.11/Plots/jl_xR7aXc".
[2327] signal 11 (2): Segmentation fault: 11
in expression starting at none:0
gks_exit_handler at /Users/hurak/.julia/artifacts/3eeeb2e4ac7317a5dd5d1cbbf5fa2cf244e8833b/lib/libGR.dylib (unknown line)
__cxa_finalize_ranges at /usr/lib/system/libsystem_c.dylib (unknown line)
Allocations: 115795466 (Pool: 115791680; Big: 3786); GC: 45

@MasonProtter
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I'm also hitting this

@fhagemann
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+1, failing some GitHub Actions that require Plots for the documentation build

@gericke-n gericke-n mentioned this issue Jan 20, 2025
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@oameye
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oameye commented Jan 20, 2025

if I downgrade to [email protected], it works again.

@fhagemann
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Yes, it seems to be related to [email protected]
jheinen/GR.jl#556

@ajinkya-k
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Downgrading to [email protected] worked for me as well

@ajinkya-k ajinkya-k mentioned this issue Jan 20, 2025
Closed
@dgomezcastro
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+1 on macOS. Downgrading seems to fix it

@Azendae-Popo
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Downgrading to [email protected] worked for me as well

Downgrading to [email protected] didn't work for me 😞

@AronT-TLV
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AronT-TLV commented Jan 20, 2025 •
edited
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+1 on MacOSx. Downgrading GR solved the problem

@sprague252
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sprague252 commented Jan 20, 2025 •
edited
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If I use juliaup to install and run Julia v1.10.7, Plots builds successfully in an empty project (on Mac OS X).

@ajinkya-k
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I guess we can close this now that GR release v0.73.12 is available. See resolution here: jheinen/GR.jl#556

@t-bltg t-bltg mentioned this issue Jan 21, 2025
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10 participants
@ajinkya-k @hurak @dgomezcastro @AronT-TLV @sprague252 @MasonProtter @fhagemann @oameye @VictorVanthilt @Azendae-Popo