Closed jemisjoky closed 7 months ago
Opening up the Julia REPL and running Base.runtests()
shows a few failed tests that seem to be related to the issue above. I'm giving the summary of failed tests first, and then the full test printout at the bottom.
Test Summary: | Pass Fail Error Broken Total Time
Overall | 40342979 6 2 352660 40695647 15m05.6s
Downloads | 1 1 8.1s
LibGit2/libgit2 | 747 6 753 1m05.9s
Pkg | 1 1 16.8s
FAILURE
The global RNG seed was 0x1749f83068514184b3f2b68c3d0939fb.
Error in testset Downloads:
Error During Test at none:1
Got exception outside of a @test
ProcessExitedException(3)
Stacktrace:
[1] try_yieldto(undo::typeof(Base.ensure_rescheduled))
@ Base ./task.jl:871
[2] wait()
@ Base ./task.jl:931
[3] wait(c::Base.GenericCondition{ReentrantLock})
@ Base ./condition.jl:124
[4] take_buffered(c::Channel{Any})
@ Base ./channels.jl:416
[5] take!(c::Channel{Any})
@ Base ./channels.jl:410
[6] take!(::Distributed.RemoteValue)
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:726
[7] remotecall_fetch(::Function, ::Distributed.Worker, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, UInt128, Tuple{Symbol}, NamedTuple{(:seed,), Tuple{UInt128}}})
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:461
[8] remotecall_fetch(::Function, ::Int64, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, UInt128, Tuple{Symbol}, NamedTuple{(:seed,), Tuple{UInt128}}})
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:492
[9] macro expansion
@ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/test/runtests.jl:260 [inlined]
[10] (::var"#43#55"{Vector{Task}, var"#print_testworker_errored#51"{ReentrantLock, Int64, Int64}, var"#print_testworker_stats#49"{ReentrantLock, Int64, Int64, Int64, Int64, Int64, Int64}, Vector{Any}, Dict{String, DateTime}})()
@ Main ./task.jl:484
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:727
Expression: LibGit2.url(remote) == repo_url
Evaluated: "ssh://git@github.com/JuliaLang/Example.jl" == "https://github.com/JuliaLang/Example.jl"
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:733
Expression: sprint(show, remote) == "GitRemote:\nRemote name: upstream url: $(repo_url)"
Evaluated: "GitRemote:\nRemote name: upstream url: ssh://git@github.com/JuliaLang/Example.jl" == "GitRemote:\nRemote name: upstream url: https://github.com/JuliaLang/Example.jl"
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:745
Expression: LibGit2.url(remote) == repo_url
Evaluated: "ssh://git@github.com/JuliaLang/Example.jl" == "https://github.com/JuliaLang/Example.jl"
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:747
Expression: sprint(show, remote) == "GitRemote:\nRemote name: upstream url: $(repo_url)"
Evaluated: "GitRemote:\nRemote name: upstream url: ssh://git@github.com/JuliaLang/Example.jl" == "GitRemote:\nRemote name: upstream url: https://github.com/JuliaLang/Example.jl"
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:759
Expression: sprint(show, remote) == "GitRemote:\nRemote name: upstream2 url: $(repo_url)"
Evaluated: "GitRemote:\nRemote name: upstream2 url: ssh://git@github.com/JuliaLang/Example.jl" == "GitRemote:\nRemote name: upstream2 url: https://github.com/JuliaLang/Example.jl"
Error in testset LibGit2/libgit2:
Test Failed at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/test/libgit2.jl:764
Expression: LibGit2.url(remote) == repo_url
Evaluated: "ssh://git@github.com/JuliaLang/Example.jl" == "https://github.com/JuliaLang/Example.jl"
Error in testset Pkg:
Error During Test at none:1
Got exception outside of a @test
ProcessExitedException(6)
Stacktrace:
[1] try_yieldto(undo::typeof(Base.ensure_rescheduled))
@ Base ./task.jl:871
[2] wait()
@ Base ./task.jl:931
[3] wait(c::Base.GenericCondition{ReentrantLock})
@ Base ./condition.jl:124
[4] take_buffered(c::Channel{Any})
@ Base ./channels.jl:416
[5] take!(c::Channel{Any})
@ Base ./channels.jl:410
[6] take!(::Distributed.RemoteValue)
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:726
[7] remotecall_fetch(::Function, ::Distributed.Worker, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, UInt128, Tuple{Symbol}, NamedTuple{(:seed,), Tuple{UInt128}}})
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:461
[8] remotecall_fetch(::Function, ::Int64, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, UInt128, Tuple{Symbol}, NamedTuple{(:seed,), Tuple{UInt128}}})
@ Distributed /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Distributed/src/remotecall.jl:492
[9] macro expansion
@ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/test/runtests.jl:260 [inlined]
[10] (::var"#43#55"{Vector{Task}, var"#print_testworker_errored#51"{ReentrantLock, Int64, Int64}, var"#print_testworker_stats#49"{ReentrantLock, Int64, Int64, Int64, Int64, Int64, Int64}, Vector{Any}, Dict{String, DateTime}})()
@ Main ./task.jl:484
ERROR: LoadError: Test run finished with errors
in expression starting at /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/test/runtests.jl:93
ERROR: A test has failed. Please submit a bug report (https://github.com/JuliaLang/julia/issues)
including error messages above and the output of versioninfo():
Julia Version 1.8.4
Commit 00177ebc4fc (2022-12-23 21:32 UTC)
Platform Info:
OS: macOS (arm64-apple-darwin21.5.0)
CPU: 10 × Apple M1 Max
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
Threads: 1 on 8 virtual cores
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] runtests(tests::Vector{String}; ncores::Int64, exit_on_error::Bool, revise::Bool, seed::Nothing)
@ Base ./util.jl:611
[3] runtests (repeats 2 times)
@ ./util.jl:587 [inlined]
[4] top-level scope
@ REPL[1]:1
caused by: failed process: Process(setenv(`/Applications/Julia-1.8.app/Contents/Resources/julia/bin/julia -Cnative -J/Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/sys.dylib -g1 /Applications/Julia-1.8.app/Contents/Resources/julia/bin/../share/julia/test/runtests.jl all`,["_CE_M=", "LSCOLORS=Gxfxcxdxbxegedabagacad", "PATH=/Users/jemis/opt/miniconda3/envs/juliacall_test/bin:/Users/jemis/opt/miniconda3/condabin:/Users/jemis/Library/Python/3.8/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/MacGPG2/bin", "CONDA_PREFIX_1=/Users/jemis/opt/miniconda3", "MANPATH=/opt/homebrew/share/man::", "ITERM_PROFILE=Default", "USER=jemis", "JULIA_DEPOT_PATH=/var/folders/lv/ygkpc9md2kb37pw5nz2mqv5w0000gn/T/jl_FTzKcE", "LESS=-R", "CONDA_PROMPT_MODIFIER=(juliacall_test) " … "PYTHONBREAKPOINT=ipdb.set_trace", "ZSH=/Users/jemis/.oh-my-zsh", "COMMAND_MODE=unix2003", "PWD=/Users/jemis", "TERM_PROGRAM=iTerm.app", "PYTHONPATH=/Users/jemis/Library/Python/3.8:", "CPPFLAGS=-I/opt/homebrew/opt/openblas/include", "LDFLAGS=-L/opt/homebrew/opt/openblas/lib", "CONDA_PREFIX=/Users/jemis/opt/miniconda3/envs/juliacall_test", "TERM_SESSION_ID=w0t4p0:8E0E6E2E-11A1-4833-B260-07DA815F549C"]), ProcessExited(1)) [1]
Stacktrace:
[1] pipeline_error
@ ./process.jl:565 [inlined]
[2] run(::Cmd; wait::Bool)
@ Base ./process.jl:480
[3] run
@ ./process.jl:477 [inlined]
[4] runtests(tests::Vector{String}; ncores::Int64, exit_on_error::Bool, revise::Bool, seed::Nothing)
@ Base ./util.jl:603
[5] runtests (repeats 2 times)
@ ./util.jl:587 [inlined]
[6] top-level scope
@ REPL[1]:1
Libgit2 test failures look unrelated. Do you have any special git configuration? You seem to be forcing SSH protocol. But the segfaults you reported are in libcurl while downloading the registry (?)
You're right @giordano, my git config is forcing SSH and that's probably the source of the Libgit2 test failures. The Pkg test failure looks like the same origin as my issue, and the Downloads test error is something I've also seen while trying to add other packages.
I just managed to add PythonCall
, but am unclear about why this eventually worked. My bug seems to be non-deterministic, and just repeating the same call multiple times eventually succeeds in installing the package. Here's an example starting from a fresh re-install of Julia (deleting ~/.julia
and /Applications/Julia-1.8.app/
, then downloading and installing the binary again):
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Installing known registries into `~/.julia`
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
signal (11): Segmentation fault: 11
in expression starting at none:1
Curl_connect_ongoing at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Allocations: 2389948 (Pool: 2387942; Big: 2006); GC: 4
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
signal (11): Segmentation fault: 11
in expression starting at none:1
Curl_connect_ongoing at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Allocations: 2447965 (Pool: 2446189; Big: 1776); GC: 4
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
signal (11): Segmentation fault: 11
in expression starting at none:1
add_next_timeout at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
override_login at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Curl_connect at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_socket at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:48 [inlined]
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:56 [inlined]
macro expansion at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/utils.jl:28 [inlined]
do_multi at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:114
#32 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:131 [inlined]
lock at ./lock.jl:185
#31 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:128 [inlined]
macro expansion at ./asyncevent.jl:281 [inlined]
#666 at ./task.jl:134
jfptr_YY.666_39069 at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
start_task at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
Allocations: 1731264 (Pool: 1730144; Big: 1120); GC: 3
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
signal (11): Segmentation fault: 11
in expression starting at none:1
add_next_timeout at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
override_login at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Curl_connect at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_socket at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:48 [inlined]
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:56 [inlined]
macro expansion at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/utils.jl:28 [inlined]
do_multi at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:114
#32 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:131 [inlined]
lock at ./lock.jl:185
#31 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:128 [inlined]
macro expansion at ./asyncevent.jl:281 [inlined]
#666 at ./task.jl:134
jfptr_YY.666_39069 at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
start_task at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
Allocations: 2434917 (Pool: 2433148; Big: 1769); GC: 4
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Installed MicroMamba ────────────────── v0.1.12
Installed TableTraits ───────────────── v1.0.1
Installed Scratch ───────────────────── v1.1.1
Installed Parsers ───────────────────── v2.5.2
Installed JSON3 ─────────────────────── v1.12.0
Installed Preferences ───────────────── v1.3.0
Installed DataAPI ───────────────────── v1.14.0
Installed Tables ────────────────────── v1.10.0
Installed JLLWrappers ───────────────── v1.4.1
Installed micromamba_jll ────────────── v1.0.0+0
Installed DataValueInterfaces ───────── v1.0.0
Installed IteratorInterfaceExtensions ─ v1.0.0
julia(20549,0x1fc627a80) malloc: *** error for object 0x600000a0ac00: pointer being freed was not allocated
julia(20549,0x1fc627a80) malloc: *** set a breakpoint in malloc_error_break to debug
signal (6): Abort trap: 6
in expression starting at none:1
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 2573584 (Pool: 2571278; Big: 2306); GC: 5
[1] 20549 abort julia -e 'import Pkg; Pkg.add("PythonCall")'
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
julia(20568,0x1fc627a80) malloc: *** error for object 0x600003880070: pointer being freed was not allocated
julia(20568,0x1fc627a80) malloc: *** set a breakpoint in malloc_error_break to debug
signal (6): Abort trap: 6
in expression starting at none:1
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 2416420 (Pool: 2414664; Big: 1756); GC: 4
[1] 20568 abort julia -e 'import Pkg; Pkg.add("PythonCall")'
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
julia(20578,0x1fc627a80) malloc: *** error for object 0x60000100f100: pointer being freed was not allocated
julia(20578,0x1fc627a80) malloc: *** set a breakpoint in malloc_error_break to debug
signal (6): Abort trap: 6
in expression starting at none:1
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 1726772 (Pool: 1725661; Big: 1111); GC: 3
[1] 20578 abort julia -e 'import Pkg; Pkg.add("PythonCall")'
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
signal (11): Segmentation fault: 11
in expression starting at none:1
add_next_timeout at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
override_login at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Curl_connect at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_socket at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:48 [inlined]
curl_multi_socket_action at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Curl.jl:56 [inlined]
macro expansion at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/utils.jl:28 [inlined]
do_multi at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:114
#32 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:131 [inlined]
lock at ./lock.jl:185
#31 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-4.0/build/default-macmini-aarch64-4-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Downloads/src/Curl/Multi.jl:128 [inlined]
macro expansion at ./asyncevent.jl:281 [inlined]
#666 at ./task.jl:134
jfptr_YY.666_39069 at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
start_task at /Applications/Julia-1.8.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.8.dylib (unknown line)
Allocations: 2436710 (Pool: 2434941; Big: 1769); GC: 4
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
julia(20587,0x1fc627a80) malloc: *** error for object 0x600002b90f00: pointer being freed was not allocated
julia(20587,0x1fc627a80) malloc: *** set a breakpoint in malloc_error_break to debug
signal (6): Abort trap: 6
in expression starting at none:1
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 2416386 (Pool: 2414632; Big: 1754); GC: 4
[1] 20587 abort julia -e 'import Pkg; Pkg.add("PythonCall")'
~ julia -e 'import Pkg; Pkg.add("PythonCall")'
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Installed Pidfile ──────── v1.3.0
Installed UnsafePointers ─ v1.0.0
Installed MacroTools ───── v0.5.10
Installed CondaPkg ─────── v0.2.15
Installed StructTypes ──── v1.10.0
Updating `~/.julia/environments/v1.8/Project.toml`
[6099a3de] + PythonCall v0.9.10
Updating `~/.julia/environments/v1.8/Manifest.toml`
[992eb4ea] + CondaPkg v0.2.15
[9a962f9c] + DataAPI v1.14.0
[e2d170a0] + DataValueInterfaces v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.4.1
[0f8b85d8] + JSON3 v1.12.0
[1914dd2f] + MacroTools v0.5.10
[0b3b1443] + MicroMamba v0.1.12
[bac558e1] + OrderedCollections v1.4.1
[69de0a69] + Parsers v2.5.2
[fa939f87] + Pidfile v1.3.0
[21216c6a] + Preferences v1.3.0
[6099a3de] + PythonCall v0.9.10
[ae029012] + Requires v1.3.0
[6c6a2e73] + Scratch v1.1.1
[66db9d55] + SnoopPrecompile v1.0.1
[856f2bd8] + StructTypes v1.10.0
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.10.0
[e17b2a0c] + UnsafePointers v1.0.0
[f8abcde7] + micromamba_jll v1.0.0+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.3
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.8.0
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[fa267f1f] + TOML v1.0.0
[a4e569a6] + Tar v1.10.1
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.1+0
[deac9b47] + LibCURL_jll v7.84.0+0
[29816b5a] + LibSSH2_jll v1.10.2+0
[c8ffd9c3] + MbedTLS_jll v2.28.0+0
[14a3606d] + MozillaCACerts_jll v2022.2.1
[4536629a] + OpenBLAS_jll v0.3.20+0
[83775a58] + Zlib_jll v1.2.12+3
[8e850b90] + libblastrampoline_jll v5.1.1+0
[8e850ede] + nghttp2_jll v1.48.0+0
[3f19e933] + p7zip_jll v17.4.0+0
Precompiling project...
27 dependencies successfully precompiled in 13 seconds
I'm closing this for now (might just be some quirk of my device), but feel free to reopen this if others run into the same issue.
@jemisjoky did you do anything specific to fix this issue? I'm seeing a nearly identical error using juliaup
on 1.9.0 and am also on an Apple M1.
I'd like to open this back up if we could. This has been broken for me for a few months now (M1 as well, but I'm on v1.8.5). I've tried both juliaup
and downloading the official binaries and its the same problem. Notably, though, is that it only happens in VSCode for me (both in the integrated REPL and calling julia
from the VSCode terminal).
This is still happening on v1.9.0 for me.
What error is printed, what macos version, what packages are you trying to add? Just to see if anyone else can reproduce?
(@v1.9) pkg> st
Status `~/.julia/environments/v1.9/Project.toml`
[6e4b80f9] BenchmarkTools v1.3.2
[c3a54625] JET v0.8.0
[1914dd2f] MacroTools v0.5.10
[5fb14364] OhMyREPL v0.5.22
[ccf2f8ad] PlotThemes v3.1.0
[c3e4b0f8] Pluto v0.19.26
[295af30f] Revise v3.5.3
julia> versioninfo()
Julia Version 1.9.1
Commit 147bdf428cd (2023-06-07 08:27 UTC)
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 8 × Apple M1
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
Threads: 1 on 4 virtual cores
Environment:
JULIA_PKG_USE_CLI_GIT = true
JULIA_EDITOR = code
JULIA_PKG_DEVDIR = /Users/jonnie.diegelman/github
(@v1.9) pkg> add Plots
Resolving package versions...
[23900] signal (11.2): Segmentation fault: 11
in expression starting at none:0
Curl_connect_ongoing at /Applications/Julia-1.9.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
multi_runsingle at /Applications/Julia-1.9.app/Contents/Resources/julia/lib/julia/libcurl.4.dylib (unknown line)
Allocations: 8522856 (Pool: 8510739; Big: 12117); GC: 15
[1] 23900 segmentation fault julia
@taranraj123 I didn't find anything to fix the issue, but also didn't try very hard. Not a regular Julia user, so having a hackey way to install one set of dependencies was good enough for my use case.
I've having the same issue on a Macbook Pro with a Mac M1 Pro chip, macOS Ventura 13.3.1
Folks, you're going to have to run this through a debugger like lldb or gdb and report back useful information if you want this to be fixed. Just saying you're experiencing an issue few people can reproduce is not helpful, does not add value to the discussion and doesn't lead anywhere.
Having a rough idea of the number of people this impacts (just one or two people? or is it a more common problem?) and whether the problem still persists for those who have it actually does add value to the discussion. I get that it's frustrating that people are sharing issues without a way to reproduce them, but chastising people for just mentioning that they are hitting this issue is not very helpful either.
I can't speak for everyone on this thread, but I had never heard of lldb before you mentioned it. I'm trying to figure it out right now. Even if I get it running (which is a big "if"; the tutorials and installation instructions are definitely not written for people at my level of understanding and I'm hitting some pretty cryptic errors just trying to install it exactly as described in the instructions), I'm not really sure what I'm supposed to be looking for. Is the right message for someone who described themselves as "not a regular Julia user" really "don't post or comment on issues with Julia until you've run your issue through some arcane debugger"?
I'm hitting this issue on Julia 1.9 while trying to instantiate a package environment for an existing internal tool.
versioninfo
Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 10 × Apple M1 Max
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
Threads: 1 on 8 virtual cores
Crash output
[42537] signal (11.2): Segmentation fault: 11
in expression starting at none:0
getproperty at ./Base.jl:37 [inlined]
macro expansion at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-R17H3W25T9.0/build/default-honeycrisp-R17H3W25T9-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/Downloads/src/Curl/utils.jl:56 [inlined]
do_multi at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-R17H3W25T9.0/build/default-honeycrisp-R17H3W25T9-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/Downloads/src/Curl/Multi.jl:116
#44 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-R17H3W25T9.0/build/default-honeycrisp-R17H3W25T9-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/Downloads/src/Curl/Multi.jl:134 [inlined]
lock at ./lock.jl:229
#43 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-R17H3W25T9.0/build/default-honeycrisp-R17H3W25T9-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/Downloads/src/Curl/Multi.jl:131 [inlined]
macro expansion at ./asyncevent.jl:281 [inlined]
#702 at ./task.jl:134
jfptr_YY.702_44726 at /Users/dfarmer/.julia/juliaup/julia-1.9.3+[0.aarch64.apple](http://0.aarch64.apple/).darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/dfarmer/.julia/juliaup/julia-1.9.3+[0.aarch64.apple](http://0.aarch64.apple/).darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
start_task at /Users/dfarmer/.julia/juliaup/julia-1.9.3+[0.aarch64.apple](http://0.aarch64.apple/).darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
Allocations: 2175297 (Pool: 2173595; Big: 1702); GC: 4
and LLDB backtrace
Process 42534 stopped
* thread #1, name = 'main', queue = '[com.apple](http://com.apple/).main-thread', stop reason = signal SIGSEGV
frame #0: 0x000000018c834764 libsystem_kernel.dylib`__pthread_kill + 8
libsystem_kernel.dylib`:
-> 0x18c834764 <+8>: b.lo 0x18c834784 ; <+40>
0x18c834768 <+12>: pacibsp
0x18c83476c <+16>: stp x29, x30, [sp, #-0x10]!
0x18c834770 <+20>: mov x29, sp
Target 0: (julia) stopped.
(lldb) thread backtrace all
* thread #1, name = 'main', queue = '[com.apple](http://com.apple/).main-thread', stop reason = signal SIGSEGV
* frame #0: 0x000000018c834764 libsystem_kernel.dylib`__pthread_kill + 8
frame #1: 0x000000018c86bc28 libsystem_pthread.dylib`pthread_kill + 288
frame #2: 0x000000018c74246c libsystem_c.dylib`raise + 32
frame #3: 0x000000010007233c julia`nix::sys::signal::raise::h0de0e49d5680a60f + 12
frame #4: 0x000000010000e7f0 julia`julialauncher::run_app::h2751dd6601e18ebc + 20276
frame #5: 0x0000000100010cf0 julia`julialauncher::main::hae74203636462b0b + 4912
frame #6: 0x00000001000042a8 julia`std::sys_common::backtrace::__rust_begin_short_backtrace::h87b7f46cd3222880 + 28
frame #7: 0x00000001000123cc julia`main + 592
frame #8: 0x000000018c513f28 dyld`start + 2236
thread #2, name = 'ctrl-c'
frame #0: 0x000000018c82cb0c libsystem_kernel.dylib`read + 8
frame #1: 0x000000010000415c julia`std::sys_common::backtrace::__rust_begin_short_backtrace::h5a806446894c8291 + 56
frame #2: 0x00000001000049fc julia`core::ops::function::FnOnce::call_once$u7b$$u7b$vtable.shim$u7d$$u7d$::he1e828b33f52c423 + 352
frame #3: 0x0000000100114ab8 julia`std::sys::unix::thread::Thread::new::thread_start::h999abeaf027c3bba + 48
frame #4: 0x000000018c86bfa8 libsystem_pthread.dylib`_pthread_start + 148
I'm not sure why, but when I run it in lldb doesn't show the exact same command output but I'm seeing the same thing as the OP (regarding add_next_timeout in libcurl) if I run it without lldb.
I'm not sure why, but when I run it in lldb doesn't show the exact same command output but I'm seeing the same thing as the OP (regarding add_next_timeout in libcurl) if I run it without lldb.
Because you're attaching lldb to the juliaup executable, not the actual Julia process which is crashing.
Same issue, lldb backtrace:
❯ rm -rf ~/.julia
❯ lldb -- julia-1.9.3/bin/julia
(lldb) target create "julia-1.9.3/bin/julia"
Current executable set to '/Users/nehal/tmp/julia-1.9.3/bin/julia' (arm64).
(lldb) r
Process 9825 launched: '/Users/nehal/tmp/julia-1.9.3/bin/julia' (arm64)
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.9.3 (2023-08-24)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(@v1.9) pkg> add JSON
Installing known registries into `~/.julia`
Process 9825 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x18)
frame #0: 0x0000000104260098 libcurl.4.dylib`add_next_timeout + 76
libcurl.4.dylib`add_next_timeout:
-> 0x104260098 <+76>: ldp x0, x1, [x26, #0x18]
0x10426009c <+80>: bl 0x10427094c ; Curl_timediff
0x1042600a0 <+84>: cmp x0, #0x0
0x1042600a4 <+88>: b.gt 0x1042600c0 ; <+116>
Target 0: (julia) stopped.
(lldb) bt all
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x18)
* frame #0: 0x0000000103960098 libcurl.4.dylib`add_next_timeout + 76
frame #1: 0x000000010397554c libcurl.4.dylib`override_login + 376
frame #2: 0x0000000103974be8 libcurl.4.dylib`Curl_connect + 4412
frame #3: 0x000000010395f1d8 libcurl.4.dylib`multi_runsingle + 572
frame #4: 0x0000000103960770 libcurl.4.dylib`multi_socket + 260
frame #5: 0x0000000103960820 libcurl.4.dylib`curl_multi_socket_action + 52
frame #6: 0x000000012365ae20 sys.dylib`julia_do_multi_62196 at Curl.jl:50
frame #7: 0x000000012365c0b4 sys.dylib`julia_lock_36792 at Multi.jl:134
frame #8: 0x000000012365c414 sys.dylib`julia_YY.702_44725 at Multi.jl:131
frame #9: 0x000000012365c4f0 sys.dylib`jfptr_YY.702_44726 + 8
frame #10: 0x00000001018195c4 libjulia-internal.1.9.dylib`ijl_apply_generic + 1732
frame #11: 0x0000000101836edc libjulia-internal.1.9.dylib`start_task + 184
thread #2
frame #0: 0x000000019f956060 libsystem_kernel.dylib`kevent + 8
frame #1: 0x000000010187220c libjulia-internal.1.9.dylib`signal_listener + 684
frame #2: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #3
frame #0: 0x000000019f94ff14 libsystem_kernel.dylib`mach_msg2_trap + 8
frame #1: 0x000000019f962240 libsystem_kernel.dylib`mach_msg2_internal + 80
frame #2: 0x000000019f958b78 libsystem_kernel.dylib`mach_msg_overwrite + 604
frame #3: 0x000000019f957f08 libsystem_kernel.dylib`mach_msg_server + 356
frame #4: 0x00000001018710b4 libjulia-internal.1.9.dylib`mach_segv_listener + 36
frame #5: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #4
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #5
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #6
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #7
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #8
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #9
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #10
frame #0: 0x000000019f953710 libsystem_kernel.dylib`__psynch_cvwait + 8
frame #1: 0x000000019f990574 libsystem_pthread.dylib`_pthread_cond_wait + 1232
frame #2: 0x000000010d930714 libopenblas64_.dylib`blas_thread_server + 388
frame #3: 0x000000019f98ffa8 libsystem_pthread.dylib`_pthread_start + 148
thread #11
frame #0: 0x000000019f951bc8 libsystem_kernel.dylib`__workq_kernreturn + 8
thread #12
frame #0: 0x000000019f951bc8 libsystem_kernel.dylib`__workq_kernreturn + 8
julia> versioninfo()
Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 10 × Apple M1 Max
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
Threads: 1 on 8 virtual cores
Environment:
JULIA_NUM_THREADS = 1
1.9.4 seems to be better for me. It has a few libcurl related commits
1.9.4 seems to be better for me.
What does it mean? You have fewer crashes or none at all so far? In v1.9.4 Libcurl was updated to the latest release.
1.9.4 fixed the issue for me 👍
I don't think thread support was present in those older version
Not sure if this can add anything to the discussion but I also got a segmentation fault error upon adding packages, but on a Linux machine (64bit, julia 1.10.5). The error disappeared, it turned out, when removing the openssl version of conda, that was interfering with the openssl version of the system. Just to let developers know that the error could be related to ssl.
That's definitely unrelated to the issue discussed above.
I have a 2021 MacBook Pro with an Apple M1 Max processor, and am having a problem with a fresh install of Julia 1.8.4 (macOS ARM binary) installed from the official downloads page. Opening the Julia REPL and calling
versioninfo()
gives:I'm trying to use
PythonCall
for my work, but attempting to import this causes Julia to crash. For example:Importing other packages has the same effect:
I'm guessing this is ultimately more of a MacOS issue than a Julia issue, but any help would be hugely appreciated here!