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JuliaPy / PythonCall.jl

Python and Julia in harmony.
https://juliapy.github.io/PythonCall.jl/stable/
MIT License
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Segfault using PythonCall on Apple M1 with Julia 1.11.0-rc4 #563

Open nhz2 opened 1 month ago

nhz2 commented 1 month ago

Affects: PythonCall

Describe the bug I got a segfault using PythonCall on GitHub CI for Apple M1.

https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82

This seems to be an intermittent issue. Your system

Julia Version 1.11.0-rc4
Commit b4b9add84db (2024-09-25 11:03 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 3 × Apple M1 (Virtual)
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 3 virtual cores)
Testing ZipArchives
      Status `/private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/Project.toml`
  [4c88cf16] Aqua v0.8.7
  [944b1d66] CodecZlib v0.7.6
  [36869731] Malt v1.1.1
  [6fe1bfb0] OffsetArrays v1.14.1
  [6099a3de] PythonCall v0.9.23
  [efcf1570] Setfield v1.1.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [49080126] ZipArchives v2.3.0 `~/work/ZipArchives.jl/ZipArchives.jl`
  [a5390f91] ZipFile v0.10.1
  [1e303b3e] LibArchive_jll v3.7.4+0
  [2a0f44e3] Base64 v1.11.0
  [a63ad114] Mmap v1.11.0
  [44cfe95a] Pkg v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [8dfed614] Test v1.11.0
  [3f19e933] p7zip_jll v17.4.0+2
      Status `/private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/Manifest.toml`
  [4c88cf16] Aqua v0.8.7
  [dce04be8] ArgCheck v2.3.0
  [6309b1aa] CodecInflate64 v0.1.3
  [944b1d66] CodecZlib v0.7.6
  [34da2185] Compat v4.16.0
  [992eb4ea] CondaPkg v0.2.23
  [187b0558] ConstructionBase v1.5.8
  [9a962f9c] DataAPI v1.16.0
  [e2d170a0] DataValueInterfaces v1.0.0
  [0c81fc1b] InputBuffers v1.0.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.6.0
  [0f8b85d8] JSON3 v1.14.0
  [1914dd2f] MacroTools v0.5.13
  [36869731] Malt v1.1.1
  [0b3b1443] MicroMamba v0.1.14
  [6fe1bfb0] OffsetArrays v1.14.1
  [bac558e1] OrderedCollections v1.6.3
  [69de0a69] Parsers v2.8.1
  [fa939f87] Pidfile v1.3.0
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [6099a3de] PythonCall v0.9.23
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [6c6a2e73] Scratch v1.2.1
  [efcf1570] Setfield v1.1.1
  [1e83bf80] StaticArraysCore v1.4.3
  [856f2bd8] StructTypes v1.11.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [e17b2a0c] UnsafePointers v1.0.0
  [49080126] ZipArchives v2.3.0 `~/work/ZipArchives.jl/ZipArchives.jl`
  [a5390f91] ZipFile v0.10.1
  [1fd713ca] Attr_jll v2.5.2+0
  [6e34b625] Bzip2_jll v1.0.8+1
  [2e619515] Expat_jll v2.6.2+0
  [1e303b3e] LibArchive_jll v3.7.4+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [5ced3[41](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:44)a] Lz4_jll v1.10.0+1
  [458c3c95] OpenSSL_jll v3.0.15+1
  [ffd25f8a] XZ_jll v5.4.6+0
  [3161d3a3] Zstd_jll v1.5.6+1
  [ed5aba05] acl_jll v2.3.2+0
  [f8abcde7] micromamba_jll v1.5.8+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b[42](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:45)a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [f489334b] StyledStrings v1.11.0
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [deac9b[47](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:50)] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [83775a58] Zlib_jll v1.2.13+1
  [8e8[50](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:53)ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2

Additional context

Stack trace:

[3148] signal 11 (2): Segmentation fault: 11
in expression starting at /Users/runner/work/ZipArchives.jl/ZipArchives.jl/test/external_unzippers.jl:7
_PyObject_Malloc at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyUnicode_New at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
unicode_decode_utf8 at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyUnicode_FromFormatV at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyErr_Format at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_GenericGetAttrWithDict at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_GetAttr at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
import_ensure_initialized at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_ImportModuleLevelObject at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_Import at /private/var/folders/0g/hj_q_pzx65bbjnslxz9n0src0000gn/T/jl_yiKQEd/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_Import at /Users/runner/.julia/packages/PythonCall/Nr75f/src/C/pointers.jl:303
unknown function (ip: 0x12ed1409b)
unknown function (ip: 0x12ece431b)
unknown function (ip: 0x12ece42b7)
macro expansion at /Users/runner/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:132 [inlined]
pyimport at /Users/runner/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:1561
unknown function (ip: 0x12ece41ff)
unknown function (ip: 0x12ecbd833)
unknown function (ip: 0x12ecbd6e3)
pyimport at /Users/runner/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:1562 [inlined]
init_consts at /Users/runner/.julia/packages/PythonCall/Nr75f/src/Core/consts.jl:205
unknown function (ip: 0x12ecbd6a7)
unknown function (ip: 0x12eca421f)
unknown function (ip: 0x12eca40df)
__init__ at /Users/runner/.julia/packages/PythonCall/Nr75f/src/Core/Core.jl:42
unknown function (ip: 0x12eca4077)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
jl_module_run_initializer at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:76
run_module_init at ./loading.jl:1336
register_restored_modules at ./loading.jl:1324
#_include_from_serialized#1066 at ./loading.jl:1213
_include_from_serialized at ./loading.jl:1169 [inlined]
_include_from_serialized at ./loading.jl:1169 [inlined]
#_require_search_from_serialized#1076 at ./loading.jl:1975
_require_search_from_serialized at ./loading.jl:1898
jfptr__require_search_from_serialized_44910.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
_require at ./loading.jl:2435
__require_prelocked at ./loading.jl:2300
jfptr___require_prelocked_70208.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
jl_f__call_in_world at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/builtins.c:894
#invoke_in_world#3 at ./essentials.jl:1088 [inlined]
invoke_in_world at ./essentials.jl:1085 [inlined]
_require_prelocked at ./loading.jl:2287
macro expansion at ./loading.jl:2226 [inlined]
macro expansion at ./lock.jl:273 [inlined]
__require at ./loading.jl:2183
jfptr___require_70144.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
jl_f__call_in_world at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/builtins.c:894
#invoke_in_world#3 at ./essentials.jl:1088 [inlined]
invoke_in_world at ./essentials.jl:1085 [inlined]
require at ./loading.jl:2176
jfptr_require_70141.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
call_require at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:486 [inlined]
eval_import_path at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:523
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:812
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:629
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:539
jl_interpret_toplevel_thunk at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:821
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:952 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
include_string at ./loading.jl:[262](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:265)8
_include at ./loading.jl:2688
include at ./sysimg.jl:38
unknown function (ip: 0x102884087)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
do_call at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:126
eval_stmt_value at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:174
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:663
jl_interpret_toplevel_thunk at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:821
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:952 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
include_string at ./loading.jl:2628
_include at ./loading.jl:[268](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:271)8
include at ./sysimg.jl:38
unknown function (ip: 0x102884087)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
do_call at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:126
eval_stmt_value at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:174
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:663
jl_interpret_toplevel_thunk at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:821
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:952 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
include_string at ./loading.jl:2628
_include at ./loading.jl:2688
include at ./sysimg.jl:38
unknown function (ip: 0x102884087)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
do_call at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:126
eval_stmt_value at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:174
eval_body at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:663
jl_interpret_toplevel_thunk at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/interpreter.c:821
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:952 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/toplevel.c:994
jlplt_ijl_toplevel_eval_in_[283](https://github.com/JuliaIO/ZipArchives.jl/actions/runs/11219970406/job/31187122812?pr=82#step:6:286)55.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
eval at ./boot.jl:430 [inlined]
exec_options at ./client.jl:296
_start at ./client.jl:531
jfptr__start_72508.1 at /Users/runner/hostedtoolcache/julia/1.11.0-rc4/aarch64/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
true_main at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-honeycrisp-XG3Q6T6R70.0/build/default-honeycrisp-XG3Q6T6R70-0/julialang/julia-release-1-dot-11/src/jlapi.c:1059
Allocations: 23655843 (Pool: 23653807; Big: 2036); GC: 20
Package ZipArchives errored during testing (received signal: 11)
tmistele commented 1 month ago

I have a very similar issue with the final julia 1.11.0. The segfault is very non-deterministic. It doesn't always happen and when it happens it doesn't always happen at the same point. Some backtraces look like this:

[36693] signal 11 (1): Segmentation fault
in expression starting at [REDACTED].jl
PyType_IsSubtype at /usr/lib64/libpython3.12.so.1.0 (unknown line)
unknown function (ip: 0x7fb959cbaf3d)
_PyEval_EvalFrameDefault at /usr/lib64/libpython3.12.so.1.0 (unknown line)
unknown function (ip: 0x7fb959cdce0a)
PyObject_CallObject at $HOME/.julia/packages/PythonCall/Nr75f/src/C/pointers.jl:303 [inlined]
macro expansion at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:132 [inlined]
pycallargs at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:220
#pycall#21 at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:243 [inlined]
pycall at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:233 [inlined]
#_#11 at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:357 [inlined]
Py at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:357 [inlined]
[...]

Others like this:

[36447] signal 11 (1): Segmentation fault
in expression starting at [REDACTED].jl
PyObject_GetAttr at /usr/lib64/libpython3.12.so.1.0 (unknown line)
PyUFuncOverride_GetNonDefaultArrayUfunc at [REDACTED]/.venv/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so (unknown line)
PyUFunc_CheckOverride at [REDACTED]/.venv/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so (unknown line)
ufunc_generic_fastcall at [REDACTED]/.venv/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so (unknown line)
PyObject_Vectorcall at /usr/lib64/libpython3.12.so.1.0 (unknown line)
_PyEval_EvalFrameDefault at /usr/lib64/libpython3.12.so.1.0 (unknown line)
unknown function (ip: 0x7f829fedce0a)
PyObject_CallObject at $HOME/.julia/packages/PythonCall/Nr75f/src/C/pointers.jl:303 [inlined]
macro expansion at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:132 [inlined]
pycallargs at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:220
#pycall#21 at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:243 [inlined]
pycall at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:233 [inlined]
#_#11 at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:357 [inlined]
Py at $HOME/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:357 [inlined]
[...]

Running the same code with julia 1.10.4 doesn't have this issue.

dpinol commented 1 month ago

I also get seg faults, on linux, only on multithread, in applications which worked with julia 1.10

tmistele commented 2 weeks ago

Fwiw, here's a somewhat self-contained example that reliably crashes for me within a handful of runs (but it's non-deterministic), see this repository. Its only dependencies are QuadGK on the julia side and camb on the python side. The crashes only happen with julia 1.11, not with julia 1.10. This is on x86_64 Linux.

import QuadGK
using PythonCall

const camb = pyimport("camb")

const Pm = let
    params = camb.set_params(H0=70)
    params.set_matter_power(redshifts=0:.1:1.5, kmax=9.5)
    res = camb.get_results(params)
    power = res.get_matter_power_interpolator(nonlinear=false, k_hunit=false, hubble_units=false, extrap_kmax=1e6).P
    (z, k) -> let
        pyval = power(z, k)
        pyconvert(Float64, pyval)
    end
end

calculate_stuff = (R, z) -> let
    θ = R/900.
    integrand = lθ -> let
        kl = lθ/((1+z) * R)
        sqrt(lθ)*cos(lθ)*Pm(z, kl) / (θ*θ)
    end
    QuadGK.quadgk(integrand, 0, 50)[1]
end

zvalues = [0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7]
Rvalues = collect(.1:.2:7.0)
@info @. calculate_stuff(Rvalues, zvalues')