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Segmentation fault on ARM Mac #680

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Closed
Segmentation fault on ARM Mac#680
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bugSomething isn't working

Description

@mhauru
mhauru
opened on Sep 29, 2025

Affects: PythonCall

Describe the bug
A segmentation fault when trying to call a constructor from an imported Python package called harmonic, installed with CondaPkg.pip_add. The MWE seems to require having a project structure in place, I'm unable to reproduce this using a plain script. The issue is deterministically reproducible, see below.

The folder structure:

$ exa -a --tree
.
├── CondaPkg.toml
├── Manifest.toml
├── Project.toml
└── src
    └── MWE.jl

Project.toml:

name = "MWE"
uuid = "4995295b-c8e1-42cb-958b-a0cc4f73796a"
authors = ["blahblah"]
version = "0.0.1"

[deps]
CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"

[compat]
CondaPkg = "=0.2.33"
PythonCall = "=0.9.28"

CondaPkg.toml:

[deps]
python = "<3.11"

[pip.deps]
harmonic = ""

Manifest.toml:

Details 
# This file is machine-generated - editing it directly is not advised

julia_version = "1.11.7"
manifest_format = "2.0"
project_hash = "d300a4187a8eae5fe37abe7ac28c490260578e63"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.2"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
version = "1.11.0"

[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
version = "1.11.0"

[[deps.CondaPkg]]
deps = ["JSON3", "Markdown", "MicroMamba", "Pidfile", "Pkg", "Preferences", "Scratch", "TOML", "pixi_jll"]
git-tree-sha1 = "bd491d55b97a036caae1d78729bdb70bf7dababc"
uuid = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
version = "0.2.33"

[[deps.DataAPI]]
git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.16.0"

[[deps.DataValueInterfaces]]
git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
version = "1.0.0"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
version = "1.11.0"

[[deps.Downloads]]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
version = "1.11.0"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
version = "1.11.0"

[[deps.IteratorInterfaceExtensions]]
git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
uuid = "82899510-4779-5014-852e-03e436cf321d"
version = "1.0.0"

[[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "0533e564aae234aff59ab625543145446d8b6ec2"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.7.1"

[[deps.JSON3]]
deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"]
git-tree-sha1 = "411eccfe8aba0814ffa0fdf4860913ed09c34975"
uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
version = "1.14.3"

    [deps.JSON3.extensions]
    JSON3ArrowExt = ["ArrowTypes"]

    [deps.JSON3.weakdeps]
    ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"

[[deps.LazyArtifacts]]
deps = ["Artifacts", "Pkg"]
uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
version = "1.11.0"

[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.4"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "8.6.0+0"

[[deps.LibGit2]]
deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
version = "1.11.0"

[[deps.LibGit2_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
version = "1.7.2+0"

[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.11.0+1"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
version = "1.11.0"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
version = "1.11.0"

[[deps.MacroTools]]
git-tree-sha1 = "1e0228a030642014fe5cfe68c2c0a818f9e3f522"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.16"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
version = "1.11.0"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.6+0"

[[deps.MicroMamba]]
deps = ["Pkg", "Scratch", "micromamba_jll"]
git-tree-sha1 = "011cab361eae7bcd7d278f0a7a00ff9c69000c51"
uuid = "0b3b1443-0f03-428d-bdfb-f27f9c1191ea"
version = "0.1.14"

[[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"
version = "1.11.0"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2023.12.12"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.OrderedCollections]]
git-tree-sha1 = "05868e21324cede2207c6f0f466b4bfef6d5e7ee"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.8.1"

[[deps.Parsers]]
deps = ["Dates", "PrecompileTools", "UUIDs"]
git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.8.3"

[[deps.Pidfile]]
deps = ["FileWatching", "Test"]
git-tree-sha1 = "2d8aaf8ee10df53d0dfb9b8ee44ae7c04ced2b03"
uuid = "fa939f87-e72e-5be4-a000-7fc836dbe307"
version = "1.3.0"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.11.0"

    [deps.Pkg.extensions]
    REPLExt = "REPL"

    [deps.Pkg.weakdeps]
    REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[deps.PrecompileTools]]
deps = ["Preferences"]
git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
version = "1.2.1"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "0f27480397253da18fe2c12a4ba4eb9eb208bf3d"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.5.0"

[[deps.Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
version = "1.11.0"

[[deps.PythonCall]]
deps = ["CondaPkg", "Dates", "Libdl", "MacroTools", "Markdown", "Pkg", "Serialization", "Tables", "UnsafePointers"]
git-tree-sha1 = "34510e11cabd7964291f32f14d28b367e9960e6e"
uuid = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
version = "0.9.28"

    [deps.PythonCall.extensions]
    CategoricalArraysExt = "CategoricalArrays"
    PyCallExt = "PyCall"

    [deps.PythonCall.weakdeps]
    CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
    PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"

[[deps.Random]]
deps = ["SHA"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
version = "1.11.0"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Scratch]]
deps = ["Dates"]
git-tree-sha1 = "9b81b8393e50b7d4e6d0a9f14e192294d3b7c109"
uuid = "6c6a2e73-6563-6170-7368-637461726353"
version = "1.3.0"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
version = "1.11.0"

[[deps.StructTypes]]
deps = ["Dates", "UUIDs"]
git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8"
uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
version = "1.11.0"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.3"

[[deps.TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]
git-tree-sha1 = "f2c1efbc8f3a609aadf318094f8fc5204bdaf344"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.12.1"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
version = "1.11.0"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
version = "1.11.0"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
version = "1.11.0"

[[deps.UnsafePointers]]
git-tree-sha1 = "c81331b3b2e60a982be57c046ec91f599ede674a"
uuid = "e17b2a0c-0bdf-430a-bd0c-3a23cae4ff39"
version = "1.0.0"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+1"

[[deps.micromamba_jll]]
deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"]
git-tree-sha1 = "2ca2ac0b23a8e6b76752453e08428b3b4de28095"
uuid = "f8abcde7-e9b7-5caa-b8af-a437887ae8e4"
version = "1.5.12+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.59.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+2"

[[deps.pixi_jll]]
deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"]
git-tree-sha1 = "f349584316617063160a947a82638f7611a8ef0f"
uuid = "4d7b5844-a134-5dcd-ac86-c8f19cd51bed"
version = "0.41.3+0"

src/MWE.jl:

module MWE

using CondaPkg: CondaPkg
using PythonCall: PythonCall

const hm = PythonCall.pyimport("harmonic")

function make(ndim)
    hm.Chains(ndim)
    return nothing
end

end

To reproduce:

$ julia --project=. -e "using MWE; MWE.make(1)"
    CondaPkg Found dev dependencies: /private/tmp/condapkg/CondaPkg.toml
    CondaPkg Found dependencies: /Users/mhauru/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
    CondaPkg Found dependencies: /Users/mhauru/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + harmonic (pip)
             + python
             + uv
    CondaPkg Initialising pixi
             │ /Users/mhauru/.julia/artifacts/d2fecc2a9fa3eac2108d3e4d9d155e6ff5dfd0b2/bin/pixi
             │ init
             │ --format pixi
             └ /private/tmp/condapkg/.CondaPkg
✔ Created /private/tmp/condapkg/.CondaPkg/pixi.toml
    CondaPkg Wrote /private/tmp/condapkg/.CondaPkg/pixi.toml
             │ [dependencies]
             │ uv = ">=0.4"
             │
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = "<3.11, >=3.9,<4"
             │
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["osx-arm64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             │ description = "automatically generated by CondaPkg.jl"
             │
             │ [pypi-dependencies]
             └ harmonic = "*"
    CondaPkg Installing packages
             │ /Users/mhauru/.julia/artifacts/d2fecc2a9fa3eac2108d3e4d9d155e6ff5dfd0b2/bin/pixi
             │ install
             └ --manifest-path /private/tmp/condapkg/.CondaPkg/pixi.toml
✔ The default environment has been installed.

[31978] signal 11 (2): Segmentation fault: 11
in expression starting at none:1
PyObject_GetAttr at /private/tmp/condapkg/.CondaPkg/.pixi/envs/default/lib/libpython3.10.dylib (unknown line)
PyObject_GetAttr at /Users/mhauru/.julia/packages/PythonCall/mkWc2/src/C/pointers.jl:300 [inlined]
macro expansion at /Users/mhauru/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:118 [inlined]
pygetattr at /Users/mhauru/.julia/packages/PythonCall/mkWc2/src/Core/builtins.jl:58
getproperty at /Users/mhauru/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:250 [inlined]
make at /private/tmp/condapkg/src/MWE.jl:9
unknown function (ip: 0x16d0480fb)
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:666
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:824
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
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]
exec_options at ./client.jl:296
_start at ./client.jl:531
jfptr__start_73909.1 at /Users/mhauru/.julia/juliaup/julia-1.11.7+0.aarch64.apple.darwin14/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: 10484352 (Pool: 10482312; Big: 2040); GC: 11
Segmentation fault: 11

Your system
macOS Sequoia 15.7 running on an M1 arm Mac.

julia> versioninfo()
Julia Version 1.11.7
Commit f2b3dbda30a (2025-09-08 12:10 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin24.0.0)
  CPU: 10 × Apple M1 Pro
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 8 virtual cores)
Environment:
  JULIA_FORMATTER_SO = /Users/mhauru/julia_formatter.so

julia> import Pkg, CondaPkg

julia> Pkg.status()
Project MWE v0.0.1
Status `/private/tmp/condapkg/Project.toml`
  [992eb4ea] CondaPkg v0.2.33
  [6099a3de] PythonCall v0.9.28

julia> CondaPkg.status()
CondaPkg Status /private/tmp/condapkg/CondaPkg.toml
Environment
  /private/tmp/condapkg/.CondaPkg/.pixi/envs/default
Packages
  python v3.10.18 (<3.11)
Pip Packages
  harmonic v1.3.0

Activity

  1. mhauru
    added
    bugSomething isn't working
    on Sep 29, 2025

  2. cjdoris commented on Oct 13, 2025

    @cjdoris
    cjdoris
    on Oct 13, 2025
    Member

    Yes your top level const hm is not allowed. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#Writing-packages-which-depend-on-PythonCall

  3. cjdoris
    closed this as completedon Oct 13, 2025
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