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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 on M1 when loading Python Package MNE. #315

Open palday opened 1 year ago

palday commented 1 year ago

Affects: PythonCall

Describe the bug On M1, I can reliably induce a segfault when loading the Python package mne via PythonCall.

(@v1.9) pkg> activate --temp
  Activating new project at `/var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_TKDOuI`

julia> versioninfo()
Julia Version 1.9.0
Commit 8e630552924 (2023-05-07 11:25 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

(jl_TKDOuI) pkg> add CondaPkg PythonCall
   Resolving package versions...
    Updating `/private/var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_TKDOuI/Project.toml`
  [992eb4ea] + CondaPkg v0.2.18
  [6099a3de] + PythonCall v0.9.13
...

julia> using CondaPkg

(jl_TKDOuI) pkg> conda add mne

julia> using PythonCall

julia> pyimport("mne")

[16152] signal (11.2): Segmentation fault: 11
in expression starting at REPL[7]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /private/var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_TKDOuI/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
Allocations: 7988242 (Pool: 7981782; Big: 6460); GC: 13

Your system Please provide detailed information about your system:

julia> versioninfo()
Julia Version 1.9.0
Commit 8e630552924 (2023-05-07 11:25 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

Additional context

I think there's some weird interaction between the Conda build, LLVM dylib and PythonCall.

cjdoris commented 1 year ago

What's the output of the conda add mne line? I'm wondering if it's installing an incompatible version of libllvm.

palday commented 1 year ago

Here's the conda resolution

conda add mne ```julia (jl_i34IKD) pkg> conda add mne CondaPkg Found dependencies: /var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_i34IKD/CondaPkg.toml CondaPkg Found dependencies: /Users/palday/.julia/packages/PythonCall/1f5yE/CondaPkg.toml CondaPkg Resolving changes + mne + python CondaPkg Creating environment │ /Users/palday/.julia/artifacts/7cfea9db5b54ceb7d9109c8728914c9459303a75/bin/micromamba │ -r /Users/palday/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root │ create │ -y │ -p /var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_i34IKD/.CondaPkg/env │ --override-channels │ --no-channel-priority │ mne[version='*'] │ python[version='>=3.7,<4',channel='conda-forge',build='*cpython*'] └ -c conda-forge __ __ ______ ___ ____ _____ ___ / /_ ____ _ / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/ / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ / / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/ /_/ conda-forge/osx-arm64 6.4MB @ 4.0MB/s 1.8s conda-forge/noarch 12.4MB @ 3.9MB/s 3.5s Transaction Prefix: /private/var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_i34IKD/.CondaPkg/env Updating specs: - mne=* - conda-forge::python[version='>=3.7,<4',build=*cpython*] Package Version Build Channel Size ──────────────────────────────────────────────────────────────────────────────────────────────────────────── Install: ──────────────────────────────────────────────────────────────────────────────────────────────────────────── + aiohttp 3.8.4 py311he2be06e_0 conda-forge/osx-arm64 534kB + aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge/noarch 13kB + anyio 3.7.0 pyhd8ed1ab_1 conda-forge/noarch 97kB + aom 3.5.0 h7ea286d_0 conda-forge/osx-arm64 2MB + appnope 0.1.3 pyhd8ed1ab_0 conda-forge/noarch 8kB + argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge/noarch 16kB + argon2-cffi-bindings 21.2.0 py311he2be06e_3 conda-forge/osx-arm64 35kB + asttokens 2.2.1 pyhd8ed1ab_0 conda-forge/noarch 28kB + async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge/noarch 9kB + attrs 23.1.0 pyh71513ae_1 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pyhd8ed1ab_0 conda-forge/noarch 103kB + pygments 2.15.1 pyhd8ed1ab_0 conda-forge/noarch 841kB + pymatreader 0.0.30 pyhd8ed1ab_0 conda-forge/noarch 11kB + pyobjc-core 9.1.1 py311h490943d_0 conda-forge/osx-arm64 452kB + pyobjc-framework-cocoa 9.1.1 py311h490943d_0 conda-forge/osx-arm64 373kB + pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge/noarch 888kB + pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge/noarch 81kB + pyqt 5.15.7 py311h7203e35_3 conda-forge/osx-arm64 4MB + pyqt5-sip 12.11.0 py311ha397e9f_3 conda-forge/osx-arm64 71kB + pyqtgraph 0.13.3 pyhd8ed1ab_0 conda-forge/noarch 686kB + pyrsistent 0.19.3 py311he2be06e_0 conda-forge/osx-arm64 119kB + pysocks 1.7.1 pyha2e5f31_6 conda-forge/noarch 19kB + pytables 3.7.0 py311h887c5ef_3 conda-forge/osx-arm64 2MB + python 3.11.3 h1456518_0_cpython conda-forge/osx-arm64 Cached + python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch 246kB + python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge/noarch 226kB + python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge/noarch 13kB + python-picard 0.7 pyh8a188c0_0 conda-forge/noarch 17kB + python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge/noarch 143kB + python_abi 3.11 3_cp311 conda-forge/osx-arm64 6kB + pytz 2023.3 pyhd8ed1ab_0 conda-forge/noarch 187kB + pyvista 0.39.1 pyhd8ed1ab_0 conda-forge/noarch 1MB + pyvistaqt 0.10.0 pyhd8ed1ab_0 conda-forge/noarch 134kB + pywavelets 1.4.1 py311h4add359_0 conda-forge/osx-arm64 4MB + pyyaml 6.0 py311he2be06e_5 conda-forge/osx-arm64 193kB + pyzmq 25.1.0 py311hb1af645_0 conda-forge/osx-arm64 507kB + qdarkstyle 3.1 pyhd8ed1ab_0 conda-forge/noarch 601kB + qt-main 5.15.8 hcac2fde_13 conda-forge/osx-arm64 51MB + qtpy 2.3.1 pyhd8ed1ab_0 conda-forge/noarch 56kB + readline 8.2 h92ec313_1 conda-forge/osx-arm64 Cached + requests 2.31.0 pyhd8ed1ab_0 conda-forge/noarch 57kB + rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge/noarch 8kB + rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge/noarch 8kB + scikit-image 0.20.0 py311h4eec4a9_1 conda-forge/osx-arm64 10MB + scikit-learn 1.2.2 py311hf0b18b8_2 conda-forge/osx-arm64 8MB + scipy 1.10.1 py311h93d07a4_3 conda-forge/osx-arm64 15MB + scooby 0.7.2 pyhd8ed1ab_0 conda-forge/noarch 21kB + seaborn 0.12.2 hd8ed1ab_0 conda-forge/noarch 6kB + seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge/noarch 232kB + send2trash 1.8.2 pyhd1c38e8_0 conda-forge/noarch 23kB + setuptools 67.7.2 pyhd8ed1ab_0 conda-forge/noarch Cached + sip 6.7.9 py311ha891d26_0 conda-forge/osx-arm64 573kB + six 1.16.0 pyh6c4a22f_0 conda-forge/noarch 14kB + snappy 1.1.10 h17c5cce_0 conda-forge/osx-arm64 34kB + sniffio 1.3.0 pyhd8ed1ab_0 conda-forge/noarch 14kB + soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge/noarch 35kB + sqlite 3.42.0 h203b68d_0 conda-forge/osx-arm64 813kB + stack_data 0.6.2 pyhd8ed1ab_0 conda-forge/noarch 26kB + statsmodels 0.14.0 py311hb49d859_1 conda-forge/osx-arm64 12MB + svt-av1 1.4.1 h7ea286d_0 conda-forge/osx-arm64 1MB + tbb 2021.9.0 hffc8910_0 conda-forge/osx-arm64 121kB + tbb-devel 2021.9.0 h4f9cb39_0 conda-forge/osx-arm64 1MB + terminado 0.17.1 pyhd1c38e8_0 conda-forge/noarch 20kB + threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge/noarch 18kB + tifffile 2020.6.3 py_0 conda-forge/noarch 111kB + tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge/noarch 23kB + tk 8.6.12 he1e0b03_0 conda-forge/osx-arm64 3MB + toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch 18kB + tomli 2.0.1 pyhd8ed1ab_0 conda-forge/noarch 16kB + toolz 0.12.0 pyhd8ed1ab_0 conda-forge/noarch 49kB + tornado 6.3.2 py311heffc1b2_0 conda-forge/osx-arm64 841kB + tqdm 4.65.0 pyhd8ed1ab_1 conda-forge/noarch 88kB + traitlets 5.9.0 pyhd8ed1ab_0 conda-forge/noarch 98kB + typing-extensions 4.6.3 hd8ed1ab_0 conda-forge/noarch 10kB + typing_extensions 4.6.3 pyha770c72_0 conda-forge/noarch 35kB + typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge/noarch 14kB + tzdata 2023c h71feb2d_0 conda-forge/noarch Cached + urllib3 2.0.2 pyhd8ed1ab_0 conda-forge/noarch 98kB + utfcpp 3.2.3 hce30654_0 conda-forge/osx-arm64 12kB + vtk 9.2.6 qt_py311h600e403_201 conda-forge/osx-arm64 31MB + wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge/noarch 29kB + webencodings 0.5.1 py_1 conda-forge/noarch 12kB + websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge/noarch 45kB + wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached + widgetsnbextension 3.6.4 pyhd8ed1ab_0 conda-forge/noarch 645kB + wrapt 1.15.0 py311he2be06e_0 conda-forge/osx-arm64 59kB + wslink 1.10.2 pyhd8ed1ab_0 conda-forge/noarch 30kB + x264 1!164.3095 h57fd34a_2 conda-forge/osx-arm64 717kB + x265 3.5 hbc6ce65_3 conda-forge/osx-arm64 2MB + xlrd 2.0.1 pyhd8ed1ab_3 conda-forge/noarch 94kB + xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge/noarch 14kB + xorg-libxau 1.0.11 hb547adb_0 conda-forge/osx-arm64 14kB + xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge/osx-arm64 18kB + xz 5.2.6 h57fd34a_0 conda-forge/osx-arm64 Cached + yaml 0.2.5 h3422bc3_2 conda-forge/osx-arm64 88kB + yarl 1.9.2 py311heffc1b2_0 conda-forge/osx-arm64 100kB + zeromq 4.3.4 hbdafb3b_1 conda-forge/osx-arm64 318kB + zipp 3.15.0 pyhd8ed1ab_0 conda-forge/noarch 17kB + zlib 1.2.13 h03a7124_4 conda-forge/osx-arm64 Cached + zstd 1.5.2 hf913c23_6 conda-forge/osx-arm64 308kB Summary: Install: 326 packages Total download: 445MB ```

I had also suspected something with libllvm and it's actually installing two different versions:

  + libllvm14                            14.0.6  hd1a9a77_3               conda-forge/osx-arm64       21MB
  + libllvm15                            15.0.7  h62b9111_1               conda-forge/osx-arm64       22MB
palday commented 1 year ago

There seems to be a related but distinct problem when doing this on MacOS on Intel, xref https://discourse.julialang.org/t/using-pymne-crashes-julia/101799

cjdoris commented 1 year ago

Same version of libllvm14 as Julia.

Maybe the presence of libllvm15 as well causes issues. Why does that get installed?

Or maybe libcxx is incompatible with Julia. What is the result of Base.BinaryPlatforms.detect_libstdcxx_version()?

palday commented 1 year ago

Or maybe libcxx is incompatible with Julia. What is the result of Base.BinaryPlatforms.detect_libstdcxx_version()?

nothing

Since we've had a few Julia patch releases in the meantime, I also tried this on 1.9.2 and 1.10-beta1 and have the same problem.

palday commented 1 year ago

I wonder if this is related:

https://github.com/JuliaLang/julia/pull/49745