Open
Description
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: 13Your 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 coresAdditional context
- I suspect this might be related to Import Python submodules crashes Julia #291, but that issue lacked sufficient detail to know for sure.
- I am unable to replicate this problem with a few other related python packages (matplotlib, fooof, neurodsp) on M1.
- The issue is not present on x86-64.
- Running Python (from the
.CondaPkg/env) and importing MNE directly does not cause a segfault. - Installing MNE from pip instead of Conda resolves the issue.
I think there's some weird interaction between the Conda build, LLVM dylib and PythonCall.