Segmentation Fault(Mac OS BigSur, Python 3.9 mini-forge dist. )

[yak-liu-NEU]

Hello,

I get this segmentation fault message when I was trying to run my code with:
kernprof -v -l
Then I got:
[1] 15207 segmentation fault kernprof -l -v mytest.py

I tried the same code and command on another windows and ubuntu machine and they all work like normal.
Does anyone know how to solve this problem? Thanks!

[Erotemic]

I'm not sure on this issue. Have you tried running with valgrind to see where the segfault is happening?

[yak-liu-NEU]

I'm not sure on this issue. Have you tried running with valgrind to see where the segfault is happening?

I follow the instruction on https://github.com/LouisBrunner/valgrind-macos/tree/feature/macos_11pp

It failed at compiling.

Last 15 lines from /Users/liu.yak/Library/Logs/Homebrew/valgrind/03.make: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/mach/i386/thread_status.h:254:9: error: unknown type name '_STRUCT_X86_DEBUG_STATE64' typedef _STRUCT_X86_DEBUG_STATE64 x86_debug_state64_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/mach/i386/thread_status.h:260:9: error: unknown type name '_STRUCT_X86_PAGEIN_STATE' typedef _STRUCT_X86_PAGEIN_STATE x86_pagein_state_t; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/mach/i386/thread_status.h:266:9: error: unknown type name '_STRUCT_X86_INSTRUCTION_STATE' typedef _STRUCT_X86_INSTRUCTION_STATE x86_instruction_state_t; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: *** [fixup_macho_loadcmds] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2

I have upgraded my CommandLineTools to the latest version.
Seems like the current macOS compatibility build is still so experimental. Don't know how to solve this.

[seanlaw]

@yak-liu-NEU I tried this on my OSX ARM64 running Python 3.9:

1. Fresh install of miniconda3
2. conda install -y -c conda-forge scikit-build cython
3. git clone https://github.com/pyutils/line_profiler.git
4. cd line_profiler && python setup.py install

This seemed to solve the problem for me and I hope that it'll work for you.

[tbenthompson]

Just a heads-up that I'm still seeing this issue. Compiling from source as @seanlaw suggested works fine so it seems like all that's needed for a fix is probably some small tweaks to the packaging pipeline.

[user799595]

I tried @seanlaw's suggestion but I'm getting an error:

ImportError: The line_profiler._line_profiler c-extension is not importable. Has it been compiled? Underlying error is ex=ModuleNotFoundError("No module named 'line_profiler._line_profiler'")

Same results with

 pip install git+https://github.com/pyutils/line_profiler.git

I had to run this before setup.py:

cmake --build .

[SimonCW]

Also didn't work for me. I get

ImportError: The line_profiler._line_profiler c-extension is not importable. Has it been compiled? Underlying error is ex=ImportError("dlopen(/opt/homebrew/Caskroom/mambaforge/base/envs/persrec/lib/python3.9/site-packages/line_profiler-3.5.2-py3.9-macosx-11.0-arm64.egg/line_profiler/_line_profiler.cpython-39-darwin.so, 0x0002): tried: '/opt/homebrew/Caskroom/mambaforge/base/envs/persrec/lib/python3.9/site-packages/line_profiler-3.5.2-py3.9-macosx-11.0-arm64.egg/line_profiler/_line_profiler.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))")

Which is a bit weird since I'm definitely on M1:

❯ uname -m
arm64

Update:

Never mind, I had the ARCHFLAGS environment variable set to x86 ... I don't know why.

❯ printenv | grep -i arch
ARCHFLAGS=-arch x86_64

Unsetting and re-compiling worked