Segmentation fault on import of scipy.integrate on Apple M1 ARM silicon

SciPy can be installed under native Python 3.9.1 on an Apple M1 system running macOS Big Sur 11.1 using these instructions. However, importing scipy.integrate gives a segmentation fault.

Reproducing code example:

$ brew install python@3.9
$ brew install openblas
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install cython --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install numpy --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install pandas --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install pybind11 --no-use-pep517
$ OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install scipy --no-use-pep517
$ python3
Python 3.9.1 (default, Dec 29 2020, 02:24:05) 
[Clang 12.0.0 (clang-1200.0.32.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.integrate

Error message:

I’m not sure how to install gdb on M1 – I’m not sure it’s possible yet. If there is another tool I can use to get a stack trace, please advise. Here is the detail on where in the import process the error occurs, via the last bit of verbose output achieved via python3 -vv:

...
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/quadpack.cpython-39-darwin.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/quadpack.abi3.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/quadpack.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/quadpack.py
# /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/__pycache__/quadpack.cpython-39.pyc matches /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/quadpack.py
# code object from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/__pycache__/quadpack.cpython-39.pyc'
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_quadpack.cpython-39-darwin.so
# extension module 'scipy.integrate._quadpack' loaded from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_quadpack.cpython-39-darwin.so'
# extension module 'scipy.integrate._quadpack' executed from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_quadpack.cpython-39-darwin.so'
import 'scipy.integrate._quadpack' # <_frozen_importlib_external.ExtensionFileLoader object at 0x116030880>
import 'scipy.integrate.quadpack' # <_frozen_importlib_external.SourceFileLoader object at 0x1151608e0>
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_ode.cpython-39-darwin.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_ode.abi3.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_ode.so
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_ode.py
# /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/__pycache__/_ode.cpython-39.pyc matches /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_ode.py
# code object from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/__pycache__/_ode.cpython-39.pyc'
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/vode.cpython-39-darwin.so
# extension module 'scipy.integrate.vode' loaded from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/vode.cpython-39-darwin.so'
# extension module 'scipy.integrate.vode' executed from '/opt/homebrew/lib/python3.9/site-packages/scipy/integrate/vode.cpython-39-darwin.so'
import 'scipy.integrate.vode' # <_frozen_importlib_external.ExtensionFileLoader object at 0x116041580>
# trying /opt/homebrew/lib/python3.9/site-packages/scipy/integrate/_dop.cpython-39-darwin.so
zsh: segmentation fault  /opt/homebrew/bin/python3 -vv -c "import scipy.integrate"

Scipy/Numpy/Python version information:

>> import sys, scipy, numpy; print(scipy.__version__, numpy.__version__, sys.version_info)
1.6.0 1.19.5 sys.version_info(major=3, minor=9, micro=1, releaselevel='final', serial=0)

[judahrand]

I believe these were the same changes as made in numpy-wheels: https://github.com/MacPython/scipy-wheels/pull/123

[isuruf]

There was one test in numpy that was marked as xfail which is the reason for the RuntimeWarnings here. https://github.com/numpy/numpy/issues/18555