Bus Error 10 on Apple Silicon compiled for python 3.8

Describe the bug

When building from source for python3.8 on an Apple Silicon Mac, the build succeeds, but you can’t import sklearn in python

Steps/Code to Reproduce

Follow directions here: https://scikit-learn.org/stable/developers/advanced_installation.html

Install libomp via brew: brew install libomp

Set libomp flags per openmp_helpers.py:

export LDFLAGS="$LDFLAGS -Wl,-rpath,/opt/homebrew/lib/ -L/usr/local/opt/libomp/lib -lomp"

export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp"

Build succeeds but testing gives the error:

Successfully installed scikit-learn
Removed build tracker: '/private/var/folders/lp/ytqhb2lj0sxf89sdd16z61pc0000gn/T/pip-req-tracker-ja_3b66l'
(tfmac) bash-3.2$ python3 -c "import sklearn; sklearn.show_versions()"
Bus error: 10
(tfmac) bash-3.2$ 

Expected Results

python3 -c “import sklearn; sklearn.show_versions()” works correctly

Actual Results

Successfully installed scikit-learn
Removed build tracker: '/private/var/folders/lp/ytqhb2lj0sxf89sdd16z61pc0000gn/T/pip-req-tracker-ja_3b66l'
(tfmac) bash-3.2$ python3 -c "import sklearn; sklearn.show_versions()"
Bus error: 10
(tfmac) bash-3.2$ 

Versions

scipy.version.version ‘1.7.0.dev0+9b9f2e8’ numpy.version.version ‘1.18.5’ Full log of install process here: https://pastebin.com/4yXK6KHS

[iRonJ]

@iRonJ how did you install python3 with homebrew? With or without arch -x86_64?

Can you please report the output of the following command on your machine?

python3 -c "import platform; print(platform.platform())"

(tfmac) bash-3.2$ python3 -c “import platform; print(platform.platform())” macOS-11.1-arm64-arm-64bit

[ogrisel]

I opened https://github.com/scikit-learn/scikit-learn/issues/19137 to track progress for this. Let’s close this issue to keep things simple.