Failed install M1/M2 extra steps

[zhywang17]

Hi Brady,
I was trying to follow the instructions for M1/M2 Mac extra steps, and when I try to run
./python3.10 -m pip install MDAnalysis --cache-dir ~/MDAnalysis-wheel this error came:

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/brecht/dev/build_darwin/deps/Release/sqlite/include -I/Users/brecht/dev/build_darwin/deps/Release/bzip2/include -I/Users/brecht/dev/build_darwin/deps/Release/lzma/include -I/Users/brecht/dev/build_darwin/deps/Release/zlib/include -mmacosx-version-min=11.00 -arch arm64 -mmacosx-version-min=11.00 -arch arm64 -I/Applications/Blender.app/Contents/Resources/3.5/python/include/python3.10 -c Bio/Align/_aligners.c -o build/temp.macosx-11.00-arm64-cpython-310/Bio/Align/_aligners.o
      Bio/Align/_aligners.c:11:10: fatal error: 'Python.h' file not found
      #include "Python.h"
               ^~~~~~~~~~
      1 error generated.
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for biopython

Would you please help me to check this out?
Thanks

[BradyAJohnston]

It seems that Blender is unable to find the pre-built .whl for MDAnalysis.

Are you able to show the location and the contents of ~/MDAnalysis-wheel? Might be that the previous steps failed and the binaries weren't compiled properly

[zhywang17]

Here it is :

(base) zhenyuwang@Zhenyu 3.5 % ls ~/MDAnalysis-wheel 
GridDataFormats-1.0.1-py3-none-any.whl			mrcfile-1.4.3-py2.py3-none-any.whl
MDAnalysis-2.2.0-cp310-cp310-macosx_10_9_x86_64.whl	msgpack-1.0.5-cp310-cp310-macosx_10_9_x86_64.whl
Pillow-9.5.0-cp310-cp310-macosx_10_10_x86_64.whl	networkx-3.1-py3-none-any.whl
biopython-1.81-cp310-cp310-macosx_10_9_x86_64.whl	numpy-1.24.3-cp310-cp310-macosx_10_9_x86_64.whl
contourpy-1.0.7-cp310-cp310-macosx_10_9_x86_64.whl	packaging-23.1-py3-none-any.whl
cycler-0.11.0-py3-none-any.whl				pyparsing-3.0.9-py3-none-any.whl
fasteners-0.18-py3-none-any.whl				python_dateutil-2.8.2-py2.py3-none-any.whl
fonttools-4.39.3-py3-none-any.whl			scipy-1.10.1-cp310-cp310-macosx_10_9_x86_64.whl
gsd-2.8.1-cp310-cp310-macosx_10_9_x86_64.whl		selfcheck
http							six-1.16.0-py2.py3-none-any.whl
joblib-1.2.0-py3-none-any.whl				threadpoolctl-3.1.0-py3-none-any.whl
kiwisolver-1.4.4-cp310-cp310-macosx_10_9_x86_64.whl	tqdm-4.65.0-py3-none-any.whl
matplotlib-3.7.1-cp310-cp310-macosx_10_12_x86_64.whl	wheels
mmtf_python-1.1.3-py2.py3-none-any.whl

Thanks for your kind reply!

[BradyAJohnston]

nothing seems obviously out of the ordinary. I would maybe suggest clearing out that file and trying the build & install again

[zhywang17]

I tried several time and all failed, I searched some case, it seems like gcc cannot locate python.h, maybe I should add the python to the gcclist somewhere, I need to find out. Anyway will keep trying, thanks!

[BradyAJohnston]

The error that you are getting is indeed an error with GCC and the python that ships with Blender. Blender is unable to install python packages into the python version that ships with Blender, as it doesn't have the required python.h and associated files that are required for compiling packages.

To get around this, the installation instructions tell you to pre-compile the MDAnalysis package with a different version of python and then install the pre-compiled version into the version that ships with Blender. Without more detailed error messages, it seems like the pre-compiled version is falling to be installed, Blender is then attempting to compile it's own version which then also fails. I am unsure why.

This thread (#108) is discussing exactly this error. There are some other solutions which are provided, perhaps try some of those.

[zhywang17]

I really appreciate your effort to help around! Now I can use a Blender on Windows with MN installed to read the file and then send the project to Blender on Mac lol, works well for me, maybe I would just looking forward to your upcoming version that officially settle this issue

[YaoYinYing]

Hi @zhywang17 I guess you are currently using a rosetta2-mediated x86-64 conda and python. To fix this ,you need to re-create a ARM based conda env for this wheel building.

Basicly, try this CONDA_SUBDIR=osx-arm64 conda create -n MN_PY310 python=3.10 -y for the armed python env.

[zhywang17]

My environment is exactly like what you said but the solution is not work for me, maybe I should reinstall blender?

[YaoYinYing]

Yes you'd better do a completely clean reinstallation of blender and MN. Just make sure EVERYTHING is ARMed.

[YaoYinYing]

the solution is not work for

And if you can share some error logs this might be more clear for me to do this help