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RuntimeError when using cell2location on MacOS (M1)

See original GitHub issue


I follow the instructions from the [scvi-tools tutorial || Quick START TUTORIAL || Mapping human lymph node cell types to 10X Visium with Cell2location] and download all required package of cell2location successfully. (


However, I encountered the following error when running the code on Python.

RuntimeError: This version of jaxlib was built using AVX instructions, which your CPU and/or operating system do not support. You may be able work around this issue by building jaxlib from source. 

it happened when reading

import jax


I guess that it occurred because of M1, I tried installing jaxlib from source by the following link, ( , but failed. I am struggling for the issue and want to find an effective way to tackle with the problem.

do you have encountered such an issue? could you please give me some suggestions?

Await your reply appreciatively!! Thanks a lot!!

Issue Analytics

  • State:open
  • Created a year ago
  • Comments:11 (4 by maintainers)

github_iconTop GitHub Comments

sarahshuangcommented, Oct 14, 2022

Hi @adamgayoso , The problem is solved now, because I realize I didn’t install scvi-tools in the proper environment. Thanks a lot!!

adamgayosocommented, Oct 14, 2022

The issue is likely related to using a version of python that is being interpreted via rosetta istead of a native M1 version of python. Cell2location will only work in the latter case (e.g., download an m1 version of homebrew, use that to install miniforge and then use conda to install scvi-tools, and then pip install cell2location)

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