"Illegal Instruction" Error When Running Python Script in Docker Container

Describe the Bug

When running a Python script (test.py) within a Docker container built from homebrew/brew:latest and using Python 3.10 installed via Homebrew, the script exits with an "Illegal instruction" error. This issue occurs when attempting to use the cellxgene_census library version 1.11.1, installed via pip. The exact cause of the illegal instruction is unclear, as the script does not successfully execute to completion.

To Reproduce

Steps to reproduce the behavior:

test.py content;

import cellxgene_census

cellxgene_census.download_source_h5ad("a5d5c529-8a1f-40b5-bda3-35208970070d",
                                      to_path="./a5d5c529-8a1f-40b5-bda3-35208970070d.h5ad")

Create a Dockerfile with the following content:

FROM homebrew/brew:latest

RUN brew install python@3.10

ENV PATH="/home/linuxbrew/.linuxbrew/opt/python@3.10/bin:$PATH"

RUN python3.10 -m pip install --upgrade pip

RUN python3.10 -m pip install cellxgene_census==1.11.1

WORKDIR /home/app

COPY test.py ./

CMD ["tail", "-f", "/dev/null"]

Build the Docker container:

docker buildx build --platform linux/arm64/v8 -t cellxgene_census_bug . --load

Run the container:
```
docker run -it cellxgene_census_bug
```
Attempt to execute test.py within the container:
```
python3.10 test.py
```

Expected Behavior

The script test.py should execute to completion without encountering an "Illegal instruction" error. Expected behavior depends on the script's functionality but generally includes successful completion of tasks without crashing.

Environment

Host:

Machine: arm64
OS: macOS 14.3.1
Docker version: Docker version 25.0.3
Software versions:

Container:

Machine: x86_64
OS: Ubuntu 22.04.3 LTS
Software versions:
- Python version: 3.10 (as installed via Homebrew in the Docker container)
- Pip packages:
  
  Click to expand

Package	Version
aiobotocore	2.12.1
aiohttp	3.9.3
aioitertools	0.11.0
aiosignal	1.3.1
anndata	0.10.6
array_api_compat	1.4.1
async-timeout	4.0.3
attrs	23.2.0
botocore	1.34.51
cellxgene-census	1.11.1
certifi	2024.2.2
charset-normalizer	3.3.2
contourpy	1.2.0
cycler	0.12.1
exceptiongroup	1.2.0
fonttools	4.50.0
frozenlist	1.4.1
fsspec	2024.3.0
h5py	3.10.0
idna	3.6
jmespath	1.0.1
joblib	1.3.2
kiwisolver	1.4.5
llvmlite	0.42.0
matplotlib	3.8.3
multidict	6.0.5
natsort	8.4.0
networkx	3.2.1
numba	0.59.0
numpy	1.26.4
packaging	24.0
pandas	2.2.1
patsy	0.5.6
pillow	10.2.0
pip	24.0
pyarrow	15.0.1
pyarrow-hotfix	0.6
pynndescent	0.5.11
pyparsing	3.1.2
python-dateutil	2.9.0.post0
pytz	2024.1
requests	2.31.0
s3fs	2024.3.0
scanpy	1.9.8
scikit-learn	1.4.1.post1
scipy	1.12.0
seaborn	0.13.2
session-info	1.0.0
setuptools	68.2.2
six	1.16.0
somacore	1.0.8
statsmodels	0.14.1
stdlib-list	0.10.0
threadpoolctl	3.3.0
tiledb	0.26.3
tiledbsoma	1.8.0
tqdm	4.66.2
typing_extensions	4.10.0
tzdata	2024.1
umap-learn	0.5.5
urllib3	2.0.7
wheel	0.41.3
wrapt	1.16.0
yarl	1.9.4

Additional Context

The issue seems related to executing Python code within the Docker container environment set up with Homebrew's Python 3.10. Identifying the instruction causing the illegal instruction error or a more specific scenario within test.py that triggers the error would require further debugging tools not accessible due to the nature of the crash.

chanzuckerberg / cellxgene-census