docker run error: Importing the numpy C-extensions failed.

[carrisonj]

docker run cli as follow:
docker run -it --volume $HOME/af_input:/root/af_input --volume $HOME/af_output:/root/af_output --volume $MODEL_PARAMETERS_DIR:/root/models --volume $DB_DIR:/root/public_databases --gpus all alphafold3 python3 run_alphafold.py --json_path=/root/af_input/fold_input.json --model_dir=/root/models --output_dir=/root/af_output

i've add lines below to run_alphafold.py,
import os
os.environ['OPENBLAS_NUM_THREADS'] = '1'
before
import numpy as np

still got same error. pls help me, thx a lot.

[carrisonj]

OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/init.py", line 23, in
from . import multiarray
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/multiarray.py", line 10, in
from . import overrides
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/overrides.py", line 8, in
from numpy._core._multiarray_umath import (
ImportError: PyCapsule_Import could not import module "datetime"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/init.py", line 114, in
from numpy.config import show as show_config
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/config.py", line 4, in
from numpy._core._multiarray_umath import (
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/_core/init.py", line 49, in
raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

• The Python version is: Python3.11 from "/alphafold3_venv/bin/python3"
• The NumPy version is: "2.1.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: PyCapsule_Import could not import module "datetime"

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/app/alphafold/run_alphafold.py", line 39, in
from alphafold3.common import folding_input
File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/common/folding_input.py", line 23, in
from alphafold3 import structure
File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/init.py", line 14, in
from alphafold3.structure.bioassemblies import BioassemblyData
File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/bioassemblies.py", line 18, in
from alphafold3.structure import mmcif
File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/structure/mmcif.py", line 29, in
import numpy as np
File "/alphafold3_venv/lib/python3.11/site-packages/numpy/init.py", line 119, in
raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
its source directory; please exit the numpy source tree, and relaunch
your python interpreter from there.

[Augustin-Zidek]

This is a duplicate of #83, let's continue the discussion there.