Scipy Import Error with a 'Symbol not found: __gfortran_stop_numeric_f08' - matlab

Question

I am getting an error when trying to import scipy in my Python venv. The full terminal commands/outputs are below. You can see that the scipy package was already installed in another terminal session within this venv. The error appears to be with some gfortran data type and the system looking for it my Matlab directory. I don't know why this would be or how to fix it. I am on a Mac. I tried these same commands on my Linux machine (which also has Matlab installed) and it worked fine. Thanks in advance.
mshafer#Michaels-MacBook-Pro-2 ~ % python3.9 -m venv /Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv
mshafer#Michaels-MacBook-Pro-2 ~ % source /Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/bin/activate
(uavrt_venv) mshafer#Michaels-MacBook-Pro-2 ~ % python3 -m pip install scipy
Requirement already satisfied: scipy in ./Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages (1.9.3)
Requirement already satisfied: numpy<1.26.0,>=1.18.5 in ./Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages (from scipy) (1.23.5)
(uavrt_venv) mshafer#Michaels-MacBook-Pro-2 ~ % python3
Python 3.9.15 (main, Oct 11 2022, 22:27:25)
[Clang 14.0.0 (clang-1400.0.29.102)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from scipy import interpolate
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/__init__.py", line 211, in __getattr__
return _importlib.import_module(f'scipy.{name}')
File "/usr/local/Cellar/python#3.9/3.9.15/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/interpolate/__init__.py", line 166, in <module>
from ._interpolate import *
File "/Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/interpolate/_interpolate.py", line 11, in <module>
import scipy.special as spec
File "/Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/special/__init__.py", line 649, in <module>
from . import _ufuncs
ImportError: dlopen(/Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/special/_ufuncs.cpython-39-darwin.so, 0x0002): Symbol not found: __gfortran_stop_numeric_f08
Referenced from: /Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/special/_ufuncs.cpython-39-darwin.so
Expected in: /Applications/MATLAB_R2022a.app/sys/os/maci64/libgfortran.3.dylib

Answer 1

This error is arising because an incorrect libgfortran is being loaded. scipy is distributed with a vendored version of libgfortran. However, for some reason a libgfortran sited in a Matlab directory is being loaded. These kinds of problems can be got to the bottom of, but it can be complicated as there are various ways that shared libraries can be loaded, and the user can change how that occurs as well.
What is the output of otool -L /Users/mshafer/Desktop/PLAYGROUND/CODE_TOEPLITZ/uavrt_venv/lib/python3.9/site-packages/scipy/special/_ufuncs.cpython-39-darwin.so?
I would expect this to be something like:
scipy/special/_ufuncs.cpython-310-darwin.so:
#loader_path/../.dylibs/libopenblasp-r0.3.20.dylib (compatibility version 0.0.0, current version 0.0.0)
#loader_path/../.dylibs/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1311.0.0)
This means that the dlopen call should go up a directory, down into .dylibs (which is where the vendored libraries are placed), then load libgfortran from there.
Have you set the LD_LIBRARY_PATH variable?
How was Python installed?