Acces violation on Windows when importing some scipy modules

[schtandard]

If I create a folder containing the file test_foo.py with the following content

from scipy.special import ellipk
from scipy.optimize import root_scalar

def test_foo():
    assert 1 == 1

and run pytest in that folder twice, I get the following output:

(test) C:\pytest_sandbox>pytest
================================================= test session starts =================================================
platform win32 -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.0
rootdir: C:\pytest_sandbox
collected 1 item

test_foo.py .                                                                                                    [100%]

================================================== 1 passed in 1.08s ==================================================

(test) C:\pytest_sandbox>pytest
================================================= test session starts =================================================
platform win32 -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.0
rootdir: C:\pytest_sandbox
collecting ... Windows fatal exception: access violation

Current thread 0x00000a20 (most recent call first):
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1053 in create_module
  File "<frozen importlib._bootstrap>", line 816 in module_from_spec
  File "<frozen importlib._bootstrap>", line 924 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1434 in _handle_fromlist
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_duccfft\basic.py", line 6 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_duccfft\__init__.py", line 3 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_helper.py", line 4 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\__init__.py", line 92 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1061 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\linalg\interpolative.py", line 360 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_remove_redundancy.py", line 9 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog_util.py", line 9 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog_ip.py", line 27 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog.py", line 22 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\__init__.py", line 435 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\pytest_sandbox\test_foo.py", line 2 in <module>
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\_pytest\assertion\rewrite.py", line 188 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked

Current thread's C stack trace (most recent call first):
  <cannot get C stack on this system>
Windows fatal exception: access violation

Current thread 0x00000a20 (most recent call first):
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1053 in create_module
  File "<frozen importlib._bootstrap>", line 816 in module_from_spec
  File "<frozen importlib._bootstrap>", line 924 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1434 in _handle_fromlist
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_duccfft\basic.py", line 6 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_duccfft\__init__.py", line 3 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\_helper.py", line 4 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\fft\__init__.py", line 92 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 1061 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\linalg\interpolative.py", line 360 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_remove_redundancy.py", line 9 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog_util.py", line 9 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog_ip.py", line 27 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\_linprog.py", line 22 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\scipy\optimize\__init__.py", line 435 in <module>
  File "<frozen importlib._bootstrap>", line 491 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 759 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
  File "C:\pytest_sandbox\test_foo.py", line 2 in <module>
  File "C:\Users\wilde02\AppData\Local\miniforge3\envs\test\Lib\site-packages\_pytest\assertion\rewrite.py", line 188 in exec_module
  File "<frozen importlib._bootstrap>", line 938 in _load_unlocked

Current thread's C stack trace (most recent call first):
  <cannot get C stack on this system>
collected 1 item

test_foo.py .                                                                                                    [100%]

================================================== 1 passed in 0.98s ==================================================

That is, the first time it runs without issues, the second time (and all subsequent times) I get an access violation, though the test still passes just fine.

• If I delete either of the folders .pytest_cache and __pycache__ that are created during the run, the error disappears again (for one run).
• If I remove either of the two scipy imports, the error disappears immediately.

I have to say that I don't quite understand what's going on here. If you need any more information or debugging done, I'm happy to provide that.

Environment

I am on Windows 11 using a conda environment. pip list reveals the following versions.

(test) C:\pytest_sandbox>pip list
Package           Version
----------------- -------
colorama          0.4.6
exceptiongroup    1.3.1
iniconfig         2.3.0
numpy             2.5.3
packaging         26.3
pip               26.2.1
pluggy            1.6.0
Pygments          2.21.0
pytest            9.1.1
scipy             1.18.1
tomli             2.4.1
typing_extensions 4.16.0

• a detailed description of the bug or problem you are having
• output of pip list from the virtual environment you are using
• pytest and operating system versions
• minimal example if possible

[RonnyPfannschmidt]

this tends to be typical sign of a memory layout triggered c level bug (not related to pytest

try if things get more stable with --assert=plain - but you will need to run this with a debugger to see where it kills itself

if you have access to an agent let it try to do the c level error finding and also try with debug builds

as those are anaconda builds this may also be a slight packaging issue - which needs knowledge for that

what i cna say with confidence is that the segfault is not from pytest

[RonnyPfannschmidt]

a key detail is that the c stacks are missing - so we have no idea where exactly it goes off the rails

[schtandard]

Hmm, ok, thanks for the pointers. Unfortunately, I do not have access to an agent and neither do I know how to run this with a debugger (a C debugger, I assume). Is there some documentation that I can follow? Or is this impractical if I don't already have a C development environment set up?

[RonnyPfannschmidt]

as you are usin conda - i presume that should enable you to get debug tools

i am however not familiar with conda and cant give recommendations