BUG: Windows fatal exception code 0xc06d007e

[Rational-IM]

Describe the issue:

When running a very simple code (see below; from a previously similar issue reported), I receive the following error:

Windows fatal exception: code 0xc06d007e

After that, the kernel is restart (using Spyder 5.5.1; but it happens with other versions of Spyder too, like 5.5.0, that works fine). I tried installing Spyder + numpy in multiple ways - with Anaconda, with miniconda and conda-standalone. Nothing worked.

Reproduce the code example:

import numpy as np

a = np.array([
    [1., 0., 0.],
    [0., 1., 0.],
    [0, 0., 1.]
])

b = np.array([
    [1., 0., 0.],
    [0., 1., 0.],
    [0, 0., 1.]
])

print(np.dot(a, b))

Error message:

Windows fatal exception: code 0xc06d007e

Main thread:
Current thread 0x00008e44 (most recent call first):
  File "c:\users\danil\onedrive\python_projects\canvas\canvas 30.py", line 23 in <module>
  File "C:\Users\danil\miniconda3\envs\spyder-5.5.1\Lib\site-packages\spyder_kernels\py3compat.py", line 356 in compat_exec
  File "C:\Users\danil\miniconda3\envs\spyder-5.5.1\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 473 in exec_code
  File "C:\Users\danil\miniconda3\envs\spyder-5.5.1\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 615 in _exec_file
  File "C:\Users\danil\miniconda3\envs\spyder-5.5.1\Lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 528 in runfile
  File "C:\Users\danil\AppData\Local\Temp\ipykernel_41640\313744497.py", line 1 in <module>

Restarting kernel...

Python and NumPy Versions:

The attached file is an export of my environment: python 3.12.1 and numpy 1.26.4

Runtime Environment:

Not sure if this is the requested outcome (as there is also an error) but here it is:

runfile('C:/Users/danil/OneDrive/Python_projects/Canvas/untitled0.py', wdir='C:/Users/danil/OneDrive/Python_projects/Canvas', current_namespace=True)
Traceback (most recent call last):

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\spyder_kernels\py3compat.py:356 in compat_exec
exec(code, globals, locals)

File c:\users\danil\onedrive\python_projects\canvas\untitled0.py:9
print(numpy.show_runtime())

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\numpy\lib\utils.py:66 in show_runtime
config_found.extend(threadpool_info())

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\threadpoolctl.py:415 in threadpool_info
return ThreadpoolController().info()

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\threadpoolctl.py:677 in info
return [lib_controller.info() for lib_controller in self.lib_controllers]

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\threadpoolctl.py:124 in info
"num_threads": self.num_threads,

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\threadpoolctl.py:139 in num_threads
return self.get_num_threads()

File ~\miniconda3\envs\spyder-5.5.1\Lib\site-packages\threadpoolctl.py:302 in get_num_threads
return get_func()

OSError: [WinError -1066598274] Windows Error 0xc06d007e

Context for the issue:

I use numpy in a code I run daily that is crucial for my business.

[Rational-IM]

Here is the environment export (couldn't attach as a .yml file):

name: spyder-5.5.1
channels:

• conda-forge
• defaults
  dependencies:
• alabaster=0.7.16=pyhd8ed1ab_0
• arrow=1.3.0=pyhd8ed1ab_0
• astroid=3.0.3=py312h2e8e312_0
• asttokens=2.4.1=pyhd8ed1ab_0
• atomicwrites=1.4.1=pyhd8ed1ab_0
• attrs=23.2.0=pyh71513ae_0
• autopep8=2.0.4=pyhd8ed1ab_0
• babel=2.14.0=pyhd8ed1ab_0
• bcrypt=4.1.2=py312hfccd98a_0
• beautifulsoup4=4.12.3=pyha770c72_0
• binaryornot=0.4.4=py_1
• black=24.1.1=py312h2e8e312_0
• bleach=6.1.0=pyhd8ed1ab_0
• brotli-python=1.1.0=py312h53d5487_1
• bzip2=1.0.8=hcfcfb64_5
• ca-certificates=2024.2.2=h56e8100_0
• certifi=2024.2.2=pyhd8ed1ab_0
• cffi=1.16.0=py312he70551f_0
• chardet=5.2.0=py312h2e8e312_1
• charset-normalizer=3.3.2=pyhd8ed1ab_0
• click=8.1.7=win_pyh7428d3b_0
• cloudpickle=3.0.0=pyhd8ed1ab_0
• colorama=0.4.6=pyhd8ed1ab_0
• comm=0.2.1=pyhd8ed1ab_0
• cookiecutter=2.5.0=pyhca7485f_0
• cryptography=42.0.2=py312he4c2ea2_0
• debugpy=1.8.1=py312h53d5487_0
• decorator=5.1.1=pyhd8ed1ab_0
• defusedxml=0.7.1=pyhd8ed1ab_0
• diff-match-patch=20230430=pyhd8ed1ab_0
• dill=0.3.8=pyhd8ed1ab_0
• docstring-to-markdown=0.13=pyhd8ed1ab_0
• docutils=0.20.1=py312h2e8e312_3
• entrypoints=0.4=pyhd8ed1ab_0
• exceptiongroup=1.2.0=pyhd8ed1ab_2
• executing=2.0.1=pyhd8ed1ab_0
• flake8=7.0.0=pyhd8ed1ab_0
• gettext=0.21.1=h5728263_0
• glib=2.78.3=h12be248_0
• glib-tools=2.78.3=h12be248_0
• gst-plugins-base=1.22.9=h001b923_0
• gstreamer=1.22.9=hb4038d2_0
• icu=73.2=h63175ca_0
• idna=3.6=pyhd8ed1ab_0
• imagesize=1.4.1=pyhd8ed1ab_0
• importlib-metadata=7.0.1=pyha770c72_0
• importlib_metadata=7.0.1=hd8ed1ab_0
• importlib_resources=6.1.1=pyhd8ed1ab_0
• inflection=0.5.1=pyh9f0ad1d_0
• intel-openmp=2024.0.0=h57928b3_49841
• intervaltree=3.1.0=pyhd8ed1ab_1
• ipykernel=6.29.2=pyha63f2e9_0
• ipython=8.21.0=pyh7428d3b_0
• isort=5.13.2=pyhd8ed1ab_0
• jaraco.classes=3.3.1=pyhd8ed1ab_0
• jedi=0.19.1=pyhd8ed1ab_0
• jellyfish=1.0.3=py312hfccd98a_0
• jinja2=3.1.3=pyhd8ed1ab_0
• jsonschema=4.21.1=pyhd8ed1ab_0
• jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
• jupyter_client=8.6.0=pyhd8ed1ab_0
• jupyter_core=5.7.1=py312h2e8e312_0
• jupyterlab_pygments=0.3.0=pyhd8ed1ab_1
• keyring=24.3.0=py312h2e8e312_0
• krb5=1.21.2=heb0366b_0
• libblas=3.9.0=21_win64_mkl
• libcblas=3.9.0=21_win64_mkl
• libclang=15.0.7=default_hde6756a_4
• libclang13=15.0.7=default_h85b4d89_4
• libexpat=2.5.0=h63175ca_1
• libffi=3.4.4=hd77b12b_0
• libglib=2.78.3=h16e383f_0
• libhwloc=2.9.3=default_haede6df_1009
• libiconv=1.17=hcfcfb64_2
• libjpeg-turbo=3.0.0=hcfcfb64_1
• liblapack=3.9.0=21_win64_mkl
• libogg=1.3.5=h2bbff1b_1
• libpng=1.6.42=h19919ed_0
• libsodium=1.0.18=h8d14728_1
• libspatialindex=1.9.3=h39d44d4_4
• libsqlite=3.45.1=hcfcfb64_0
• libvorbis=1.3.7=h0e60522_0
• libxml2=2.12.5=hc3477c8_0
• libzlib=1.2.13=hcfcfb64_5
• markdown-it-py=3.0.0=pyhd8ed1ab_0
• markupsafe=2.1.5=py312he70551f_0
• matplotlib-inline=0.1.6=pyhd8ed1ab_0
• mccabe=0.7.0=pyhd8ed1ab_0
• mdurl=0.1.2=pyhd8ed1ab_0
• mistune=3.0.2=pyhd8ed1ab_0
• mkl=2024.0.0=h66d3029_49657
• more-itertools=10.2.0=pyhd8ed1ab_0
• mypy_extensions=1.0.0=pyha770c72_0
• nbclient=0.8.0=pyhd8ed1ab_0
• nbconvert=7.16.0=pyhd8ed1ab_0
• nbconvert-core=7.16.0=pyhd8ed1ab_0
• nbconvert-pandoc=7.16.0=pyhd8ed1ab_0
• nbformat=5.9.2=pyhd8ed1ab_0
• nest-asyncio=1.6.0=pyhd8ed1ab_0
• numpy=1.26.4=py312h8753938_0
• numpydoc=1.6.0=pyhd8ed1ab_0
• openssl=3.2.1=hcfcfb64_0
• packaging=23.2=pyhd8ed1ab_0
• pandoc=3.1.11.1=h57928b3_0
• pandocfilters=1.5.0=pyhd8ed1ab_0
• paramiko=3.4.0=pyhd8ed1ab_0
• parso=0.8.3=pyhd8ed1ab_0
• pathspec=0.12.1=pyhd8ed1ab_0
• pcre2=10.42=h17e33f8_0
• pexpect=4.9.0=pyhd8ed1ab_0
• pickleshare=0.7.5=py_1003
• pip=24.0=pyhd8ed1ab_0
• pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
• platformdirs=4.2.0=pyhd8ed1ab_0
• pluggy=1.4.0=pyhd8ed1ab_0
• ply=3.11=py_1
• prompt-toolkit=3.0.43=py312haa95532_0
• psutil=5.9.8=py312he70551f_0
• pthreads-win32=2.9.1=hfa6e2cd_3
• ptyprocess=0.7.0=pyhd3deb0d_0
• pure_eval=0.2.2=pyhd8ed1ab_0
• pycodestyle=2.11.1=pyhd8ed1ab_0
• pycparser=2.21=pyhd8ed1ab_0
• pydocstyle=6.3.0=pyhd8ed1ab_0
• pyflakes=3.2.0=pyhd8ed1ab_0
• pygments=2.17.2=pyhd8ed1ab_0
• pylint=3.0.3=pyhd8ed1ab_0
• pylint-venv=3.0.3=pyhd8ed1ab_0
• pyls-spyder=0.4.0=pyhd8ed1ab_0
• pynacl=1.5.0=py312hc560f31_3
• pyqt=5.15.10=py312hd77b12b_0
• pyqt5-sip=12.13.0=py312h2bbff1b_0
• pyqtwebengine=5.15.10=py312hd77b12b_0
• pysocks=1.7.1=pyh0701188_6
• python=3.12.1=h2628c8c_1_cpython
• python-dateutil=2.8.2=pyhd8ed1ab_0
• python-fastjsonschema=2.19.1=pyhd8ed1ab_0
• python-lsp-black=2.0.0=pyhd8ed1ab_0
• python-lsp-jsonrpc=1.1.2=pyhd8ed1ab_0
• python-lsp-server=1.10.0=pyhd8ed1ab_0
• python-lsp-server-base=1.10.0=pyhd8ed1ab_0
• python-slugify=8.0.4=pyhd8ed1ab_0
• python_abi=3.12=4_cp312
• pytoolconfig=1.2.6=py312haa95532_0
• pytz=2024.1=pyhd8ed1ab_0
• pywin32=306=py312h53d5487_2
• pywin32-ctypes=0.2.2=py312h2e8e312_1
• pyyaml=6.0.1=py312he70551f_1
• pyzmq=25.1.2=py312h1ac6f91_0
• qdarkstyle=3.2.3=pyhd8ed1ab_0
• qstylizer=0.2.2=pyhd8ed1ab_0
• qt-main=5.15.8=h9e85ed6_18
• qt-webengine=5.15.9=h5bd16bc_7
• qtawesome=1.3.0=pyh9208f05_0
• qtconsole=5.5.1=pyhd8ed1ab_0
• qtconsole-base=5.5.1=pyha770c72_0
• qtpy=2.4.1=pyhd8ed1ab_0
• referencing=0.33.0=pyhd8ed1ab_0
• requests=2.31.0=pyhd8ed1ab_0
• rich=13.7.0=pyhd8ed1ab_0
• rope=1.12.0=pyhd8ed1ab_0
• rpds-py=0.17.1=py312hfccd98a_0
• rtree=1.2.0=py312h72b5f30_0
• setuptools=69.0.3=pyhd8ed1ab_0
• sip=6.7.12=py312h53d5487_0
• six=1.16.0=pyh6c4a22f_0
• snowballstemmer=2.2.0=pyhd8ed1ab_0
• sortedcontainers=2.4.0=pyhd8ed1ab_0
• soupsieve=2.5=pyhd8ed1ab_1
• sphinx=7.2.6=pyhd8ed1ab_0
• sphinxcontrib-applehelp=1.0.8=pyhd8ed1ab_0
• sphinxcontrib-devhelp=1.0.6=pyhd8ed1ab_0
• sphinxcontrib-htmlhelp=2.0.5=pyhd8ed1ab_0
• sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
• sphinxcontrib-qthelp=1.0.7=pyhd8ed1ab_0
• sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
• spyder=5.5.1=py312h2e8e312_0
• spyder-kernels=2.5.0=win_pyh7428d3b_0
• stack_data=0.6.2=pyhd8ed1ab_0
• tabulate=0.9.0=pyhd8ed1ab_1
• tbb=2021.11.0=h91493d7_1
• text-unidecode=1.3=pyhd8ed1ab_1
• textdistance=4.5.0=pyhd8ed1ab_0
• three-merge=0.1.1=pyh9f0ad1d_0
• tinycss2=1.2.1=pyhd8ed1ab_0
• tk=8.6.13=h5226925_1
• tomli=2.0.1=pyhd8ed1ab_0
• tomlkit=0.12.3=pyha770c72_0
• tornado=6.3.3=py312he70551f_1
• traitlets=5.14.1=pyhd8ed1ab_0
• types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0
• typing_extensions=4.9.0=pyha770c72_0
• tzdata=2024a=h0c530f3_0
• ucrt=10.0.22621.0=h57928b3_0
• ujson=5.9.0=py312h53d5487_0
• urllib3=2.2.0=pyhd8ed1ab_0
• vc=14.3=hcf57466_18
• vc14_runtime=14.38.33130=h82b7239_18
• vs2015_runtime=14.38.33130=hcb4865c_18
• watchdog=4.0.0=py312h2e8e312_0
• wcwidth=0.2.13=pyhd8ed1ab_0
• webencodings=0.5.1=pyhd8ed1ab_2
• whatthepatch=1.0.5=pyhd8ed1ab_0
• wheel=0.42.0=pyhd8ed1ab_0
• win_inet_pton=1.1.0=pyhd8ed1ab_6
• xz=5.4.5=h8cc25b3_0
• yaml=0.2.5=h8ffe710_2
• yapf=0.40.1=pyhd8ed1ab_0
• zeromq=4.3.5=h63175ca_0
• zipp=3.17.0=pyhd8ed1ab_0
• zstd=1.5.5=h12be248_0
  prefix: C:\Users\danil\miniconda3\envs\spyder-5.5.1

[seberg]

Unlikely to be NumPy related, dot calls blas, which is MKL. So it should be either MKL or some other odd interaction. You might want to try what happens outside of spyder, maybe this is Qt or so.

My suspicion would be that somehow your blas install is broken, but I don't know how (I assume Numpy is not pip installed but installed through conda/mamba)

[AbeCoull]

Currently, I am also seeing some threading issues (example execution). It is notable that these failures were only see on MacOS runners but I will confirm whether this is the case for other OS's.

When constraining numpy to numpy<=1.26.3, the issue went away. I am still looking into what changed but for now, there seems to be a correlation.

[Yeop-Jung]

Could be an issue with Spyder 5.
I tried the same code above on pycharm community version and it was fine.

[seberg]

I am not sure why the Mac issue is supposed to be related. I still don't think this is related to NumPy, but it would help to have a core dump or running with the visual studio debugger attached and looking at that backtrace (I assume it gives one).

The Python backtrace/snippet just won't give you much except: it's almost certainly BLAS related (and not NumPy).

[sgwu]

I came across a similar issue yesterday, not using numpy, but matplotlib + spyder, below is the error message:

Windows fatal exception: code 0xc06d007e


Main thread:
Current thread 0x000023f0 (most recent call first):
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\transforms.py", line 2436 in get_affine
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\transforms.py", line 2437 in get_affine
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\patches.py", line 587 in draw
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\artist.py", line 72 in draw_wrapper
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\figure.py", line 3153 in draw
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\artist.py", line 72 in draw_wrapper
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\artist.py", line 95 in draw_wrapper
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\backends\backend_agg.py", line 388 in draw
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\matplotlib\backends\backend_qt.py", line 459 in _draw_idle
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\ipykernel\eventloops.py", line 128 in loop_qt
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\ipykernel\kernelbase.py", line 487 in advance_eventloop
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\tornado\ioloop.py", line 738 in _run_callback
  File "C:\Users\wdsyy\anaconda3\lib\asyncio\events.py", line 80 in _run
  File "C:\Users\wdsyy\anaconda3\lib\asyncio\base_events.py", line 1905 in _run_once
  File "C:\Users\wdsyy\anaconda3\lib\asyncio\base_events.py", line 601 in run_forever
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\tornado\platform\asyncio.py", line 195 in start
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\ipykernel\kernelapp.py", line 739 in start
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\spyder_kernels\console\start.py", line 330 in main
  File "C:\Users\wdsyy\anaconda3\lib\site-packages\spyder_kernels\console\__main__.py", line 24 in <module>
  File "C:\Users\wdsyy\anaconda3\lib\runpy.py", line 87 in _run_code
  File "C:\Users\wdsyy\anaconda3\lib\runpy.py", line 197 in _run_module_as_main


Restarting kernel...

Here is my code:

import matplotlib.pyplot as plt

plt.plot([0,1,2])

Like @Yeop-Jung , I tried my code in jupyter lab and it runs fine.

Could be an issue with Spyder 5. I tried the same code above on pycharm community version and it was fine.

The bug appeared after I updated my packages in conda by conda update --all. I tried downgrading spyder to previous versions, didn't work.

[seberg]

This should probably be floated to conda-forge. Maybe it is a Spyder issue, maybe an MKL issue, or maybe a pacakging one, I don't know.

[Yeop-Jung]

FYI, I installed spyder 5.4 and it works fine now.

[Rational-IM]

I reported the issue at Spyder's GitHub. I will close the issue here due to @Yeop-Jung reporting a similar issue with matplotlib.

[GitKia1392]

Its 92% an issue with yo pc.

Windows fatal exception 0xc06d007e means a unknown software/antivirus is trying to disable the software/module/whatever; if you have a antivirus like MalwareBytes/Hitman pro/Kaspersky then try adding it to the "excluded list" of "unwanted" programs.

Reg
Kiamehr