Jupyter crahses inside a linux/amd64 docker container running on arm64 chip

[emielvb]

Description

Jupyter crashes after running jupyter execute inside a docker container after specifying to build on amd64 architecture (--platform=linux/amd64) from a Mac with arm64 architecture.
Downstream effect is that trying to run a VSCode interactive notebook session causes VSCode to crash.

Reproduce

1. From a MacOS system with arm64 architecture, run any docker container built using the flag --platform=linux/amd64.

Option A: from CLI
2. Install jupyterlab and ipykernel using pip3 install ipykernel jupyterlab
3. try to run any notebook using jupyter execute notebook.ipynb
4. observe CLI hanging, giving error after 60 seconds

Option B: interactive notebook session on VSCode
2. Open any .ipynb file
3. Select kernel
4. Press run on any executable cell
5. Observe VSCode hanging indefinitely

Running those same steps on the same system but without the flag --platform=linux/amd64 gives no issues.
Within the same setup, running ipython notebook.ipynb does not give any issues. The problem lies with running the jupyter command.

This repo provides a fully reproducible setup with an example devcontainer: https://github.com/emielvb/bug-report-jupyter
Multiple images have been explored, the issue appears solely with the flag --platform=linux/amd64.

Expected behavior

Running a notebook inside a container without crashes

Context

• Operating System and version: MacOS Tahoe - Version 26.2 (25C56)
• Chip: Apple M4 Pro (arm64)
• Linux version inside container: Debian GNU/Linux 13 (trixie)
• JupyterLab version:

  jupyter --version
  Selected Jupyter core packages...
  IPython          : 9.9.0
  ipykernel        : 7.1.0
  ipywidgets       : not installed
  jupyter_client   : 8.8.0
  jupyter_core     : 5.9.1
  jupyter_server   : 2.17.0
  jupyterlab       : 4.5.2
  nbclient         : 0.10.4
  nbconvert        : 7.16.6
  nbformat         : 5.10.4
  notebook         : not installed
  qtconsole        : not installed
  traitlets        : 5.14.3

Troubleshoot Output

vscode ➜ /workspaces/bug-report-jupyter/amd64-example (develop) $ jupyter troubleshoot
$PATH:
        /vscode/vscode-server/bin/linux-x64/994fd12f8d3a5aa16f17d42c041e5809167e845a/bin/remote-cli
        /usr/local/python/current/bin
        /usr/local/py-utils/bin
        /usr/local/jupyter
        /usr/local/share/nvm/current/bin
        /usr/local/bin
        /usr/local/python/current/bin
        /usr/local/py-utils/bin
        /usr/local/jupyter
        /usr/local/share/nvm/current/bin
        /usr/local/bin
        /usr/local/sbin
        /usr/local/bin
        /usr/sbin
        /usr/bin
        /sbin
        /bin
        /home/vscode/.local/bin
sys.path:

/home/vscode/.local/bin

/usr/local/lib/python312.zip

/usr/local/lib/python3.12

/usr/local/lib/python3.12/lib-dynload

/home/vscode/.local/lib/python3.12/site-packages

/usr/local/lib/python3.12/site-packages
sys.executable:

/usr/local/bin/python3.12
sys.version:

3.12.12 (main, Oct  9 2025, 22:39:36) [GCC 14.2.0]
platform.platform():

Linux-6.10.14-linuxkit-x86_64-with-glibc2.41
which -a jupyter:

/home/vscode/.local/bin/jupyter
pip list:

Package                   Version

------------------------- -----------

anyio                     4.12.1

argon2-cffi               25.1.0

argon2-cffi-bindings      25.1.0

arrow                     1.4.0

asttokens                 3.0.1

async-lru                 2.1.0

attrs                     25.4.0

babel                     2.17.0

beautifulsoup4            4.14.3

bleach                    6.3.0

certifi                   2026.1.4

cffi                      2.0.0

charset-normalizer        3.4.4

comm                      0.2.3

debugpy                   1.8.19

decorator                 5.2.1

defusedxml                0.7.1

executing                 2.2.1

fastjsonschema            2.21.2

fqdn                      1.5.1

gitdb                     4.0.12

GitPython                 3.1.41

h11                       0.16.0

httpcore                  1.0.9

httpx                     0.28.1

idna                      3.11

ipykernel                 7.1.0

ipython                   9.9.0

ipython_pygments_lexers   1.1.1

isoduration               20.11.0

jedi                      0.19.2

Jinja2                    3.1.6

json5                     0.13.0

jsonpointer               3.0.0

jsonschema                4.26.0

jsonschema-specifications 2025.9.1

jupyter_client            8.8.0

jupyter_core              5.9.1

jupyter-events            0.12.0

jupyter-lsp               2.3.0

jupyter_server            2.17.0

jupyter_server_terminals  0.5.4

jupyterlab                4.5.2

jupyterlab_pygments       0.3.0

jupyterlab_server         2.28.0

lark                      1.3.1

MarkupSafe                3.0.3

matplotlib-inline         0.2.1

mistune                   3.2.0

nbclient                  0.10.4

nbconvert                 7.16.6

nbformat                  5.10.4

nest-asyncio              1.6.0

notebook_shim             0.2.4

packaging                 25.0

pandocfilters             1.5.1

parso                     0.8.5

pexpect                   4.9.0

pip                       25.0.1

platformdirs              4.5.1

prometheus_client         0.24.1

prompt_toolkit            3.0.52

psutil                    7.2.1

ptyprocess                0.7.0

pure_eval                 0.2.3

pycparser                 2.23

Pygments                  2.19.2

python-dateutil           2.9.0.post0

python-json-logger        4.0.0

PyYAML                    6.0.3

pyzmq                     27.1.0

referencing               0.37.0

requests                  2.32.5

rfc3339-validator         0.1.4

rfc3986-validator         0.1.1

rfc3987-syntax            1.1.0

rpds-py                   0.30.0

Send2Trash                2.1.0

setuptools                78.1.1

six                       1.17.0

smmap                     5.0.2

soupsieve                 2.8.3

stack-data                0.6.3

terminado                 0.18.1

tinycss2                  1.4.0

tornado                   6.5.4

traitlets                 5.14.3

typing_extensions         4.15.0

tzdata                    2025.3

uri-template              1.3.0

urllib3                   2.6.3

wcwidth                   0.2.14

webcolors                 25.10.0

webencodings              0.5.1

websocket-client          1.9.0

Command Line Output

vscode ➜ /workspaces/bug-report-jupyter/amd64-example (develop) $ jupyter execute test.ipynb 
[NbClientApp] Executing test.ipynb
[NbClientApp] ERROR | Error occurred while starting new kernel client for kernel 94f9ddce-fe98-4d7a-b0b2-b3140c08c494: Kernel didn't respond in 60 seconds
Traceback (most recent call last):
  File "/home/vscode/.local/bin/jupyter-execute", line 8, in 
    sys.exit(main())
             ^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/jupyter_core/application.py", line 284, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/home/vscode/.local/lib/python3.12/site-packages/traitlets/config/application.py", line 1074, in launch_instance
    app.initialize(argv)
  File "/home/vscode/.local/lib/python3.12/site-packages/traitlets/config/application.py", line 118, in inner
    return method(app, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/cli.py", line 161, in initialize
    self.run_notebook(path)
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/cli.py", line 215, in run_notebook
    client.execute()
  File "/home/vscode/.local/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/asyncio/base_events.py", line 691, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/client.py", line 693, in async_execute
    async with self.async_setup_kernel(**kwargs):
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/contextlib.py", line 210, in __aenter__
    return await anext(self.gen)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/client.py", line 651, in async_setup_kernel
    await self.async_start_new_kernel_client()
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/client.py", line 566, in async_start_new_kernel_client
    await ensure_async(self.kc.wait_for_ready(timeout=self.startup_timeout))
  File "/home/vscode/.local/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 214, in ensure_async
    result = await obj
             ^^^^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/jupyter_client/client.py", line 208, in _async_wait_for_ready
    raise RuntimeError("Kernel didn't respond in %d seconds" % timeout)
RuntimeError: Kernel didn't respond in 60 seconds
Exception ignored in atexit callback: .wrapped of >
Traceback (most recent call last):
  File "/home/vscode/.local/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/asyncio/base_events.py", line 691, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/home/vscode/.local/lib/python3.12/site-packages/nbclient/client.py", line 504, in _async_cleanup_kernel
    assert self.km is not None
           ^^^^^^^^^^^^^^^^^^^
AssertionError: 
vscode ➜ /workspaces/bug-report-jupyter/amd64-example (develop) $