Slower atexit methods do not run to completion

[parantapa]

Description

Cleanup methods that are slower do not run to completion when restarting kernel.

Reproduce

1. Create a new IPython notebook
2. Create and execute a new cell with the following code

Example code:

import atexit
import time
from pathlib import Path

def write_hello():
    time.sleep(5)
    Path("hello.txt").write_text("hello")

atexit.register(write_hello)

4. Click on "Restart kernel"
5. The new file "hello.txt" was not created.

Expected behavior

The "hello.txt" should have been created.

Context

• Operating System and version: ArchLinux
• Browser and version: Firefox Developer version 125.0b6
• JupyterLab version: 4.1.6

Additional info

Jupyter lab shows a TimeoutError on console.

[E 2024-05-02 10:50:31.388 ServerApp] Uncaught exception GET /api/kernels/28d27336-01eb-4fed-9b24-e5b4a1ae8ef4/channels?session_id=3fa3bd68-c341-4029-b71b-92c68bdc3ba6 (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/api/kernels/28d27336-01eb-4fed-9b24-e5b4a1ae8ef4/channels?session_id=3fa3bd68-c341-4029-b71b-92c68bdc3ba6', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/parantapa/miniconda3/envs/notebook_env/lib/python3.11/site-packages/tornado/web.py", line 1790, in _execute
        result = await result
                 ^^^^^^^^^^^^
      File "/home/parantapa/miniconda3/envs/notebook_env/lib/python3.11/site-packages/jupyter_server/services/kernels/websocket.py", line 65, in get
        await self.pre_get()
      File "/home/parantapa/miniconda3/envs/notebook_env/lib/python3.11/site-packages/jupyter_server/services/kernels/websocket.py", line 59, in pre_get
        await self.connection.prepare()
      File "/home/parantapa/miniconda3/envs/notebook_env/lib/python3.11/site-packages/jupyter_server/services/kernels/connection/channels.py", line 318, in prepare
        raise TimeoutError(msg)
    TimeoutError: Kernel never reached an 'alive' state.

This error is gone when using a larger kernel_info_timeout.
However, the atexit method still does not run to completion.

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[JasonWeill]

@parantapa Thank you for opening this issue! Does this also happen when you use other apps, like VS Code, that support ipykernel? If so, this may be an issue upstream, which you can report here: https://github.com/ipython/ipykernel/issues

[parantapa]

@JasonWeill It works as expected on when using IPython from shell. I do not use VS Code so I am unable to test on that.

I have been trying to find the spot in Jupyter Lab, Jupyter Server and Ipython that is responsible for killing the kernel. But I since I am not familiar enough, I haven't figured it out.

[krassowski]

I have been trying to find the spot in Jupyter Lab, Jupyter Server and Ipython that is responsible for killing the kernel. But I since I am not familiar enough, I haven't figured it out.

This would be jupyter_client or ipykernel.

[krassowski]

Though the timeout is raised from jupyter_server as your traceback indicates, so maybe you problem is that the timeout in jupyter_server is too short for your usecase? In any case the code you are looking for is not in this repository.