Finding "Kernel Errors"

[jlperla]

Description

I am using Quarto 1.6.39 with Julia 1.11 (through jupyter kernel). I have tried these issues on windows, macos, and on linux (in CI).

When I generate output with my .qmd it usually (always?) says "KERNEL EXCEPTION" at the end of the execution. Something like the following:

Starting julia-1.11 kernel...Done

Executing 'problem_set_3.quarto_ipynb'
  Cell 1/25: ''...Done
... ETC...
  Cell 25/25: ''...Done

KERNEL EXCEPTION
Starting julia-1.11 kernel...Done

Executing 'problem_set_3.quarto_ipynb'
  Cell 1/25: ''...Done

However, the output seems to be fine, as far as I can tell? Is there a way to debug the reasons to post a minimum working example.

I would ignore the error, but I am also having intermittent problems with the output generation stalling when runnning in a github action - which I worry is related.

[mcanouil]

First sharing a reproducible document that exhibits the message would help.
Unfortunately, sharing only the latter does not allow us to really help you.

Regarding debugging, see https://quarto.org/docs/troubleshooting/index.html.

[jlperla]

Thanks! I played around with it, including putting in the https://quarto.org/docs/troubleshooting/index.html#debugging-jupyter-engine-issues

And in the output I see a little more info. In particular, it says something like this now:

KERNEL EXCEPTION- Checking for existing kernel
- No existing kernel found

Starting julia-1.11 kernel...- Executing notebook with oneshot kernel
2025-01-05 11:04:33,881 - root - Level 25 - /Applications/quarto/share/jupyter/jupyter.py:283 - running notebook without keepalive
2025-01-05 11:04:33,882 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:165 - inside notebook_execute
2025-01-05 11:04:33,898 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:187 - notebook was read
2025-01-05 11:04:33,898 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:435 - {
  "name": "julia-1.11",
  "language": "julia",
  "display_name": "Julia 1.11.2",
  "path": "/Users/jlperla/Library/Jupyter/kernels/julia-1.11"
}
2025-01-05 11:04:33,899 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:121 - using cache
2025-01-05 11:04:33,899 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:124 - getting cache
2025-01-05 11:04:33,977 - root - Level 25 - /Applications/quarto/share/jupyter/notebook.py:468 - nb_from_cache match

i.e., is the KERNEL EXCEPTION just that it can't find an existing kernel you are keeping running? If so, then is this exceptiono innocuous? Is there a setting to always use a new kernel each time it executes to avoid this?

[cderv]

Is there a setting to always use a new kernel each time it executes to avoid this?

You can ask for a new kernel each time by opting out keep-alive. See about Kernel https://quarto.org/docs/computations/python.html#kernel-daemon

Inside a document

execute:
  daemon: false

At command line this is --no-execute-daemon flag.

• Executing notebook with oneshot kernel

Thought it seems to already be calling one shot kernel without keep-alive.

Do you have this KERNEL EXCEPTION only with Julia Kernel ?

Could you share full log from a document render that give you this ? Where does this KERNEL EXCEPTION happens ?

It seems to be even before Jupyter gives us some log information by setting

execute:
  debug: true

🤔