[guix-jupyter] timeout issue running the kernel

DoneSubmitted by Domagoj Stolfa.
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2 participants
  • Domagoj Stolfa
  • Ludovic Courtès
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unassigned
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normal
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Domagoj Stolfa wrote on 3 Jul 2021 17:30
(address . bug-guix@gnu.org)
YOCCnDGOaRLj06mV@pepehands
Hello:

I've been trying to set up a Jupyter environment with the Guix kernel inside a
guix environment using:

`guix environment --ad-hoc guix-jupyter jupyter -- jupyter notebook`.

Jupyter starts up fine, but when I create an empty notebook with the Guix kernel
it spams Nudge messages in the console, followed by a crash:

```
[W 16:25:40.117 NotebookApp] Nudge: attempt 120 on kernel 14569df8-e4d1-4847-ae1f-c68e13feeed8
[E 16:25:40.479 NotebookApp] Uncaught exception GET /api/kernels/14569df8-e4d1-4847-ae1f-c68e13feeed8/channels?session_id=05319f9c28b3455cad1b9f4fcf9e0e41 (127.0.0.1)
HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/api/kernels/14569df8-e4d1-4847-ae1f-c68e13feeed8/channels?session_id=05319f9c28b3455cad1b9f4fcf9e0e41', version='HTTP/1.1', remote_ip='127.0.0.1')
Traceback (most recent call last):
File "/gnu/store/zkjmzfd8li7p7yaihm9rs617vqq9n5qh-python-tornado-6.1/lib/python3.8/site-packages/tornado/websocket.py", line 956, in _accept_connection
await open_result
tornado.util.TimeoutError: Timeout
```

Attempting to run anything in the notebook such as

`;;guix environment matplotlib-env <- python-ipykernel python-numpy python-matplotlib`

simply does nothing. I'm not sure if this is an issue with me misconfiguring
something or if it's actually a bug, but I haven't been able to chase it down
as I don't really understand the internals of Jupyter all that well.

Adding `python-ipykernel` and using a Python kernel works fine.

--
Domagoj
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Domagoj Stolfa wrote on 5 Jul 2021 22:54
(address . 49355@debbugs.gnu.org)
YONxeahruuTTnUXP@pepehands
Having done some time-machining, I can confirm that
68c9e0a56e008f19427bd213cf5b24bdd8fe5922 is a good commit. The guix kernel
works fine on it. I don't however yet know which commit caused the regression,
but if nobody finds it until I have more time to bisect, I'll report back.

--
Domagoj
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Domagoj Stolfa wrote on 6 Jul 2021 03:31
(address . 49355@debbugs.gnu.org)
YOOyi0jCB3naP8R8@pepehands
After a very painful bisect with various issues appearing in jupyter (unrelated
to this one), I've identified the first good commit and the first bad commit.

The commit range which caused the problem is between

95f25c9b13e22603c35f3acd9048fbd1c8671925

and

9e7f09cbec40257619e57edfdd700c775e96833d

which is a series of commits by Ricardo updating a bunch of python stuff,
including jupyter. My suspicion is that the update to jupyter-core from 4.4.0 to
4.7.1 (2a12cbaaab970bcab09002e952e062da0274f0b6) caused jupyter-core to no
longer agree with the guix kernel. I haven't diagnosed further.

The first good commit is 85788dd64d5c54ff52f19c8bb6c8c522ed581b2c and the first
bad commit I was able to actually get jupyter to work on is
9e7f09cbec40257619e57edfdd700c775e96833d.

--
Domagoj
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Ludovic Courtès wrote on 6 Jul 2021 17:48
(name . Domagoj Stolfa)(address . ds815@gmx.com)(address . 49355@debbugs.gnu.org)
87zguzphnc.fsf@gnu.org
Hi,

Domagoj Stolfa <ds815@gmx.com> skribis:

Toggle quote (20 lines)
> After a very painful bisect with various issues appearing in jupyter (unrelated
> to this one), I've identified the first good commit and the first bad commit.
>
> The commit range which caused the problem is between
>
> 95f25c9b13e22603c35f3acd9048fbd1c8671925
>
> and
>
> 9e7f09cbec40257619e57edfdd700c775e96833d
>
> which is a series of commits by Ricardo updating a bunch of python stuff,
> including jupyter. My suspicion is that the update to jupyter-core from 4.4.0 to
> 4.7.1 (2a12cbaaab970bcab09002e952e062da0274f0b6) caused jupyter-core to no
> longer agree with the guix kernel. I haven't diagnosed further.
>
> The first good commit is 85788dd64d5c54ff52f19c8bb6c8c522ed581b2c and the first
> bad commit I was able to actually get jupyter to work on is
> 9e7f09cbec40257619e57edfdd700c775e96833d.

Thanks for bisecting!

I believe this is fixed by

You should be able to try it out by running:

guix environment --ad-hoc jupyter guix-jupyter \
--with-branch=guix-jupyter=master -- \
jupyter notebook --debug --no-browser

Hmm now that I re-test it seems to be unreliable. Perhaps I’m missing
something else.

Let me know if it works for you!

Ludo’.
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Domagoj Stolfa wrote on 6 Jul 2021 18:12
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 49355@debbugs.gnu.org)
YOSA4scUbctikQk6@pepehands
Hi:

Toggle quote (2 lines)
> Let me know if it works for you!

Thanks for the quick fix!

So far it has worked well -- I haven't yet run into any unreliable behaviour,
but my notebooks are extremely simple at the moment, at most simply plotting
some stuff with matplotlib!

--
Domagoj
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Domagoj Stolfa wrote on 8 Jul 2021 18:42
[guix-jupyter] timeout issue running the kernel
(address . control@debbugs.gnu.org)
YOcq53TOKyWjNXud@pepehands
close 49355
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