GNU bug report logs -
#49355
[guix-jupyter] timeout issue running the kernel
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Reported by: Domagoj Stolfa <ds815 <at> gmx.com>
Date: Sat, 3 Jul 2021 15:31:02 UTC
Severity: normal
Done: Domagoj Stolfa <ds815 <at> gmx.com>
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
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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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Message #8 received at 49355 <at> debbugs.gnu.org (full text, mbox):
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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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(Tue, 06 Jul 2021 01:33:02 GMT)
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Message #11 received at 49355 <at> debbugs.gnu.org (full text, mbox):
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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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(Tue, 06 Jul 2021 15:50:01 GMT)
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Message #14 received at 49355 <at> debbugs.gnu.org (full text, mbox):
Hi,
Domagoj Stolfa <ds815 <at> gmx.com> skribis:
> 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
<https://gitlab.inria.fr/guix-hpc/guix-kernel/-/commit/bc81615c11b67abe6533d7e076cf152d06618866>.
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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(Tue, 06 Jul 2021 16:13:02 GMT)
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Message #17 received at 49355 <at> debbugs.gnu.org (full text, mbox):
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Hi:
> 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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bug closed, send any further explanations to
49355 <at> debbugs.gnu.org and Domagoj Stolfa <ds815 <at> gmx.com>
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Domagoj Stolfa <ds815 <at> gmx.com>
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control <at> debbugs.gnu.org
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(Thu, 08 Jul 2021 16:43:02 GMT)
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bug archived.
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(Fri, 06 Aug 2021 11:24:08 GMT)
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This bug report was last modified 2 years and 234 days ago.
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