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jupyter notebook immediately crashes with dead kernel

Started by"D. R. Evans" <doc.evans@gmail.com>
First post2018-11-06 01:10 +0100
Last post2018-11-07 17:30 +0100
Articles 7 — 3 participants

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  jupyter notebook immediately crashes with dead kernel "D. R. Evans" <doc.evans@gmail.com> - 2018-11-06 01:10 +0100
    Re: jupyter notebook immediately crashes with dead kernel vipul kumar <finn98@protonmail.com> - 2018-11-06 01:40 +0100
      Re: jupyter notebook immediately crashes with dead kernel "D. R. Evans" <doc.evans@gmail.com> - 2018-11-06 02:20 +0100
        Re: jupyter notebook immediately crashes with dead kernel "D. R. Evans" <doc.evans@gmail.com> - 2018-11-06 16:00 +0100
          Re: jupyter notebook immediately crashes with dead kernel "D. R. Evans" <doc.evans@gmail.com> - 2018-11-07 15:40 +0100
            Re: jupyter notebook immediately crashes with dead kernel finn <finn98@protonmail.com> - 2018-11-07 16:50 +0100
              Re: jupyter notebook immediately crashes with dead kernel "D. R. Evans" <doc.evans@gmail.com> - 2018-11-07 17:30 +0100

#202171 — jupyter notebook immediately crashes with dead kernel

From"D. R. Evans" <doc.evans@gmail.com>
Date2018-11-06 01:10 +0100
Subjectjupyter notebook immediately crashes with dead kernel
Message-ID<wQX6p-38t-13@gated-at.bofh.it>

[Multipart message — attachments visible in raw view] — view raw

Running current debian stable (64-bit).

I installed the jupyter-notebook package (which caused several other packages
associated with python3 to be installed).

There was no indication of any problems with the installation, and I didn't
see any messages suggesting that anything else needs to be done to run jupyter.

But when I run the application and try to create a new notebook using File |
New Notebook | Python3 on the web page
http://localhost:8888/notebooks/Untitled1.ipynb?kernel_name=python3, the
python3 kernel will not start and I get a message saying that it has died.
Attempts to restart the kernel produce the same result.

What else do I need to do to get this package to work? Or is there somewhere
on the system where I can find a more useful error message?

  Doc Evans

-- 
Web:  http://enginehousebooks.com/drevans

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#202172

Fromvipul kumar <finn98@protonmail.com>
Date2018-11-06 01:40 +0100
Message-ID<wQXzr-3hy-1@gated-at.bofh.it>
In reply to#202171
Run Jupyter-notebook from terminal. Send log report which you'll get on terminal while running jupyter-notebook.


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Tuesday, November 6, 2018 5:30 AM, D. R. Evans <doc.evans@gmail.com> wrote:

> Running current debian stable (64-bit).
>
> I installed the jupyter-notebook package (which caused several other packages
> associated with python3 to be installed).
>
> There was no indication of any problems with the installation, and I didn't
> see any messages suggesting that anything else needs to be done to run jupyter.
>
> But when I run the application and try to create a new notebook using File |
> New Notebook | Python3 on the web page
> http://localhost:8888/notebooks/Untitled1.ipynb?kernel_name=python3, the
> python3 kernel will not start and I get a message saying that it has died.
> Attempts to restart the kernel produce the same result.
>
> What else do I need to do to get this package to work? Or is there somewhere
> on the system where I can find a more useful error message?
>
> Doc Evans
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Web: http://enginehousebooks.com/drevans

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#202174

From"D. R. Evans" <doc.evans@gmail.com>
Date2018-11-06 02:20 +0100
Message-ID<wQYc9-3Jq-5@gated-at.bofh.it>
In reply to#202172

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vipul kumar wrote on 11/05/2018 05:35 PM:
> Run Jupyter-notebook from terminal. Send log report which you'll get on terminal while running jupyter-notebook.
> 
> 

----

[W 18:07:15.047 NotebookApp] Widgets are unavailable. On Debian, notebook
support for widgets is provided by the package
jupyter-nbextension-jupyter-js-widgets
[I 18:07:15.100 NotebookApp] Serving notebooks from local directory: /home/n7dr
[I 18:07:15.100 NotebookApp] 0 active kernels
[I 18:07:15.100 NotebookApp] The Jupyter Notebook is running at:
http://localhost:8888/
[I 18:07:15.100 NotebookApp] Use Control-C to stop this server and shut down
all kernels (twice to skip confirmation)

----

I was going to add the widget support after the basic notebook is working, but
installed jupyter-nbextension-jupyter-js-widgets anyway and tried again:

----

[HN:~] jupyter-notebook
[I 18:11:04.210 NotebookApp] Serving notebooks from local directory: /home/n7dr
[I 18:11:04.211 NotebookApp] 0 active kernels
[I 18:11:04.211 NotebookApp] The Jupyter Notebook is running at:
http://localhost:8888/
[I 18:11:04.211 NotebookApp] Use Control-C to stop this server and shut down
all kernels (twice to skip confirmation).

----

So the warning message goes away (as expected) but the behaviour is unchanged:
the kernel still dies when I try to create a notebook.

  Doc

-- 
Web:  http://enginehousebooks.com/drevans

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#202191

From"D. R. Evans" <doc.evans@gmail.com>
Date2018-11-06 16:00 +0100
Message-ID<wRaZH-2Nl-1@gated-at.bofh.it>
In reply to#202174

[Multipart message — attachments visible in raw view] — view raw

D. R. Evans wrote on 11/05/2018 06:14 PM:
> vipul kumar wrote on 11/05/2018 05:35 PM:
>> Run Jupyter-notebook from terminal. Send log report which you'll get on terminal while running jupyter-notebook.
>>
>

> 
> [HN:~] jupyter-notebook
> [I 18:11:04.210 NotebookApp] Serving notebooks from local directory: /home/n7dr
> [I 18:11:04.211 NotebookApp] 0 active kernels
> [I 18:11:04.211 NotebookApp] The Jupyter Notebook is running at:
> http://localhost:8888/
> [I 18:11:04.211 NotebookApp] Use Control-C to stop this server and shut down
> all kernels (twice to skip confirmation).
> 
> ----

I see additional messages when I actually try to create the notebook (sorry; I
wasn't looking for those yesterday):

----

HN:~] jupyter-notebook
[I 07:37:19.123 NotebookApp] Serving notebooks from local directory: /home/n7dr
[I 07:37:19.124 NotebookApp] 0 active kernels
[I 07:37:19.124 NotebookApp] The Jupyter Notebook is running at:
http://localhost:8888/
[I 07:37:19.124 NotebookApp] Use Control-C to stop this server and shut down
all kernels (twice to skip confirmation).
[I 07:37:29.629 NotebookApp] Creating new notebook in
[I 07:37:32.575 NotebookApp] Kernel started: 00f6d461-87f1-410e-9963-5f5db91602f3
/usr/bin/python: No module named ipykernel_launcher
[I 07:37:35.561 NotebookApp] KernelRestarter: restarting kernel (1/5)
/usr/bin/python: No module named ipykernel_launcher
[I 07:37:38.571 NotebookApp] KernelRestarter: restarting kernel (2/5)
/usr/bin/python: No module named ipykernel_launcher
[I 07:37:41.582 NotebookApp] KernelRestarter: restarting kernel (3/5)
/usr/bin/python: No module named ipykernel_launcher
[W 07:37:42.678 NotebookApp] Timeout waiting for kernel_info reply from
00f6d461-87f1-410e-9963-5f5db91602f3
[I 07:37:44.592 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted
/usr/bin/python: No module named ipykernel_launcher
[W 07:37:47.604 NotebookApp] KernelRestarter: restart failed
[W 07:37:47.605 NotebookApp] Kernel 00f6d461-87f1-410e-9963-5f5db91602f3 died,
removing from map.
ERROR:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted failed!
[W 07:37:47.654 NotebookApp] Kernel deleted before session
[W 07:37:47.656 NotebookApp] 410 DELETE
/api/sessions/56ef952c-800c-448f-baf0-857081b87abc (::1) 3.46ms
referer=http://localhost:8888/notebooks/Untitled4.ipynb?kernel_name=python3

----

The strange thing here is:
  /usr/bin/python: No module named ipykernel_launcher

Why is it running /usr/bin/python, which is a link to python2??

----

HN:~] ls -al /usr/bin/python
lrwxrwxrwx 1 root root 9 Jan 24  2017 /usr/bin/python -> python2.7

----

I would have thought that, since the package installed the ipython3 kernel for
jupyter, and when I try to create a notebook, it's python3 that is in the
"New" drop-down menu on the jupyter page, then it should be executing
/usr/bin/python3, not /usr/bin/python.

Is this perhaps an error in the packaging?

  Doc

-- 
Web:  http://enginehousebooks.com/drevans

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#202227

From"D. R. Evans" <doc.evans@gmail.com>
Date2018-11-07 15:40 +0100
Message-ID<wRx9T-7IF-3@gated-at.bofh.it>
In reply to#202191

[Multipart message — attachments visible in raw view] — view raw

D. R. Evans wrote on 11/06/2018 07:56 AM:
> D. R. Evans wrote on 11/05/2018 06:14 PM:
>> vipul kumar wrote on 11/05/2018 05:35 PM:
>>> Run Jupyter-notebook from terminal. Send log report which you'll get on terminal while running jupyter-notebook.
>>>
>>
> 
>>
>> [HN:~] jupyter-notebook
>> [I 18:11:04.210 NotebookApp] Serving notebooks from local directory: /home/n7dr
>> [I 18:11:04.211 NotebookApp] 0 active kernels
>> [I 18:11:04.211 NotebookApp] The Jupyter Notebook is running at:
>> http://localhost:8888/
>> [I 18:11:04.211 NotebookApp] Use Control-C to stop this server and shut down
>> all kernels (twice to skip confirmation).
>>
>> ----
> 
> I see additional messages when I actually try to create the notebook (sorry; I
> wasn't looking for those yesterday):
> 
> ----
> 
> HN:~] jupyter-notebook
> [I 07:37:19.123 NotebookApp] Serving notebooks from local directory: /home/n7dr
> [I 07:37:19.124 NotebookApp] 0 active kernels
> [I 07:37:19.124 NotebookApp] The Jupyter Notebook is running at:
> http://localhost:8888/
> [I 07:37:19.124 NotebookApp] Use Control-C to stop this server and shut down
> all kernels (twice to skip confirmation).
> [I 07:37:29.629 NotebookApp] Creating new notebook in
> [I 07:37:32.575 NotebookApp] Kernel started: 00f6d461-87f1-410e-9963-5f5db91602f3
> /usr/bin/python: No module named ipykernel_launcher
> [I 07:37:35.561 NotebookApp] KernelRestarter: restarting kernel (1/5)
> /usr/bin/python: No module named ipykernel_launcher
> [I 07:37:38.571 NotebookApp] KernelRestarter: restarting kernel (2/5)
> /usr/bin/python: No module named ipykernel_launcher
> [I 07:37:41.582 NotebookApp] KernelRestarter: restarting kernel (3/5)
> /usr/bin/python: No module named ipykernel_launcher
> [W 07:37:42.678 NotebookApp] Timeout waiting for kernel_info reply from
> 00f6d461-87f1-410e-9963-5f5db91602f3
> [I 07:37:44.592 NotebookApp] KernelRestarter: restarting kernel (4/5)
> WARNING:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted
> /usr/bin/python: No module named ipykernel_launcher
> [W 07:37:47.604 NotebookApp] KernelRestarter: restart failed
> [W 07:37:47.605 NotebookApp] Kernel 00f6d461-87f1-410e-9963-5f5db91602f3 died,
> removing from map.
> ERROR:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted failed!
> [W 07:37:47.654 NotebookApp] Kernel deleted before session
> [W 07:37:47.656 NotebookApp] 410 DELETE
> /api/sessions/56ef952c-800c-448f-baf0-857081b87abc (::1) 3.46ms
> referer=http://localhost:8888/notebooks/Untitled4.ipynb?kernel_name=python3
> 
> ----
> 
> The strange thing here is:
>   /usr/bin/python: No module named ipykernel_launcher
> 
> Why is it running /usr/bin/python, which is a link to python2??
> 
> ----
> 
> HN:~] ls -al /usr/bin/python
> lrwxrwxrwx 1 root root 9 Jan 24  2017 /usr/bin/python -> python2.7
> 
> ----
> 
> I would have thought that, since the package installed the ipython3 kernel for
> jupyter, and when I try to create a notebook, it's python3 that is in the
> "New" drop-down menu on the jupyter page, then it should be executing
> /usr/bin/python3, not /usr/bin/python.
> 
> Is this perhaps an error in the packaging?

This is now bug 913110:
  https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=913110

The bug report includes a simple fix.

  Doc

-- 
Web:  http://enginehousebooks.com/drevans

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#202232

Fromfinn <finn98@protonmail.com>
Date2018-11-07 16:50 +0100
Message-ID<wRyfE-8l9-9@gated-at.bofh.it>
In reply to#202227
Solution 1:
sudo apt purge python3-ipykernel
sudo apt install python3-ipykernel

Solution 2:
OR, purge python-notebook package and install it again, it will automatically install ipykernel package while resolving its dependency.
sudo apt purge python-notebook
sudo apt install python-notebook

Should fix you're issue.

By the way, installing python-notebook from official debian repo(http://deb.debian.org/debian) works for me without a singal error.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Wednesday, November 7, 2018 7:59 PM, D. R. Evans <doc.evans@gmail.com> wrote:

> D. R. Evans wrote on 11/06/2018 07:56 AM:
>
> > D. R. Evans wrote on 11/05/2018 06:14 PM:
> >
> > > vipul kumar wrote on 11/05/2018 05:35 PM:
> > >
> > > > Run Jupyter-notebook from terminal. Send log report which you'll get on terminal while running jupyter-notebook.
> >
> > > [HN:~] jupyter-notebook
> > > [I 18:11:04.210 NotebookApp] Serving notebooks from local directory: /home/n7dr
> > > [I 18:11:04.211 NotebookApp] 0 active kernels
> > > [I 18:11:04.211 NotebookApp] The Jupyter Notebook is running at:
> > > http://localhost:8888/
> > > [I 18:11:04.211 NotebookApp] Use Control-C to stop this server and shut down
> > > all kernels (twice to skip confirmation).
> >
> > I see additional messages when I actually try to create the notebook (sorry; I
> > wasn't looking for those yesterday):
> >
> > HN:~] jupyter-notebook
> > [I 07:37:19.123 NotebookApp] Serving notebooks from local directory: /home/n7dr
> > [I 07:37:19.124 NotebookApp] 0 active kernels
> > [I 07:37:19.124 NotebookApp] The Jupyter Notebook is running at:
> > http://localhost:8888/
> > [I 07:37:19.124 NotebookApp] Use Control-C to stop this server and shut down
> > all kernels (twice to skip confirmation).
> > [I 07:37:29.629 NotebookApp] Creating new notebook in
> > [I 07:37:32.575 NotebookApp] Kernel started: 00f6d461-87f1-410e-9963-5f5db91602f3
> > /usr/bin/python: No module named ipykernel_launcher
> > [I 07:37:35.561 NotebookApp] KernelRestarter: restarting kernel (1/5)
> > /usr/bin/python: No module named ipykernel_launcher
> > [I 07:37:38.571 NotebookApp] KernelRestarter: restarting kernel (2/5)
> > /usr/bin/python: No module named ipykernel_launcher
> > [I 07:37:41.582 NotebookApp] KernelRestarter: restarting kernel (3/5)
> > /usr/bin/python: No module named ipykernel_launcher
> > [W 07:37:42.678 NotebookApp] Timeout waiting for kernel_info reply from
> > 00f6d461-87f1-410e-9963-5f5db91602f3
> > [I 07:37:44.592 NotebookApp] KernelRestarter: restarting kernel (4/5)
> > WARNING:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted
> > /usr/bin/python: No module named ipykernel_launcher
> > [W 07:37:47.604 NotebookApp] KernelRestarter: restart failed
> > [W 07:37:47.605 NotebookApp] Kernel 00f6d461-87f1-410e-9963-5f5db91602f3 died,
> > removing from map.
> > ERROR:root:kernel 00f6d461-87f1-410e-9963-5f5db91602f3 restarted failed!
> > [W 07:37:47.654 NotebookApp] Kernel deleted before session
> > [W 07:37:47.656 NotebookApp] 410 DELETE
> > /api/sessions/56ef952c-800c-448f-baf0-857081b87abc (::1) 3.46ms
> > referer=http://localhost:8888/notebooks/Untitled4.ipynb?kernel_name=python3
> >
> > The strange thing here is:
> > /usr/bin/python: No module named ipykernel_launcher
> > Why is it running /usr/bin/python, which is a link to python2??
> >
> > HN:~] ls -al /usr/bin/python
> > lrwxrwxrwx 1 root root 9 Jan 24 2017 /usr/bin/python -> python2.7
> >
> > I would have thought that, since the package installed the ipython3 kernel for
> > jupyter, and when I try to create a notebook, it's python3 that is in the
> > "New" drop-down menu on the jupyter page, then it should be executing
> > /usr/bin/python3, not /usr/bin/python.
> > Is this perhaps an error in the packaging?
>
> This is now bug 913110:
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=913110
>
> The bug report includes a simple fix.
>
> Doc
>
> -------------------------------------------------------------------------------------------------------------------------------
>
> Web: http://enginehousebooks.com/drevans

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#202233

From"D. R. Evans" <doc.evans@gmail.com>
Date2018-11-07 17:30 +0100
Message-ID<wRySm-ln-5@gated-at.bofh.it>
In reply to#202232

[Multipart message — attachments visible in raw view] — view raw

finn wrote on 11/07/2018 08:45 AM:
> Solution 1:
> sudo apt purge python3-ipykernel
> sudo apt install python3-ipykernel
> 
> Solution 2:
> OR, purge python-notebook package and install it again, it will automatically install ipykernel package while resolving its dependency.
> sudo apt purge python-notebook
> sudo apt install python-notebook
> 
> Should fix you're issue.
> 

Nope. They don't. I reinstalled a few times while figuring out what the real
issue is.

> By the way, installing python-notebook from official debian repo(http://deb.debian.org/debian) works for me without a singal error.
> 

Perhaps you don't have python2 installed. The official stable package looks
like it probably works fine if you don't have python2 installed.

But if you do have both official pythons installed from the stable
repositories, as I do, then /usr/bin/python points to python2 (at least it
does here) so that when jupyter tries to create a python3 notebook and
executes "python", then it executes python2,not python3, and hence there's a
rapid failure.

Easy to fix, per bug 913110, but it /is/ a bug.

  Doc

-- 
Web:  http://enginehousebooks.com/drevans

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