jupyter notebook problem with 8,3

[John Cremona]

I just updagred to 8.3 on a machine (ubuntu 16.04) where I have frequently run Sage both command-line and jupyter notebook previously.  Now when I type

sage --notebook=jupyter

I see

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 8.3, Release Date: 2018-08-03                     │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

Please wait while the Sage Jupyter Notebook server starts...

[I 16:32:21.039 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js

[I 16:32:21.347 NotebookApp] The port 8888 is already in use, trying another port.

[I 16:32:21.353 NotebookApp] Serving notebooks from local directory: /home/jec/sage-scripts

[I 16:32:21.353 NotebookApp] 0 active kernels

[I 16:32:21.353 NotebookApp] The Jupyter Notebook is running at:

[I 16:32:21.353 NotebookApp] http://localhost:8889/

[I 16:32:21.354 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Gtk-Message: Failed to load module "pk-gtk-module"

Gtk-Message: Failed to load module "pk-gtk-module"

[54010:54010:0808/163222.159037:ERROR:sandbox_linux.cc(378)] InitializeSandbox() called with multiple threads in process gpu-process.

[53973:54212:0808/163222.855277:ERROR:bus.cc(394)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix")

[53973:53973:0808/163222.961497:ERROR:gpu_process_transport_factory.cc(1016)] Lost UI shared context.

(chromium-browser:53973): LIBDBUSMENU-GLIB-WARNING **: Unable to get session bus: Unknown or unsupported transport 'disabled' for address 'disabled:'

[I 16:32:22.976 NotebookApp] 302 GET /tree (::1) 2.53ms

and the browser which pops up has a plain login page asking for a password.  There is a different user currently running some sessions (2 of which look stale as they have been running since 2017) which is why it switched from port 8888 to 8889, but I think from the above output that the switch is incomplete and it wants me to log into his session on port 8888.  Perhaps.

John

[Volker Braun]

The token does get generated for me, are you sure you don't have any funny configuration files in ~/.jupyter

Unless you override it in the config, the generated url should have this form (including the access token):

[I 09:21:59.267 NotebookApp] The Jupyter Notebook is running at:

[I 09:21:59.267 NotebookApp] http://localhost:8889/?token=0df6ca362c920415eb1990bcfa4122baa094a3fdfa0f3709

[Dima Pasechnik]

Did you try

apt-get install packagekit-gtk3-module

At least this should fix

Gtk-Message: Failed to load module "pk-gtk-module"

[John Cremona]

On 9 August 2018 at 08:26, Volker Braun <vbrau...@gmail.com> wrote:

The token does get generated for me, are you sure you don't have any funny configuration files in ~/.jupyter

The is nothing in there except for a file 'migrated' containing 

2016-09-02T15:23:38.838391

(with no newline).  I have never done anything to configure jupyter.

As I said, it worked always before I built 8.3.

Unless you override it in the config, the generated url should have this form (including the access token):

[I 09:21:59.267 NotebookApp] The Jupyter Notebook is running at:

[I 09:21:59.267 NotebookApp] http://localhost:8889/?token=0df6ca362c920415eb1990bcfa4122baa094a3fdfa0f3709

Yes, that is what I have always seen before.

I installed the package Dima suggested but that does not affect this issue.  It still behaves as it did yesterday.  Now the output is

$ sage --notebook=jupyter

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 8.3, Release Date: 2018-08-03                     │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

Please wait while the Sage Jupyter Notebook server starts...

[I 09:13:40.197 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js

[I 09:13:40.455 NotebookApp] The port 8888 is already in use, trying another port.

[I 09:13:40.460 NotebookApp] Serving notebooks from local directory: /home/jec/.jupyter

[I 09:13:40.460 NotebookApp] 0 active kernels

[I 09:13:40.460 NotebookApp] The Jupyter Notebook is running at:

[I 09:13:40.461 NotebookApp] http://localhost:8889/

[I 09:13:40.461 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

[68140:68140:0809/091341.230252:ERROR:sandbox_linux.cc(378)] InitializeSandbox() called with multiple threads in process gpu-process.

[I 09:13:41.671 NotebookApp] 302 GET /tree (::1) 1.48ms

Created new window in existing browser session.

and the new window asks or a password.  I still think it is something to do with this:

$ ps aux | grep jupyt

lowry    12387  0.0  0.0 137702340 844 ?       S     2017   0:00 python -m sage.repl.ipython_kernel -f /run/user/1074/jupyter/kernel-6a00c63e-3725-4a1f-9675-d31f3ca4346d.json

lowry    13787  0.0  0.0 146488296 3404 ?      S     2017   0:00 python -m sage.repl.ipython_kernel -f /run/user/1074/jupyter/kernel-6a00c63e-3725-4a1f-9675-d31f3ca4346d.json

lowry    49983  0.0  0.0 137942964 330344 ?    Ssl  Jul27   9:19 python -m sage.repl.ipython_kernel -f /run/user/1074/jupyter/kernel-10384626-e3c4-4112-99fc-c9f3f72db136.json

lowry    51560  0.0  0.0 138009880 336400 ?    Ssl  Jul27   0:54 python -m sage.repl.ipython_kernel -f /run/user/1074/jupyter/kernel-234bb5d0-b319-4b11-91bb-b8a5d0bb4a9d.json

lowry    56073  0.0  0.0 415368 36708 pts/51   Sl+  Feb11  41:44 python /usr/local/sage/sage-2/src/bin/sage-notebook --notebook=jupyter --port=8888

lowry    56179  0.0  0.4 3498740 2449576 ?     Ssl  Feb11  15:55 /usr/local/sage/sage-2/local/bin/python -m ipykernel_launcher -f /run/user/1074/jupyter/kernel-10500b86-2757-4ba6-9504-7ad81c57e5c4.json

jec      67068  0.0  0.0  14220  1012 pts/5    S+   09:12   0:00 grep --color=auto jupyt

but the user in question is currently somewhere in deepest Iceland.

If I simply run chromium-browser on this machine (which I am logging in to remotely) I see those error messages:

$ chromium-browser 

[68969:68969:0809/091759.024888:ERROR:sandbox_linux.cc(378)] InitializeSandbox() called with multiple threads in process gpu-process.

[68932:69172:0809/091759.442701:ERROR:bus.cc(394)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix")

[68932:68932:0809/091759.537307:ERROR:gpu_process_transport_factory.cc(1016)] Lost UI shared context.

(chromium-browser:68932): LIBDBUSMENU-GLIB-WARNING **: Unable to get session bus: Unknown or unsupported transport 'disabled' for address 'disabled:'

which at least shows that some of the error messages I get when trying to run Sage jupyter notebook are nothing to do with Sage.

 

On Wednesday, August 8, 2018 at 5:38:03 PM UTC+2, John Cremona wrote:

I just updagred to 8.3 on a machine (ubuntu 16.04) where I have frequently run Sage both command-line and jupyter notebook previously.  Now when I type

sage --notebook=jupyter

I see

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 8.3, Release Date: 2018-08-03                     │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

Please wait while the Sage Jupyter Notebook server starts...

[I 16:32:21.039 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js

[I 16:32:21.347 NotebookApp] The port 8888 is already in use, trying another port.

[I 16:32:21.353 NotebookApp] Serving notebooks from local directory: /home/jec/sage-scripts

[I 16:32:21.353 NotebookApp] 0 active kernels

[I 16:32:21.353 NotebookApp] The Jupyter Notebook is running at:

[I 16:32:21.353 NotebookApp] http://localhost:8889/

[I 16:32:21.354 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Gtk-Message: Failed to load module "pk-gtk-module"

Gtk-Message: Failed to load module "pk-gtk-module"

[54010:54010:0808/163222.159037:ERROR:sandbox_linux.cc(378)] InitializeSandbox() called with multiple threads in process gpu-process.

[53973:54212:0808/163222.855277:ERROR:bus.cc(394)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix")

[53973:53973:0808/163222.961497:ERROR:gpu_process_transport_factory.cc(1016)] Lost UI shared context.

(chromium-browser:53973): LIBDBUSMENU-GLIB-WARNING **: Unable to get session bus: Unknown or unsupported transport 'disabled' for address 'disabled:'

[I 16:32:22.976 NotebookApp] 302 GET /tree (::1) 2.53ms

and the browser which pops up has a plain login page asking for a password.  There is a different user currently running some sessions (2 of which look stale as they have been running since 2017) which is why it switched from port 8888 to 8889, but I think from the above output that the switch is incomplete and it wants me to log into his session on port 8888.  Perhaps.

John

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[Dima Pasechnik]

note the warning

The port 8888 is already in use, trying another port.

And that it tries to get you started on port 8889 instead.

Perhaps this is somehow broken...

What do you have on 8888?

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[John Cremona]

On 9 August 2018 at 10:28, Dima Pasechnik <dim...@gmail.com> wrote:

note the warning

The port 8888 is already in use, trying another port.

And that it tries to get you started on port 8889 instead.

Perhaps this is somehow broken...

That was my theory

 

What do you have on 8888?

That's where another user is running sage/jupyter,

 

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[Volker Braun]

The token is generated before launching the browser, and conflicting ports aren't a problem (jupyter just picks an unused one). Check for pesky environment variables like JUPYTER_TOKEN and/or try

sage --notebook=jupyter --no-browser --debug

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[John Cremona]

On 9 August 2018 at 12:09, Volker Braun <vbrau...@gmail.com> wrote:

The token is generated before launching the browser, and conflicting ports aren't a problem (jupyter just picks an unused one). Check for pesky environment variables like JUPYTER_TOKEN and/or try

sage --notebook=jupyter --no-browser --debug

No funny environment, I think:

$ env | grep J

(returns nothing)

$ sage --notebook=jupyter --no-browser --debug

┌────────────────────────────────────────────────────────────────────┐

│ SageMath version 8.3, Release Date: 2018-08-03                     │

│ Type "notebook()" for the browser-based notebook interface.        │

│ Type "help()" for help.                                            │

└────────────────────────────────────────────────────────────────────┘

Please wait while the Sage Jupyter Notebook server starts...

[D 12:11:45.311 NotebookApp] Searching [u'/home/jec', '/home/jec/.sage//jupyter-4.1', '/usr/local/sage/sage-2/local/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files

[D 12:11:45.311 NotebookApp] Looking for jupyter_config in /etc/jupyter

[D 12:11:45.311 NotebookApp] Looking for jupyter_config in /usr/local/etc/jupyter

[D 12:11:45.311 NotebookApp] Looking for jupyter_config in /usr/local/sage/sage-2/local/etc/jupyter

[D 12:11:45.312 NotebookApp] Looking for jupyter_config in /home/jec/.sage//jupyter-4.1

[D 12:11:45.312 NotebookApp] Looking for jupyter_config in /home/jec

[D 12:11:45.313 NotebookApp] Looking for jupyter_notebook_config in /etc/jupyter

[D 12:11:45.313 NotebookApp] Looking for jupyter_notebook_config in /usr/local/etc/jupyter

[D 12:11:45.313 NotebookApp] Looking for jupyter_notebook_config in /usr/local/sage/sage-2/local/etc/jupyter

[D 12:11:45.313 NotebookApp] Loaded config file: /usr/local/sage/sage-2/local/etc/jupyter/jupyter_notebook_config.py

[D 12:11:45.314 NotebookApp] Looking for jupyter_notebook_config in /home/jec/.sage//jupyter-4.1

[D 12:11:45.314 NotebookApp] Loaded config file: /home/jec/.sage/jupyter-4.1/jupyter_notebook_config.json

[D 12:11:45.314 NotebookApp] Looking for jupyter_notebook_config in /home/jec

[I 12:11:45.315 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js

[I 12:11:45.637 NotebookApp] The port 8888 is already in use, trying another port.

[D 12:11:45.641 NotebookApp] Paths used for configuration of jupyter_notebook_config: 

    /etc/jupyter/jupyter_notebook_config.json

[D 12:11:45.641 NotebookApp] Paths used for configuration of jupyter_notebook_config: 

    /usr/local/etc/jupyter/jupyter_notebook_config.json

[D 12:11:45.642 NotebookApp] Paths used for configuration of jupyter_notebook_config: 

    /usr/local/sage/sage-2/local/etc/jupyter/jupyter_notebook_config.json

[D 12:11:45.642 NotebookApp] Paths used for configuration of jupyter_notebook_config: 

    /home/jec/.sage//jupyter-4.1/jupyter_notebook_config.json

[I 12:11:45.645 NotebookApp] Serving notebooks from local directory: /home/jec

[I 12:11:45.645 NotebookApp] 0 active kernels

[I 12:11:45.645 NotebookApp] The Jupyter Notebook is running at:

[I 12:11:45.645 NotebookApp] http://localhost:8889/

[I 12:11:45.645 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

If I then open the browser and put localhost:8889/  in, I still get the password prompt and the command lone shows

[I 12:15:00.552 NotebookApp] 302 GET / (::1) 0.93ms

[I 12:15:00.607 NotebookApp] 302 GET /tree? (::1) 1.87ms

[D 12:15:00.617 NotebookApp] Using contents: services/contents

[D 12:15:00.674 NotebookApp] Path base/images/favicon.ico served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/base/images/favicon.ico

[D 12:15:00.675 NotebookApp] Path components/jquery-ui/themes/smoothness/jquery-ui.min.css served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/jquery-ui/themes/smoothness/jquery-ui.min.css

[D 12:15:00.675 NotebookApp] Path components/jquery-typeahead/dist/jquery.typeahead.min.css served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/jquery-typeahead/dist/jquery.typeahead.min.css

[D 12:15:00.675 NotebookApp] Path style/style.min.css served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/style/style.min.css

[D 12:15:00.677 NotebookApp] Path auth/css/override.css served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/auth/css/override.css

[D 12:15:00.677 NotebookApp] Path components/es6-promise/promise.min.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/es6-promise/promise.min.js

[D 12:15:00.677 NotebookApp] Path components/preact/index.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/preact/index.js

[D 12:15:00.677 NotebookApp] Path components/proptypes/index.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/proptypes/index.js

[D 12:15:00.678 NotebookApp] Path components/preact-compat/index.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/preact-compat/index.js

[D 12:15:00.678 NotebookApp] Path components/requirejs/require.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/components/requirejs/require.js

[D 12:15:00.679 NotebookApp] Path base/images/logo.png served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/base/images/logo.png

[D 12:15:00.680 NotebookApp] 200 GET /login?next=%2Ftree%3F (::1) 70.99ms

[D 12:15:00.710 NotebookApp] Path custom.css served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/custom/custom.css

[D 12:15:00.711 NotebookApp] 304 GET /custom/custom.css (::1) 2.39ms

[D 12:15:00.763 NotebookApp] Path auth/js/main.min.js served from /usr/local/sage/sage-2/local/lib/python2.7/site-packages/notebook/static/auth/js/main.min.js

[D 12:15:00.764 NotebookApp] 304 GET /static/auth/js/main.min.js (::1) 2.14ms

and still no token is appearing.

Luckily I have other computers all working fine with 8.3, on which I have moved my current work...

John

 

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[Volker Braun]

So whats in  /home/jec/.sage/jupyter-4.1/jupyter_notebook_config.json

[John Cremona]

On 9 August 2018 at 12:20, Volker Braun <vbrau...@gmail.com> wrote:

So whats in  /home/jec/.sage/jupyter-4.1/jupyter_notebook_config.json

Ah!  It contains

{

  "NotebookApp": {

    "password": "sha1:af540ed8f4........"

  }

}

 

(where I have deleted most of the password).  I moved that file away and now all is well.

I will leave it to others to work out how that got there, but it may be worth remembering in case this happens to anyone else.  I have no idea why that file gets created or what I did/didn't do for it to be there when no sessions were running.

Thanks for the suggestions, and especially to Volker.

John

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