Cannot install Jupyter Lab (continuation)

martinrame

martinrame

Well, after solving the issue I posted on #478525, now I'm getting this after calling jupyter notebook --generate-config:

Code: 
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-notebook", line 6, in <module>
    from notebook.notebookapp import main
  File "/usr/local/lib/python3.7/site-packages/notebook/notebookapp.py", line 51, in <module>
    from zmq.eventloop import ioloop
  File "/usr/local/lib/python3.7/site-packages/zmq/__init__.py", line 50, in <module>
    from zmq import backend
  File "/usr/local/lib/python3.7/site-packages/zmq/backend/__init__.py", line 40, in <module>
    reraise(*exc_info)
  File "/usr/local/lib/python3.7/site-packages/zmq/utils/sixcerpt.py", line 34, in reraise
    raise value
  File "/usr/local/lib/python3.7/site-packages/zmq/backend/__init__.py", line 27, in <module>
    _ns = select_backend(first)
  File "/usr/local/lib/python3.7/site-packages/zmq/backend/select.py", line 28, in select_backend
    mod = __import__(name, fromlist=public_api)
  File "/usr/local/lib/python3.7/site-packages/zmq/backend/cython/__init__.py", line 6, in <module>
    from . import (constants, error, message, context,
ImportError: /usr/local/lib/python3.7/site-packages/zmq/backend/cython/error.so: Undefined symbol "zmq_strerror"
 
Thanks, that solved the issue.

Now I can start the service and access to the user interface. Btw, this is Jupyter Notebook, not Jupyter Lab.

Here's a screenshot:

1600512620368.png


When I click run or ctrl+enter, the calc is not done, and the server's console shows this:

Code: 
[root@jupyterlab ~]# service jupyter start
[root@jupyterlab ~]# Need to remove all those ^M characters from a DOS file? Try

    tr -d \\r < dosfile > newfile
        -- Originally by Dru <genesis@istar.ca>
[W 07:44:22.156 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[I 07:44:22.157 NotebookApp] Serving notebooks from local directory: /usr/home/jupyter
[I 07:44:22.157 NotebookApp] Jupyter Notebook 6.1.4 is running at:
[I 07:44:22.158 NotebookApp] http://jupyterlab:8888/
[I 07:44:22.158 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 07:44:29.710 NotebookApp] 302 POST /login?next=%2Ftree%3F (192.168.0.110) 26.92ms
^C
[root@jupyterlab ~]# [I 07:44:56.509 NotebookApp] Creating new notebook in
[I 07:44:56.569 NotebookApp] Writing notebook-signing key to /usr/home/jupyter/.local/share/jupyter/notebook_secret
/usr/local/lib/python3.7/site-packages/jupyter_client/connect.py:164: RuntimeWarning: Failed to set sticky bit on '/usr/home/jupyter/.local/share/jupyter/runtime/kernel-62f2b91b-2285-4250-b316-d9fb4e786415.json': [Errno 79] Inappropriate file type or format: '/usr/home/jupyter/.local/share/jupyter/runtime/kernel-62f2b91b-2285-4250-b316-d9fb4e786415.json'
Probably not a big deal, but runtime files may be cleaned up periodically.
  RuntimeWarning,
[I 07:44:58.331 NotebookApp] Kernel started: 62f2b91b-2285-4250-b316-d9fb4e786415, name: python3
/usr/local/lib/python3.7/site-packages/jupyter_client/connect.py:164: RuntimeWarning: Failed to set sticky bit on '/usr/home/jupyter/.local/share/jupyter/runtime/kernel-62f2b91b-2285-4250-b316-d9fb4e786415.json': [Errno 79] Inappropriate file type or format: '/usr/home/jupyter/.local/share/jupyter/runtime/kernel-62f2b91b-2285-4250-b316-d9fb4e786415.json'
Probably not a big deal, but runtime files may be cleaned up periodically.
  RuntimeWarning,
[W 07:45:19.514 NotebookApp] Replacing stale connection: 62f2b91b-2285-4250-b316-d9fb4e786415:c5d00131b1f547b780b108da491e5a77
[W 07:45:41.442 NotebookApp] Replacing stale connection: 62f2b91b-2285-4250-b316-d9fb4e786415:c5d00131b1f547b780b108da491e5a77
[W 07:45:58.426 NotebookApp] Timeout waiting for kernel_info reply from 62f2b91b-2285-4250-b316-d9fb4e786415
 
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Reactions: a6h
A few month ago I had to learn python, to produce graphical representation of some statistical analytics result. I merely used python and pip to install 3rd library packages (seaborn). May I ask you is there any specific reason to use Jupyter Lab? I know 3rd party products such as Jupyter provide some convenient, but I'm not very familiar with them. Thanks
 
vigole said:
... May I ask you is there any specific reason to use Jupyter Lab? I know 3rd party products such as Jupyter provide some convenient, but I'm not very familiar with them. Thanks
Click to expand...

Yes, I created a set of "notebooks" for options trading inside JupyterLab running on a Linux machine, now I'm trying to migrate it to a jail in my new home server.
 
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Reactions: a6h
If I create an 11.1 jail or even an older version, the packages installed using pkg will be older than those of 12.1?.
 
martinrame said:
If I create an 11.1 jail or even an older version, the packages installed using pkg will be older than those of 12.1?.
Click to expand...
The jail uses the same kernel as the host. The package repository is given in /etc/pkg/FreeBSD.conf (override by creating /usr/local/etc/pkg/repos/FreeBSD.conf) via the ABI macro, which is autogenerated to match the kernel version by default, but can be set in /usr/local/etc/pkg.conf.
 
Thanks. But I would like to create a jail trying to reproduce the behavior of an old FreeBSD system, if I create an 11.1 jail it will point to 11.1 packages?. That way I could try jupyter lab or jupyter notebook from that FreeBSD version, to check if that works.
 
From jail(8):
osrelease
The string for the jail's kern.osrelease sysctl and uname -r.

osreldate
The number for the jail's kern.osreldate and uname -K.
So that's what the userland inside the jail sees. Still, the jail runs on exactly the host's kernel; that's what jails are about.
 
Ok, I created a new jail with iocage create newjail -r 11.2-RELEASE, but the Jupyter notebook package is exactly the same as in the 12.1 jail.
 
Maybe iocage(8) does not set these two knobs osrelease & osreldate? Then you can decide that's a bug and submit a PR (see @top of the forum page). Please supply
  • freebsd-version on the host & from inside the jail
  • /etc/pkg/FreeBSD.conf, /usr/local/etc/pkg/repos/FreeBSD.conf (if it exists) & grep ABI /usr/local/etc/pkg.conf, all from inside the jail.
  • Remember that you have to give pkg(8) on the host the -j or --jail parameter to install packages into the jail.
 
Hi mjollnir, thanks for your help. I don't know if this is a bug yet.

Here are the values:

freebsd-version:

Host: 12.1-RELEASE-p8
Jail: 11.2-RELEASE-p15

From inside the jail:

Code: 
cat /etc/pkg/FreeBSD.conf
# $FreeBSD: releng/11.2/etc/pkg/FreeBSD.conf 333474 2018-05-10 23:58:33Z gjb $
#
# To disable this repository, instead of modifying or removing this file,
# create a /usr/local/etc/pkg/repos/FreeBSD.conf file:
#
#   mkdir -p /usr/local/etc/pkg/repos
#   echo "FreeBSD: { enabled: no }" > /usr/local/etc/pkg/repos/FreeBSD.conf
#

FreeBSD: {
  url: "pkg+http://pkg.FreeBSD.org/${ABI}/quarterly",
  mirror_type: "srv",
  signature_type: "fingerprints",
  fingerprints: "/usr/share/keys/pkg",
  enabled: yes
}

Code: 
grep ABI /usr/local/etc/pkg.conf
#ABI = "freebsd:10:x86:64";     # Autogenerated

Code: 
cat /usr/local/etc/pkg/repos/FreeBSD.conf
cat: /usr/local/etc/pkg/repos/FreeBSD.conf: No such file or directory

Do you see something strange?
 
Mmm, I think I'm having a network related issue. The Jupyter notebook web app tries to open a websocket connection, but as the jail is behind a pf firewall the app cannot connect to it.

Resuming, the web app runs on port 8888, as this port is allowed on the firewall I can connect without issues, but it cannot connect to the websockets server.

Now I wonder what's the websocket server port...
 
I'm not familiar with Jupyter web/server but AFAIK, if the server understand websocket and configure properly => it's possible that websocket uses the same ports aka 8888 (80 or 443, etc) through the Upgrade Header: Websocket protocol handshake:
Code: 
Connection: Upgrade
 
vigole said:
I'm not familiar with Jupyter web/server but AFAIK, if the server understand websocket and configure properly => it's possible that websocket uses the same ports aka 8888 (80 or 443, etc) through the Upgrade Header: Websocket protocol handshake:
Code: 
Connection: Upgrade
Click to expand...

Yes, you are right.

After reading here https://github.com/jupyter/notebook/issues/4457 it looks like an upgrade or downgrade of the package py37-tornado: 5.1.1 (the websockets server) could fix the issue.

Now, how can I upgrade a package using pkg?.

If I do pkg install py37-tornado6-6.0.4 I get this:

Code: 
root@jupyter11:~ # pkg install py37-tornado6-6.0.4
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
The following 1 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    py37-tornado6: 6.0.4

Number of packages to be installed: 1

The process will require 4 MiB more space.
582 KiB to be downloaded.

Proceed with this action? [y/N]: y
[jupyter11.1] [1/1] Fetching py37-tornado6-6.0.4.txz: 100%  582 KiB 297.7kB/s    00:02    
Checking integrity... done (1 conflicting)
  - py37-tornado6-6.0.4 conflicts with py37-tornado-5.1.1 on /usr/local/lib/python3.7/site-packages/tornado/__init__.py
Checking integrity... done (0 conflicting)
Conflicts with the existing packages have been found.
One more solver iteration is needed to resolve them.
The following 7 package(s) will be affected (of 0 checked):

Installed packages to be REMOVED:
    py37-ipykernel5: 5.3.0
    py37-jupyter_client: 6.1.3
    py37-nbconvert: 5.6.1_1
    py37-notebook: 6.0.3_2
    py37-terminado: 0.8.3
    py37-tornado: 5.1.1

New packages to be INSTALLED:
    py37-tornado6: 6.0.4

Number of packages to be removed: 6
Number of packages to be installed: 1

The operation will free 38 MiB.

Proceed with this action? [y/N]:

But I don't want to uninstall anything else, I just want to replace py37-tornado: 5.1.1 with py37-tornado6: 6.0.4.
 
After hours and hours of trying I gave up on the jail and installed right on the host. And it worked without issues, so, yes, it's a bug that only appears on jails. How can I report it?.
 
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