jupyterhub

references

VirtualEnv

First we create a virtual environment under '/opt/jupyterhub'. Both jupyterlab and jupyterhub will be installed into this virtualenv

[root@jhub ~]# python3 -m venv /opt/jupyterhub/

now we have a virtual env for python3 in /opt/jupyterhub

[root@jhub ~]# ls /opt/jupyterhub/bin/
activate  activate.csh  activate.fish  easy_install  easy_install-3.6  pip  pip3  pip3.6  python  python3

wheel package

this wheel package is hence installed in /opt

[root@jhub ~]# ls -ltr /opt/jupyterhub/lib/python3.6/site-packages
total 36
-rw-r--r--  1 root root  126 10 juil. 19:28 easy_install.py
drwxr-xr-x  6 root root 4096 10 juil. 19:28 setuptools
drwxr-xr-x  2 root root 4096 10 juil. 19:28 __pycache__
drwxr-xr-x  5 root root 4096 10 juil. 19:28 pkg_resources
drwxr-xr-x  2 root root 4096 10 juil. 19:28 setuptools-39.2.0.dist-info
drwxr-xr-x 11 root root 4096 10 juil. 19:28 pip
drwxr-xr-x  2 root root 4096 10 juil. 19:28 pip-9.0.3.dist-info
drwxr-xr-x  5 root root 4096 10 juil. 19:34 wheel
drwxr-xr-x  2 root root 4096 10 juil. 19:34 wheel-0.36.2.dist-info

upgrade pip

because of this warning

You are using pip version 9.0.3, however version 21.1.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.


[root@jhub ~]# /opt/jupyterhub/bin/python3 -m pip install --upgrade pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/47/ca/f0d790b6e18b3a6f3bd5e80c2ee4edbb5807286c21cdd0862ca933f751dd/pip-21.1.3-py3-none-any.whl (1.5MB)
    100% |████████████████████████████████| 1.6MB 755kB/s 
Installing collected packages: pip
  Found existing installation: pip 9.0.3
    Uninstalling pip-9.0.3:
      Successfully uninstalled pip-9.0.3
Successfully installed pip-21.1.3

jupyterhub & lab packages

[root@jhub ~]# /opt/jupyterhub/bin/python3 -m pip install jupyterhub jupyterlab
Successfully installed Mako-1.1.4 SQLAlchemy-1.4.20 alembic-1.6.5 anyio-3.2.1 babel-2.9.1 certifi-2021.5.30 certipy-0.1.3 chardet-4.0.0 contextvars-2.4 cryptography-3.4.7 dataclasses-0.8 greenlet-1.1.0 idna-2.10 immutables-0.15 json5-0.9.6 jupyter-server-1.9.0 jupyter-telemetry-0.1.0 jupyterhub-1.4.1 jupyterlab-3.0.16 jupyterlab-server-2.6.1 nbclassic-0.3.1 oauthlib-3.1.1 pamela-1.0.0 pyopenssl-20.0.1 python-editor-1.0.4 python-json-logger-2.0.1 pytz-2021.1 requests-2.25.1 requests-unixsocket-0.2.0 ruamel.yaml-0.17.10 ruamel.yaml.clib-0.2.6 sniffio-1.2.0 urllib3-1.26.6 websocket-client-1.1.0

ipywidgets

then also ipywidgets is installed in /opt because this is needed to allow connection between interactive tools running in the kernel and the user interface. other python scientific package can be installed in the traditional system paths

[root@jhub ~]# /opt/jupyterhub/bin/python3 -m pip install ipywidgets
Successfully installed MarkupSafe-2.0.1 Send2Trash-1.7.1 argon2-cffi-20.1.0 async-generator-1.10 attrs-21.2.0 backcall-0.2.0 bleach-3.3.0 cffi-1.14.6 decorator-5.0.9 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.6.1 ipykernel-5.5.5 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.6.3 jedi-0.18.0 jinja2-3.0.1 jsonschema-3.2.0 jupyter-client-6.2.0 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 jupyterlab-widgets-1.0.0 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nest-asyncio-1.5.1 notebook-6.4.0 packaging-21.0 pandocfilters-1.4.3 parso-0.8.2 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.11.0 prompt-toolkit-3.0.19 ptyprocess-0.7.0 pycparser-2.20 pygments-2.9.0 pyparsing-2.4.7 pyrsistent-0.18.0 python-dateutil-2.8.1 pyzmq-22.1.0 six-1.16.0 terminado-0.10.1 testpath-0.5.0 tornado-6.1 traitlets-4.3.3 typing-extensions-3.10.0.0 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.5.0

nodejs npm

JupyterHub also currently defaults to requiring configurable-http-proxy, which needs nodejs and npm.

[root@jhub ~]# dnf install nodejs npm
Installé:
  nodejs-1:10.24.0-1.module_el8.3.0+717+fa496f1d.x86_64      nodejs-full-i18n-1:10.24.0-1.module_el8.3.0+717+fa496f1d.x86_64      npm-1:6.14.11-1.10.24.0.1.module_el8.3.0+717+fa496f1d.x86_64 

JupyterHub Configuration

Create directory for jupyterhub config file and cd into it,

[root@jhub ~]#  mkdir -p /opt/jupyterhub/etc/jupyterhub/
[root@jhub ~]# cd /opt/jupyterhub/etc/jupyterhub/

Then generate the default configuration file

[root@jhub jupyterhub]# /opt/jupyterhub/bin/jupyterhub --generate-config
Writing default config to: jupyterhub_config.py

The generated jupyterhub_config.py file is nearly 1000 lines of commented configuration options. We will only change 1 line at this point, setting the default “spawner” to launch JupyterLab from the http-proxy URL. `grep -n c.Spawner.default jupyterhub_config.py` will show the line number that needs to be changed, 668 in my case.

Edit jupyterhub_config.py,

You will need to edit the configuration file to make the JupyterLab interface by the default. Set the following configuration option in your jupyterhub_config.py file:

#  - You can set this to `/lab` to have JupyterLab start by default, rather than Jupyter Notebook.
#c.Spawner.default_url = ''
c.Spawner.default_url = '/lab'

Further configuration options may be found in the documentation.

systemd startup

Create a systemd “Unit” file for starting jupyterhub,

[root@jhub jupyterhub]# mkdir -p /opt/jupyterhub/etc/systemd​​​​​​​

edit the Unit file /opt/jupyterhub/etc/systemd/jupyterhub.service

[root@jhub jupyterhub]# vim /opt/jupyterhub/etc/systemd​​​​​​​/jupyterhub.service
[Unit]

Description=JupyterHub
After=syslog.target network.target

[Service]

User=root
Environment="PATH=/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/jupyterhub/bin"
ExecStart=/opt/jupyterhub/bin/jupyterhub -f /opt/jupyterhub/etc/jupyterhub/jupyterhub_config.py

[Install]
WantedBy=multi-user.target

Now link that file to the directory with the system's systemd Unit files,

[root@jhub systemd​​​​​​​]# ln -s /opt/jupyterhub/etc/systemd​​​​​​​/jupyterhub.service /etc/systemd/system/jupyterhub.service
[root@jhub systemd​​​​​​​]# ls -l /etc/systemd/system/jupyterhub.service
lrwxrwxrwx 1 root root 67 10 juil. 22:07 /etc/systemd/system/jupyterhub.service -> /opt/jupyterhub/etc/systemd​​​​​​​/jupyterhub.service

Then tell systemd to reload its configuration files so that it knows about that new jupyterhub.service

[root@jpthub systemd​​​​​​​]# systemctl daemon-reload

start it and enable it at boot

[root@jhub systemd​​​​​​​]# systemctl start jupyterhub.service
[root@jhub systemd​​​​​​​]# systemctl status jupyterhub.service
● jupyterhub.service - JupyterHub
   Loaded: loaded (/opt/jupyterhub/etc/systemd​​​​​​​/jupyterhub.service; linked; vendor preset: disabled)
   Active: active (running) since Sat 2021-07-10 22:10:04 CEST; 8s ago
   
[root@jhub systemd​​​​​​​]# systemctl enable jupyterhub.service
Created symlink /etc/systemd/system/multi-user.target.wants/jupyterhub.service → /opt/jupyterhub/etc/systemd​​​​​​​/jupyterhub.service.
   

firewall

open jupyterhub webservice to our local ip network

[root@jhub systemd​​​​​​​]# firewall-cmd --permanent --add-rich-rule 'rule family="ipv4" source address="172.168.0.0/16" port port=8000 protocol=tcp  accept'
success
[root@jhub systemd​​​​​​​]# firewall-cmd --reload
success

jupyterhub webservice

now the jupyterhub webservice is available at http://jhub.domain.fr:8000

https and reverse proxy with apache

change the c.JupyterHub.bind_url on jupyterhub config file

[root@jhub jupyterhub]# grep c.JupyterHub.bind_url  /opt/jupyterhub/etc/jupyterhub/jupyterhub_config.py
#c.JupyterHub.bind_url = 'http://:8000'
c.JupyterHub.bind_url = 'http://127.0.0.1:8000'

apache

install httpd and mod_ssl package

[root@jhub certs]# yum install httpd mod_ssl

jupyterhub vhost configuration

[root@jhub certs]# cat /etc/httpd/conf.d/jupyterhub.conf

# redirect HTTP to HTTPS
Listen 80
<VirtualHost jhub.domain.fr:80>
  ServerName jhub.domain.fr
  Redirect / https://jhub.domain.fr/
</VirtualHost>

Listen 443
<VirtualHost jhub.domain.fr:443>

  ServerName jhub.domain.fr

  # configure SSL
  SSLEngine on
  SSLCertificateFile /etc/pki/tls/certs/domain.fr_eu_cert.cer
  SSLCertificateKeyFile /etc/pki/tls/private/domain.fr.key
  SSLProtocol All -SSLv2 -SSLv3
#  SSLOpenSSLConfCmd DHParameters /etc/ssl/certs/dhparam.pem
  SSLCipherSuite EECDH+AESGCM:EDH+AESGCM:AES256+EECDH:AES256+EDH

  # Use RewriteEngine to handle websocket connection upgrades
  RewriteEngine On
  RewriteCond %{HTTP:Connection} Upgrade [NC]
  RewriteCond %{HTTP:Upgrade} websocket [NC]
  RewriteRule /(.*) ws://127.0.0.1:8000/$1 [P,L]

  <Location "/">
    # preserve Host header to avoid cross-origin problems
    ProxyPreserveHost on
    # proxy to JupyterHub
    ProxyPass         http://127.0.0.1:8000/
    ProxyPassReverse  http://127.0.0.1:8000/
  </Location>
</VirtualHost>

firewall

open https service in the firewall to our IP subnet

[root@jpthub certs]# firewall-cmd --permanent --add-rich-rule 'rule family="ipv4" source address="172.168.0/16" service name="https" log prefix="https" accept'
success
[root@jpthub certs]# firewall-cmd --reload
success

SAML authenticator

[root@jhub jupyterhub]#  /opt/jupyterhub/bin/python3 -m pip install jupyterhub-samlauthenticator
Collecting jupyterhub-samlauthenticator
  Downloading jupyterhub_samlauthenticator-0.0.9-py3-none-any.whl (17 kB)
Requirement already satisfied: jupyterhub>=0.9.0 in ./lib/python3.6/site-packages (from jupyterhub-samlauthenticator) (1.4.1)
...
Installing collected packages: pyopenssl, future, lxml, eight, signxml, jupyterhub-samlauthenticator
  Attempting uninstall: pyopenssl
    Found existing installation: pyOpenSSL 20.0.1
    Uninstalling pyOpenSSL-20.0.1:
      Successfully uninstalled pyOpenSSL-20.0.1
Successfully installed eight-1.0.1 future-0.18.2 jupyterhub-samlauthenticator-0.0.9 lxml-4.6.3 pyopenssl-19.1.0 signxml-2.8.2

it installed those directories/files

[root@jhub jupyterhub]# ls -ltr /opt/jupyterhub/lib/python3.6/site-packages/samlauthenticator/
total 44
-rw-r--r-- 1 root root 36101 12 juil. 16:33 samlauthenticator.py
-rw-r--r-- 1 root root  1144 12 juil. 16:33 __init__.py
drwxr-xr-x 2 root root  4096 12 juil. 16:33 __pycache__
[root@jhub jupyterhub]# ls -ltr /opt/jupyterhub/lib/python3.6/site-packages/jupyterhub_samlauthenticator-0.0.9.dist-info
total 40
-rw-r--r-- 1 root root  1085 12 juil. 16:33 LICENSE.txt
-rw-r--r-- 1 root root    92 12 juil. 16:33 WHEEL
-rw-r--r-- 1 root root    18 12 juil. 16:33 top_level.txt
-rw-r--r-- 1 root root 17256 12 juil. 16:33 METADATA
-rw-r--r-- 1 root root     0 12 juil. 16:33 REQUESTED
-rw-r--r-- 1 root root     4 12 juil. 16:33 INSTALLER
-rw-r--r-- 1 root root  1026 12 juil. 16:33 RECORD

REMOTE_USER auth

we'll try to authenticate through a shibboleth SP proxy to benefit from federated access , then redirect that REMOTE_USER to jupyterhub

[root@jhub jupyterhub]#  /opt/jupyterhub/bin/python3 -m pip  install jhub_remote_user_authenticator
Collecting jhub_remote_user_authenticator
  Downloading jhub_remote_user_authenticator-0.1.0-py3-none-any.whl (3.6 kB)
  ...
  Installing collected packages: jhub-remote-user-authenticator
Successfully installed jhub-remote-user-authenticator-0.1.0
docpublic/systemes/systemes/jupyter/jupyterhub.txt · Last modified: 2021/07/12 20:58 by adminjp
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