Missing module sqlite3 when running Jupyterhub on Rocky9

JupyterHub
1

I’m trying to install Jupyterhub for my users on a Rocky9 Linux system. Most of the installation went fine. There were no errors for the following commands:

useradd -m -c 'Runs the JupyterHub server' jupyterhub
passwd -l jupyterhub
su - jupyterhub
python3.12 -m venv jupyterhub-env
source jupyterhub-env/bin/activate
pip install jupyterhub notebook configurable-http-proxy

Then, generate a configuration file, which is ~/jupyterhub_config.py

jupyterhub --generate-config

I only changed the port number in the config file.

Finally, I started the server:

jupyterhub
[I 2024-08-21 15:55:29.320 JupyterHub app:3307] Running JupyterHub version 5.1.0
[I 2024-08-21 15:55:29.320 JupyterHub app:3337] Using Authenticator: jupyterhub.auth.PAMAuthenticator-5.1.0
[I 2024-08-21 15:55:29.320 JupyterHub app:3337] Using Spawner: jupyterhub.spawner.LocalProcessSpawner-5.1.0
[I 2024-08-21 15:55:29.320 JupyterHub app:3337] Using Proxy: jupyterhub.proxy.ConfigurableHTTPProxy-5.1.0
[I 2024-08-21 15:55:29.326 JupyterHub app:1837] Loading cookie_secret from /home/jupyterhub/jupyterhub_cookie_secret
[E 2024-08-21 15:55:29.342 JupyterHub app:3873]
    Traceback (most recent call last):
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/jupyterhub/app.py", line 3870, in launch_instance_async
        await self.initialize(argv)
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/jupyterhub/app.py", line 3349, in initialize
        self.init_db()
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/jupyterhub/app.py", line 2009, in init_db
        self.session_factory = orm.new_session_factory(
                               ^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/jupyterhub/orm.py", line 1564, in new_session_factory
        engine = create_engine(url, **kwargs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "<string>", line 2, in create_engine
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/sqlalchemy/util/deprecations.py", line 281, in warned
        return fn(*args, **kwargs)  # type: ignore[no-any-return]
               ^^^^^^^^^^^^^^^^^^^
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/sqlalchemy/engine/create.py", line 599, in create_engine
        dbapi = dbapi_meth(**dbapi_args)
                ^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/jupyterhub/jupyterhub-env/lib/python3.12/site-packages/sqlalchemy/dialects/sqlite/pysqlite.py", line 508, in import_dbapi
        from sqlite3 import dbapi2 as sqlite
      File "/usr/local/lib/python3.12/sqlite3/__init__.py", line 57, in <module>
        from sqlite3.dbapi2 import *
      File "/usr/local/lib/python3.12/sqlite3/dbapi2.py", line 27, in <module>
        from _sqlite3 import *
    ModuleNotFoundError: No module named '_sqlite3'

I googled for solutions, but came up empty, so I hope someone here can help.

Thanks in advance!

Scott Anderson

2

In a rockylinux:9 container:

# dnf install python3.12
...

# which python3.12
/usr/bin/python3.12

If I copy your commands I end up with a working JupyterHub.

It looks like you’re using a non-standard version of Python under /usr/local:

Is it possible your Python isn’t correctly installed, or has somehow become corrupted due to conflicting packages?

3

It’s certainly possible that I made a mistake in installing Python 3.12. I followed these directions: CrownCloud Wiki - How To Install Python 3 12 On RockyLinux 9

but only recently, so not a lot of people have used the Python 3.12 yet.

I’ll try Python 3.9, which Rocky9 came with.

Thanks for the suggestion!

4

Using the Python 3.9 worked fine, so suspicion now falls on the Python 3.12. Thanks for the suggestion!

5

installing Python from source has a number of ‘optional’ dependencies that shouldn’t really be optional, and are available in ~all Python installations except some manual ones. sqlite is one of them. To install python from source, make sure you have sqlite-devel before compiling Python:

dnf install sqlite-devel

You can also look in the (very long) output of compiling Python for hints about missing optional dependencies.

6

Thank you! I’ll look into that. It’s good to know that I might not have botched the installation; it might just need some additions.

Scott