Jupyter permission denied error

nsonoda · March 22, 2024, 2:14pm

Hi!

I’ve been getting the following error when trying to start an interactive session with Jupyter:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/traitlets/traitlets.py", line 528, in get
    value = obj._trait_values[self.name]
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/jupyter-notebook", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/jupyter_core/application.py", line 264, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "/usr/local/lib/python3.6/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/usr/local/lib/python3.6/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/notebook/notebookapp.py", line 2148, in initialize
    self.init_configurables()
  File "/usr/local/lib/python3.6/site-packages/notebook/notebookapp.py", line 1650, in init_configurables
    connection_dir=self.runtime_dir,
  File "/usr/local/lib/python3.6/site-packages/traitlets/traitlets.py", line 556, in __get__
    return self.get(obj, cls)
  File "/usr/local/lib/python3.6/site-packages/traitlets/traitlets.py", line 535, in get
    value = self._validate(obj, dynamic_default())
  File "/usr/local/lib/python3.6/site-packages/jupyter_core/application.py", line 95, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/usr/local/lib/python3.6/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/usr/lib64/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/lib64/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/lib64/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  [Previous line repeated 1 more time]
  File "/usr/lib64/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/home/myuser'

Unfortunately, in this case, I don’t have the /home directory exported to the nodes, so it’s necessary to use another directory to store $HOME/.local. I tried modifying the c.NotebookApp.notebook_dir option in config.py, but I’m still getting the error.
Could you assist me?

Thanks!
Nícolas

jeff.ohrstrom · March 22, 2024, 3:47pm

From looking at the stacktrace here - looks like current versions of jupyter respond to the JUPYTER_RUNTIME_DIR environment variable. Though previous versions seemed to have responded to XDG_RUNTIME_DIR though I can’t tell what version you’re on and what will work.

github.com

jupyter/jupyter_core/blob/18cc67e2f32d32ae3cebc6725251a597a4971851/jupyter_core/paths.py#L189


      
                  if appdata:
                      return str(Path(appdata, "jupyter").resolve())
                  return pjoin(jupyter_config_dir(), "data")
              # Linux, non-OS X Unix, AIX, etc.
              xdg = env.get("XDG_DATA_HOME", None)
              if not xdg:
                  xdg = pjoin(home, ".local", "share")
              return pjoin(xdg, "jupyter")
          
          
          def jupyter_runtime_dir() -> str:
              """Return the runtime dir for transient jupyter files.
          
              Returns JUPYTER_RUNTIME_DIR if defined.
          
              The default is now (data_dir)/runtime on all platforms;
              we no longer use XDG_RUNTIME_DIR after various problems.
              """
              env = os.environ
          
              if env.get("JUPYTER_RUNTIME_DIR"):

After you resolve that you may also run into issues with JUPYTER_DATA_DIR which is similar.

github.com

jupyter/jupyter_core/blob/18cc67e2f32d32ae3cebc6725251a597a4971851/jupyter_core/paths.py#L158


      
              if env.get("JUPYTER_CONFIG_DIR"):
                  return env["JUPYTER_CONFIG_DIR"]
          
              if use_platform_dirs():
                  return platformdirs.user_config_dir(APPNAME, appauthor=False)
          
              home_dir = get_home_dir()
              return pjoin(home_dir, ".jupyter")
          
          
          def jupyter_data_dir() -> str:
              """Get the config directory for Jupyter data files for this platform and user.
          
              These are non-transient, non-configuration files.
          
              Returns JUPYTER_DATA_DIR if defined, else a platform-appropriate path.
              """
              env = os.environ
          
              if env.get("JUPYTER_DATA_DIR"):
                  return env["JUPYTER_DATA_DIR"]

nsonoda · March 22, 2024, 4:52pm

Hi Jeff!

Thank you very much! Setting the JUPYTER_RUNTIME_DIR and JUPYTER_DATA_DIR variables solved the issue.

Thanks again!

system · September 18, 2024, 4:53pm

This topic was automatically closed 180 days after the last reply. New replies are no longer allowed.

Topic		Replies	Views
Jupyter startup issues Get Help	4	1529	May 26, 2022
Jupyter failing to start Get Help question	5	1268	May 26, 2022
Timed out waiting for Jupyter Notebook/permission denied Get Help	3	1960	May 26, 2022
Jupyter notebook 'Connect to Jupyter' button not rendering Get Help	2	1100	May 26, 2022
Jupyter Notebook Fails Get Help	4	104	November 13, 2024

Jupyter permission denied error

Related topics