Jupyterhub batchsawner permission error

[Evan Clark]

When attempting to use batchspawner with slurm I get the following error and I'm not sure how to resolve it. It is similar to the XDG_Environment variable issue some users have reported, however it is inserting the proper UID for the user that is spawning a notebook. The run folder with the proper UID does have read and execute permissions for the individual user so that doesn't appear to be the issue either.

  File "/var/web_services/galaxy/jupyter_conda/bin/jupyterhub-singleuser", line 6, in <module>

    main()

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/jupyterhub/singleuser.py", line 455, in main

    return SingleUserNotebookApp.launch_instance(argv)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/jupyter_core/application.py", line 266, in launch_instance

    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/traitlets/config/application.py", line 657, in launch_instance

    app.initialize(argv)

  File "<decorator-gen-7>", line 2, in initialize

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/traitlets/config/application.py", line 87, in catch_config_error

    return method(app, *args, **kwargs)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/notebook/notebookapp.py", line 1505, in initialize

    self.init_configurables()

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/notebook/notebookapp.py", line 1209, in init_configurables

    connection_dir=self.runtime_dir,

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/traitlets/traitlets.py", line 556, in __get__

    return self.get(obj, cls)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/traitlets/traitlets.py", line 535, in get

    value = self._validate(obj, dynamic_default())

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/jupyter_core/application.py", line 99, in _runtime_dir_default

    ensure_dir_exists(rd, mode=0o700)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/site-packages/jupyter_core/utils/__init__.py", line 13, in ensure_dir_exists

    os.makedirs(path, mode=mode)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/os.py", line 210, in makedirs

    makedirs(head, mode, exist_ok)

  File "/var/web_services/galaxy/jupyter_conda/lib/python3.6/os.py", line 220, in makedirs

    mkdir(name, mode)

PermissionError: [Errno 13] Permission denied: '/run/user/1261'

[Thomas Kluyver]

I'm not familiar with how Slurm works, but I'd guess that it's running the job in a context which doesn't have access to that directory; either it's not really running as that user, or it's running after the user has 'logged out', so the directory has been deleted. The simplest workaround is to unset the XDG_RUNTIME_DIR environment variable; it should use a fallback directory instead.

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[Evan Clark]

I did unset that variable however, I still get the same error. The
directories still exist on the servers where the tasks run from as well.

Thomas Kluyver wrote:
> running after the user has 'l

--

[Carol Willing]

Hi Evan,

Which version of batchspawner are you using? https://github.com/jupyterhub/batchspawner/releases

Feel free to open an issue at the batchspawner or jupyterhub repo and we can continue troubleshooting there too :-)

Carol

[Evan Clark]

I'm using batchspawner==0.8.0rc0. I can open an issue on the github repo.

Carol Willing

April 20, 2018 6:42 PM

Hi Evan,

Which version of batchspawner are you using? https://github.com/jupyterhub/batchspawner/releases

Feel free to open an issue at the batchspawner or jupyterhub repo and we can continue troubleshooting there too :-)

Carol

On Friday, April 20, 2018 at 3:33:22 PM UTC-7, Evan Clark wrote:

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Thomas Kluyver

April 20, 2018 4:23 PM

I'm not familiar with how Slurm works, but I'd guess that it's running the job in a context which doesn't have access to that directory; either it's not really running as that user, or it's running after the user has 'logged out', so the directory has been deleted. The simplest workaround is to unset the XDG_RUNTIME_DIR environment variable; it should use a fallback directory instead.

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Evan Clark

April 20, 2018 10:55 AM

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