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'
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