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.
On 20 April 2018 at 16:55, Evan Clark <[email protected]> wrote: > 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' > > -- > You received this message because you are subscribed to the Google Groups > "Project Jupyter" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > To view this discussion on the web visit https://groups.google.com/d/ > msgid/jupyter/cd0dc951-5df0-4c03-8c8a-f5cb7aded66e%40googlegroups.com > <https://groups.google.com/d/msgid/jupyter/cd0dc951-5df0-4c03-8c8a-f5cb7aded66e%40googlegroups.com?utm_medium=email&utm_source=footer> > . > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "Project Jupyter" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/jupyter/CAOvn4qjskc_vC8TRo%2Bm4G%3DkR52_59QGQH%2B9MJE0jryVB%2Bj%2B9QQ%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
