User symlink files in /run/ are not deleted when server is stopped, causing 500 internal server error

[gmboyer]

Bug:

If a user stops their JupyterHub server through their control panel and then attempts to start it again, they will receive an error when systemdspawner spawns the user:

"500 : Internal Server Error Error in Authenticator.pre_spawn_start: FileExistsError [Errno 17] File exists: '/run/jupyter-username-singleuser'

The user cannot connect until I manually delete the user's symlink file in /run/.

Perhaps this is a bug where the user's symlink isn't automatically deleted from /run/ when they stop their server. When the spawner tries to start their server again, it erroneously thinks the server is already running and throws the 500 error.

Additional information:

I'm using a GitLab OAuthenticator with systemdspawner's dynamic_spawning set to true, if that helps.

Ubuntu 20.04 JupyterHub 1.2.2 Latest version of systemdspawner as of Dec. 15, 2020

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[yuvipanda]

@minrk do you think this is related to the recent fix to hide tokens from the process list?

[bcbnz]

I encountered the same problem (except in my case the links were at /run/jupyterhub-username). I have temporarily solved it by adding the following code to systemdspawner/systemdspawner.py at line 219 (just after the 'check if service failed' block):

        runlink = '/run/jupyterhub-{}'.format(self.user.name)
        if os.path.lexists(runlink) and not os.path.exists(runlink):
            self.log.info('Removing stale link %s', runlink)
            os.unlink(runlink)

os.path.exists returns False for broken symlinks while os.path.lexists returns True, so this should avoid trying to remove the link if its target still exists.

This is too hard-coded to be a general solution (especially since the path in my case is different to the original report), but may be useful to others until a proper solution is developed.

Also, I see the following messages in the logs when a user server is started up. I'm not sure if the migration message is relevant to this issue.

Jan 05 12:14:33 image systemd[1]: Started /bin/bash -c cd /var/lib/jupyterhub_users/username && exec jupyterhub-singleuser --port=47567.
Jan 05 12:14:33 image jupyterhub[108]: Running as unit: jupyterhub-username.service
Jan 05 12:14:33 image systemd[110]: Found pre-existing public RuntimeDirectory= directory /run/jupyterhub-username, migrating to /run/private/jupyterhub-username.
Jan 05 12:14:33 image systemd[110]: Apparently, service previously had DynamicUser= turned off, and has now turned it on.

[gmboyer]

@bcbnz Your solution worked like a charm. Thank you for taking the time to post this workaround. For those who have the same symlink format I did, modify the first line of bcbnz's code to:

runlink = '/run/jupyter-{}-singleuser'.format(self.user.name)

[fracaron]

For me adding c.SystemdSpawner.unit_extra_properties = {'RuntimeDirectoryPreserve': 'no'} to jupyterhub config resolved the issue. The user's environment file was deleted after restarting the jupyterhub service while the symlink to it was preserved.

The default set by systemdspawner 'RuntimeDirectoryPreserve': 'restart' will only work if used with c.JupyterHub.cleanup_servers = False. cleanup_servers = False will avoid shuting down the single-user servers with jupyterhub restart.

Using Ubuntu 20.04 and jupyterhub 1.3.0

[doyeonkp]

change the code in systemd.py Currently it looks like this

def ensure_environment_directory(environment_file_directory):
    """Ensure directory for environment files exists and is private"""
    # ensure directory exists
    os.makedirs(environment_file_directory, mode=0o700, exist_ok=True)
    # validate permissions
    mode = os.stat(environment_file_directory).st_mode
    if mode & 0o077:
        warnings.warn(
            f"Fixing permissions on environment directory {environment_file_directory}: {oct(mode)}",
            RuntimeWarning,
        )
        os.chmod(environment_file_directory, 0o700)

The log said [Error17] File exists, so I assume os.makedirs(environment_file_directory, mode=0o700, exist_ok=True) this line is cause of the error.

so changed as

def ensure_environment_directory(environment_file_directory):
    """Ensure directory for environment files exists and is private"""
    # ensure directory exists
    if not os.path.isdir(environment_file_directory):
        os.makedirs(environment_file_directory, mode=0o700, exist_ok=True)
    # validate permissions
    mode = os.stat(environment_file_directory).st_mode
    if mode & 0o077:
        warnings.warn(
            f"Fixing permissions on environment directory {environment_file_directory}: {oct(mode)}",
            RuntimeWarning,
        )
        os.chmod(environment_file_directory, 0o700)

so check the file exist then create. Now mine is work fine. Hope it helps someone face the same issue like me

[adsche]

Hey all, I believe the more straightforward solution might be to just set RUN_ROOT='/run/private if DynamicUser==True. This works for me and is in accordance with the systemd documentation on DynamicUser [1]. Sure, skipping the check as in the above solutions also works, but it will also modify the mode of the symlink (causing a warning message from systemd) instead of the actual state dir in /run/private...

[1] https://www.freedesktop.org/software/systemd/man/latest/systemd.exec.html - but look for the section starting with RuntimeDirectory= ...