Existing stopped container is not removed when newly requested image is different and remove = False

[dijksterhuis]

Bug description

Previously stopped container 1 derived from image A that is different to the latest image B chosen by a user from the options form is not removed when it should be in order to create container 2. Instead, container 1 is simply restarted.

Potential FIx

An additional if block can be added around here:

# if current stopped container's image != image that was just requested
if obj and obj["Config"]["Image"] != image:
    self.log.warning(
        "Removing %s of previously selected image %s that should be cleaned up: %s (id: %s)",
        self.object_type,
        self.image,
        self.object_name,
        self.object_id[:7],
    )
    await self.remove_object()
    
    obj = None

Can put together a PR. Just tested by editing current master branch install on the host myself and works perfectly well (although jouranlctl doesn't seem to be logging things correctly).

Expected behaviour

A user stopping their server and selecting image B should cause the existing stopped container 1 based on image A to be removed and a new container 2 created based on image B.

Actual behaviour

A user stops their server and selects image B but existing container 1 is restarted.

How to reproduce

With c.Spawner.remove = False and c.Spawner.allowed_images = {image_name_a: image_a, image_name_b: image_b} and a Lab ide.

1. User clicks Start Server and selects image A in the option form
2. User waits for server to load.
3. User goes to File > Hub Control Panel > Stop My Server
4. User clicks Start Server and selects image B in the option form
5. User waits for server to load.
6. User is presented with the container 1 as before (original container 1 is not removed)

Your personal set up

• OS: Ubuntu 18.04
• Version(s): On host:

$ docker --version && pip3 list | grep jupy && pip3 list | grep docker
Docker version 20.10.3, build 48d30b5
jupyter-client                6.1.3
jupyter-core                  4.6.3
jupyter-telemetry             0.1.0
jupyterhub                    1.1.0
jupyterhub-dummyauthenticator 0.3.1
jupyterlab                    2.1.3
jupyterlab-server             1.1.5
docker                        4.2.0
dockerspawner                 12.0.0

• Full environment

Container installs (we use custom images available at dockerhub and/or GitHub):

notebook==6.1.5
jupyter==1.0.0
jupyterhub==1.1.0
jupyter_core==4.6.1
jupyterlab==1.2.1
ipython==7.9.0
jupyter-tensorboard
ipykernel==5.0.0

• Configuration

Output of: $ grep -v '\(^#\|^[[:space:]]*$\)' /etc/jupyterhub/config.py

import os
import requests
from jupyter_client.localinterfaces import public_ips
from jupyterhub.auth import PAMAuthenticator as Auth
SRV = "/srv/jupyterhub/"
VAR = "/var/opt/jupyterhub/"
CONF = "/etc/jupyterhub"
USR = "/usr/local/bin"
c = get_config()
c.JupyterHub.allow_named_servers = True
c.JupyterHub.cookie_secret_file = os.path.join(VAR, 'jupyterhub_cookie_secret')
c.JupyterHub.cookie_max_age_days = 60.0
c.JupyterHub.pid_file = os.path.join(VAR, 'jupyterhub.pid')
c.JupyterHub.named_server_limit_per_user = 4
c.JupyterHub.admin_access = True
c.JupyterHub.db_url = os.path.join('sqlite:/', VAR, 'jupyterhub.sqlite')
c.JupyterHub.hub_ip = public_ips()[0]
c.JupyterHub.bind_url = 'http://127.0.0.1:8000/jupyterhub/'
c.JupyterHub.hub_port = 8080
c.JupyterHub.proxy_api_ip = '0.0.0.0'
secret_token = os.urandom(64)
c.ConfigurableHTTPProxy.auth_token = secret_token.hex()
c.ConfigurableHTTPProxy.pid_file = os.path.join(VAR, "jupyterhub-proxy.pid")
c.JupyterHub.logo_file = os.path.abspath(os.path.join(SRV, '<logo_file>.png'))
c.JupyterHub.authenticator_class = Auth
c.Authenticator.admin_users = {'<admin user name>'}
c.Authenticator.create_system_users = False
c.Authenticator.delete_invalid_users = True
c.JupyterHub.spawner_class = 'dockerspawner.SystemUserSpawner'
c.Spawner.debug = True
c.Spawner.remove = True
c.Spawner.name_template = "{username}-{servername}"
def get_image_allowlist(Spawner):
    """
    Load the allowlist file and provide the mappings as options to users
    """
    allowlist_file_path = os.path.join(CONF, 'image_allowlist.txt')
    with open(allowlist_file_path, 'r') as f:
        data = f.readlines()
    data = [i.rstrip('\n').split(',') for i in data if i != '\n']
    image_allowlist = {k: v.replace(' ', '') for k, v in data}
    return image_allowlist

c.Spawner.allowed_images = get_image_allowlist

# entrypoint.sh will always call start.sh from docker stacks once it's done doing any fancy business
spawn_cmd = os.environ.get('DOCKER_SPAWN_CMD', "entrypoint.sh")
c.Spawner.extra_create_kwargs.update({'command': spawn_cmd})

# need to mount and chown extra volume/bind mounts
c.Spawner.run_as_root = True
c.Spawner.mem_guarantee = 17179869184
c.Spawner.cpu_guarantee = 10.0
c.Spawner.extra_host_config = {
    'runtime': 'nvidia',
    'pid_mode': 'host',
    'shm_size': '16G',
}
c.Spawner.volumes = {
    '<host_volume_name>': '/shares/local/<mount point>',
    '<host_bind_mount_path>': '/shares/network/<mount_point>',
}

• Logs

journalctl -u jupyterhub since last hub restart:

Mar 29 23:52:31 <servernamee> systemd[1]: Started JupyterHub.
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [W 2021-03-29 23:52:31.947 JupyterHub app:678] JupyterHub.proxy_api_ip is deprecated in JupyterHub 0.8, use ConfigurableHTTPProxy.api_url
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.947 JupyterHub app:2240] Running JupyterHub version 1.1.0
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.948 JupyterHub app:2271] Using Authenticator: jupyterhub.auth.PAMAuthenticator-1.1.0
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.948 JupyterHub app:2271] Using Spawner: dockerspawner.systemuserspawner.SystemUserSpawner-12.0.0
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.948 JupyterHub app:2271] Using Proxy: jupyterhub.proxy.ConfigurableHTTPProxy-1.1.0
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.955 JupyterHub app:1349] Loading cookie_secret from /var/opt/jupyterhub/jupyterhub_cookie_secret
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [W 2021-03-29 23:52:31.969 JupyterHub configurable:168] Config option `delete_invalid_users` not recognized by `PAMAuthenticator`.
Mar 29 23:52:31 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:31.987 JupyterHub app:1655] Not using whitelist. Any authenticated user will be allowed.
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:32.004 JupyterHub app:2311] Initialized 0 spawners in 0.005 seconds
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [W 2021-03-29 23:52:32.006 JupyterHub proxy:643] Running JupyterHub without SSL.  I hope there is SSL termination happening somewhere else...
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:32.006 JupyterHub proxy:646] Starting proxy @ http://127.0.0.1:8000/jupyterhub/
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.405 [ConfigProxy] info: Proxying http://127.0.0.1:8000 to (no default)
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.408 [ConfigProxy] info: Proxy API at http://0.0.0.0:8001/api/routes
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.877 [ConfigProxy] info: 200 GET /api/routes
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:32.878 JupyterHub app:2556] Hub API listening on http://<ip addr>:8080/jupyterhub/hub/
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.879 [ConfigProxy] info: 200 GET /api/routes
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:32.879 JupyterHub proxy:320] Checking routes
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: [I 2021-03-29 23:52:32.879 JupyterHub proxy:400] Adding default route for Hub: /jupyterhub/ => http://<ip addr>:8080
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.880 [ConfigProxy] info: Adding route /jupyterhub -> http://<ip addr>:8080
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.881 [ConfigProxy] info: Route added /jupyterhub -> http://<ip addr>:8080
Mar 29 23:52:32 <servernamee> jupyterhub[25964]: 23:52:32.881 [ConfigProxy] info: 201 POST /api/routes/jupyterhub
Mar 29 23:52:32 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:32.882 JupyterHub app:2631] JupyterHub is now running at http://127.0.0.1:8000/jupyterhub/
Mar 29 23:52:36 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:36.567 JupyterHub log:174] 200 GET /jupyterhub/hub/home (<username>@<user IP>) 78.24ms
Mar 29 23:52:37 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:37.937 JupyterHub log:174] 200 GET /jupyterhub/hub/spawn/<username> (<username>@<user IP>) 8.33ms
Mar 29 23:52:42 <servername> python3[25964]: pam_loginuid(login:session): Error writing /proc/self/loginuid: Operation not permitted
Mar 29 23:52:42 <servername> python3[25964]: pam_loginuid(login:session): set_loginuid failed
Mar 29 23:52:42 <servername> python3[25964]: pam_unix(login:session): session opened for user <username> by (uid=0)
Mar 29 23:52:42 <servername> jupyterhub[25964]: [W 2021-03-29 23:52:42.665 JupyterHub auth:956] Failed to open PAM session for <username>: [PAM Error 14] Cannot make/remove an entry for the specified session
Mar 29 23:52:42 <servername> jupyterhub[25964]: [W 2021-03-29 23:52:42.666 JupyterHub auth:957] Disabling PAM sessions from now on.
Mar 29 23:52:42 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:42.837 JupyterHub dockerspawner:942] Container '<username>-' is gone
Mar 29 23:52:43 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:43.261 JupyterHub dockerspawner:1167] Created container <username>- (id: 8f74cbc) from image <imageA>
Mar 29 23:52:43 <servername> jupyterhub[25964]: [I 2021-03-29 23:52:43.261 JupyterHub dockerspawner:1190] Starting container <username>- (id: 8f74cbc)

Second container start doesn't seemed to be caught by logs and/or our server's journalctl isn't updating.

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[manics]

There was a discussion on the community forum recently:
https://discourse.jupyter.org/t/dockerspawner-container-deletion-by-user-choice/8024/4
Please add your thoughts there since it's a good forum for getting input from the rest of the community.

Setting remove = True should always remove the existing container. The problem with only removing the container if a different image is requested is that a user may not know whether their container will be deleted or not. It's therefore better to always remove the container and document which directories can be used for persistant data.

[dijksterhuis]

Hey @manics hadn't seen that forum post so thanks for the link. Was an interesting read. Will add a new post (and link back here) as it's not exactly the same. Still think that this is weird/unexpected behaviour that should be handled if remove = False is made available as a configuration option.

[meeseeksmachine]

This issue has been mentioned on Jupyter Community Forum. There might be relevant details there:

https://discourse.jupyter.org/t/dockerspawner-undocumented-behaviour-remove-false-does-not-replace-existing-image-a-with-new-image-b/8576/1

[minrk]

Summarizing what I think we should do from the forum:

1. better document that remove=False is really just for testing and requires manual intervention to delete data
2. warn when using remove=True about pitfalls that it’s not really what should be used
3. persist a user home directory volume by default in a manner that's easily overridden by default
4. switch to remove=True as the default, once home directories are persisted

There is no general 'home directory' persistence that will work in general, but we can pick a default that works for jupyter docker-stacks and make it easy to override. KubeSpawner's been doing this for ages and it works great.