Cases2 cases

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1. IL-0489 Rejoining a failed node of Magic Pages' three-node MySQL cluster broke its metadata and took customer websites down

   Magic Pages2025

   Symptoms

   On 15 January 2025, from about 09:55 to 11:36 CET, a database outage at Magic Pages took down customer websites. It began when the founder tried to reconnect a failed third node to the high-availability MySQL cluster and the database server reported ambiguous errors about missing metadata information.

   Service outage

   Trigger

   One of the three nodes of the MySQL cluster went down, and reconnecting it failed with errors about missing metadata information.

   Root cause

   Dependency failure

   Component

   DatabasePersistent volumes and stateful sets

   Contributing factor

   Harmful manual actionSingle point of failureMonitoring blind spot

   Remediation

   • Restarted the storage server to fix PVC provisioning
   • Let the MySQL nodes restore and sync with each other for about 45 minutes to rebuild the cluster metadata
   • Cleaned up the corrupted cluster metadata
   • Redeployed MySQL Router

   Action items

   • Monitor the health of the storage system more closely
   • Improve the failover procedures for MySQL Router
   • Investigate and fix the status page so it shows reliable information

   Lessons

   The cluster survived the first node failure as designed and lost no data, but its metadata turned out to be a single point of failure. Better monitoring of PVC health could help prevent similar issues, the 45-minute recovery leaves room for improvement, and the status page has to detect failing customer sites reliably.

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2. IL-0506 UC Berkeley DataHub logins failed and students got empty home directories after the JupyterHub database was overwritten

   UC Berkeley2017

   Symptoms

   At about 1 AM on 9 February 2017, UC Berkeley's DataHub was reported down: users trying to log in got a proxy error. The hub pod was running, but its log was full of sqlite errors.

   Service outageData lossMisrouted requests

   Trigger

   While debugging, an operator ran `.save jupyterhub.sqlite` in sqlite3 inside the hub pod without having attached the database, which replaced the JupyterHub database file with an empty one.

   Root cause

   Operator error

   Component

   DatabasePersistent volumes and stateful setsJupyterHub

   Contributing factor

   No safeguard on destructive changeUnsafe failure behaviourHarmful manual action

   Detection

   DataHub was reported down at about 1 AM, when users got a proxy error at login. At 1:12 AM a user reported that he could log in but all his notebooks were gone.

   Remediation

   • Scaled the hub to 0 replicas
   • Rebuilt the JupyterHub sqlite database by matching Kubernetes PVC names back to user ids
   • Set cookie_id to null instead of a dummy value and attached the rebuilt database to the hub
   • Changed the cookie secret in the hub pod and restarted it to log all users out
   • Deleted all user pods to log everyone out
   • Ran a script that filled in cookie_id for all users, restarted the hub and deleted all user pods again
   • Dropped the new users with a '.' in their name and renamed the older users from '-' to '.'

   Action items

   • Report upstream that JupyterHub uses only part of the cookie secret and discards the rest
   • Report upstream that the cookie_id column of the users table should have UNIQUE and NOT NULL constraints
   • Ask KubeSpawner to support username hashes in PVC and pod names so the names stay the same when the database is deleted
   • Ask OAuthenticator to support using the id from the Google authenticator as the user id, giving stable user ids
   • Switch to Google Cloud SQL, a hosted and managed MySQL database
   • Take regular and tested backups of the database
   • Start an operational FAQ of things to do and not to do
   • Set up better monitoring and paging
   • Document escalation procedures explicitly

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