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Incidents Log

2023/05/24 Mongodb session service crash

  • Issue with session-service reported at 3.30PM
  • We identified that the mongo session service was down and had used up all disk space (20Gi) shortly. That same day we created a new session service with 100Gi storage but weren't able to recover all old sessions
  • On 2023/05/26 we were able to restore old sessions. We did lose two days of saved sessions (5/24-5/25)

Remediation

Bring mongodb back

  • Take snapshot of existing EBS volume using AWS (no auto snapshots were set up)
  • Set up new mongo database with helm: helm install cbioportal-session-service-mongo-20230524 --version 7.3.1 --set image.tag=4.2,persistence.size=100Gi bitnami/mongodb
  • Connect the session service to use that one (see commit)

Bring session data back

The mongo data was stored in an AWS snapshot in mongo's binary format, so not immediately accessible for re-import into another database. First we had to bring that back.

What didn't work:

  • Tried various approach of expanding existing k8s volume, but was tricky b/c volume expansion wasn't enabled for existing PersistenceVolumeClaims

What did work:

  • Instead, started a new AWS EC2 instance with that volume attached. For whatever reason i couldn’t see the attached volume within ubuntu at first (had to use lsblk and mount). Might be something you always have to do
  • Once the volume was accessible, we ran docker run bitnami/mongodb with the correct mount location specified to load the data
  • From a separate shell used mongodump as described (cmds are described in cbioportal/README)
  • Now that we got the dump, we set up a new mongo database in the k8s cluster to load the data: helm install cbioportal-session-service-mongo-4dot2-20230525 --set image.tag=4.2,persistence.size=100Gi bitnami/mongodb
  • Then we had to copy over the data into that k8s volume. Unf kubectl cp didn't work (some TCP timeout error). Instead we figured we could create a 2nd container int he mongodb pod with rsync to copy over the data into a container in the existing k8s deployment: 
    kubectl edit deployment cbioportal-session-service-mongo-4dot2-20230525-mongodb
# add an ubuntu container
   - args:
     - infinity
     command:
     - sleep
     image: ubuntu
     imagePullPolicy: Always
     name: ubuntu
     resources: {}
     terminationMessagePath: /dev/termination-log
     terminationMessagePolicy: File
     volumeMounts:
     - mountPath: /bitnami/mongodb
       name: datadir
# wait for it to be deployed
kubectl exec -it cbioportal-session-service-mongo-4dot2-20230525-mongodb-f6wp9vx -c ubuntu -- /bin/sh
# now you can apt-get install rsync, ssh, whatev into that container and rsync the mongo dump
# then re-import the mongo database dump using instructions in cbioportal/README