Add node selector for the check-new-samples job and a livenessProbe. #35
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bpblanken
commented
Jan 24, 2024
| @@ -53,6 +53,12 @@ spec: | |||
| resources: | |||
| {{- toYaml .Values.resources | nindent 10 }} | |||
| {{- include "seqr.environment" $ | nindent 8 }} | |||
| livenessProbe: | |||
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We've seen some strange behavior recently with the seqr service failing to come up correctly during a re-spin.
My best guess at what's been happening here:
- our container runs regardless of whether or not the backgrounded server is actually running or not (
sleep 100000) - gunicorn never comes up successfully if
gcloudor something elseinit-related is failing. Testing this locally showed that only a single worker failing will bring down all N worker processes. - the readiness probe never succeeds on that pod/
- we can end up in a serving-traffic-correctly state if we have multiple pods running (1 running correctly and 1 not running).
- we can also end up in a fully down state if both pods happen to have an init issue. I'm not sure this can happen during a deployment (the internet points to the rolling deploy mechanism using "readiness" rather than liveness), but it has happened during standard pod rotations.
Adding the livenessProbe will help k8s know the container is DOA and should be kicked.
This got mentioned in slack many months ago: https://the-tgg.slack.com/archives/C01FRFB36LR/p1682518495987779
bpblanken
commented
Jan 24, 2024
| @@ -55,5 +55,9 @@ spec: | |||
| {{- with $.Values.deployment_sidecars }} | |||
| {{- tpl . $ | nindent 8 }} | |||
| {{- end }} | |||
| {{- with $.Values.nodeSelector }} | |||
| nodeSelector: | |||
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I just saw this missing and added. I'm not sure if we've ever seen this workload assigned off default-pool, but certainly a possibility.
bpblanken
changed the title
bpblanken
requested review from
sjahl and
hanars
and removed request for
sjahl
hanars
approved these changes
Jan 29, 2024
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Result from investigation into the downtime incident.