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1. IL-0462 Some MySQL pods on Shopify's GKE clusters took up to 30 minutes to start, slowing instance replacement

   Shopify2021

   Symptoms

   In 2021 Shopify's KateSQL, a database-as-a-service platform that runs several hundred production MySQL instances on GKE, found that some MySQL pods started and shut down much more slowly than similar pods with the same data set. Instance replacement, the procedure that creates a new MySQL replica pod and stops the old one, showed pod creation times ranging from 10 to 30 minutes, which held up maintenance such as configuration changes and upgrades.

   Slow pod startup or shutdownHigh latency

   Root cause

   Software defect

   Component

   Linux kernelNode operating system imageDatabase

   Contributing factor

   Unpatched known bug

   Detection

   KateSQL's instance replacement operations showed inconsistent MySQL pod creation times, and the team then measured the mysql-init container and MySQL startup times across pods.

   Remediation

   • Cordoned older nodes, moved MySQL pods to new nodes through instance replacement and drained the old nodes
   • Forced the kubepods memory cgroup to empty its dead cgroups on an affected node to test the fix
   • Created new GKE 1.18 clusters and started creating MySQL pods on them

   Lessons

   The investigation was one of the longest the Database Platform group had carried out, because of the nature of the problem, how hard it was to reproduce and the lack of an established method to follow; once the cause was known, there were several ways to fix it.

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