Cases6 cases

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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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2. IL-0041 fluent-bit silently stopped shipping application logs from one node to Elasticsearch

   PrometheusKube2020

   Symptoms

   On a Tuesday morning a developer reported that some production logs were missing. Only the logs from a single node were gone; the other nodes kept shipping normally through fluent-bit, the log shipper the team had run for more than three years.

   Monitoring outage

   Root cause

   Software defect

   Component

   Telemetry agentElasticsearch or OpenSearch

   Contributing factor

   Monitoring blind spotUnpatched known bug

   Detection

   A developer reported missing production logs; no alert fired because fluent-bit's metrics showed no errors.

   Remediation

   • added CPU to the Elasticsearch virtual machines, which cleared the write queue rejections
   • rolled out Fluentd one node at a time, using node affinity to place Fluentd and anti-affinity to remove fluent-bit
   • lowered Fluentd's flush_thread_count to 1 and set flush_interval to 5 seconds so the backlog of old logs did not overflow the buffer
   • enabled Fluentd's Position DB so already-ingested data was skipped

   Action items

   • Build monitoring for Fluentd on its Prometheus integration, including a throughput alert with separate day and night thresholds or a black-box log check

   Lessons

   A log shipper can fail without an error message and with metrics that simply stop moving, so error-based alerts never fire; throughput alerts or end-to-end checks can catch it. Open source software can break in ways nobody expects, and sometimes the way out is to switch to a different shipper fast, node by node. A new shipper that starts from scratch replays every old log on the node and needs to be slowed down.

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3. IL-0029 Slow user-facing services from CPU throttling on containers that used far less CPU than their limit

   Buffer2020

   Symptoms

   Services on Buffer's kops-managed cluster on AWS (about 60 nodes and 1500 containers) answered more slowly than they should have. The container throttling metric showed that many containers were being throttled whatever their CPU usage was, including containers that never came close to their CPU limit.

   CPU throttlingHigh latencyNode NotReady

   Trigger

   CPU limits on user-facing services, enforced through CFS quota by a Linux kernel with a bug that throttled containers even when they were well under their limit.

   Root cause

   Software defect

   Component

   Container CPU limitLinux kernelNode operating system image

   Contributing factor

   Unpatched known bugUnverified assumption

   Detection

   While reviewing the container throttling metric, the team noticed many containers being throttled even though their CPU usage stayed far below their limits.

   Remediation

   • removed CPU limits from all services directly or indirectly on the users' critical path
   • moved those services to dedicated tainted nodes and gave them matching tolerations
   • set each service's CPU request to its peak usage over a few months plus a margin of more than 20%, and set memory requests the same way

   Action items

   • Move nodes to a kernel that contains the CFS throttling fix (4.19 or later), which for Buffer means a kops version whose host image is Ubuntu 20.04
   • After the kernel upgrade, check whether throttling is fully gone and update the post

   Lessons

   A CPU limit can slow a service down even when the service uses a small part of it, because of how the kernel enforces CFS quota on older kernels; the throttling metric shows it, the CPU usage graph does not. Upgrading the kernel is the safer fix. Removing limits works for latency, but only together with honest CPU and memory requests, isolation of the unbounded services, and monitoring of node usage, since unbounded containers can starve the kubelet.

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4. IL-0012 CPU limits and an unpatched kernel CFS quota bug throttled multi-threaded services into stalls, failed health checks and timeouts

   Omio2020

   Symptoms

   For about six months, applications on Omio's Google Kubernetes Engine clusters stalled at random: they got stuck, stopped answering health check requests or lost network connections, and nothing the team looked at explained why.

   CPU throttlingProbe failuresHigh error rateHigh latencyIntermittent timeoutsIntermittent connection failures

   Trigger

   Multi-threaded workloads running with CPU limits on nodes whose kernel did not yet have the fix for a known CFS quota bug that causes unnecessary throttling.

   Root cause

   Software defect

   Component

   Container CPU limitLinux kernelkubelet

   Contributing factor

   Unknown limitMonitoring blind spotUnpatched known bug

   Detection

   Months of random stalls and failed health checks led the team to read the cgroup cpu.stat throttling counters inside the pods, which showed far more throttling than the limits should allow.

   Remediation

   • removed CPU limits until the kernel with the CFS bug fix was deployed across all clusters

   Action items

   • Deploy the kernel with the CFS quota bug fix across all clusters
   • Monitor utilisation, saturation and error metrics, API latency and error rates to confirm the change behaves as expected

   Lessons

   A CPU limit is a time quota per 100 ms period, not a share of cores, so a multi-threaded container can be stopped for most of each period long before it uses the cores it was given, and a kernel bug can make that worse. Throttling is invisible in standard Kubernetes metrics and has to be read from the cgroup counters. Removing limits trades away protection against a container that takes a whole node, which is only acceptable when runtimes are tuned.

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5. IL-0030 Most nodes of a cluster went NotReady together for 15 minutes while the API server sat behind an AWS ELB

   Zalando2019

   Symptoms

   Fewer than 20% of the nodes in one Zalando cluster were available. Most nodes reported NotReady at the same moment, and only a handful stayed Ready.

   Node NotReady

   Root cause

   Software defect

   Component

   Kubernetes API serverCloud load balancer

   Contributing factor

   Unpatched known bug

   Remediation

   • none; the nodes recovered on their own after about 15 minutes

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