Cases17 cases

7 to 11 of 17

1. IL-0112 The daily node rollover put DFDS's EKS nodes on an AMI later recalled for a kernel issue, causing "PLEG is not healthy" NodeNotReady flaps and pod network timeouts

   DFDS2022

   Symptoms

   On 2022-10-31 a planned upgrade of the vpc-cni EKS add-on, started from the deployment pipeline at 13:45 UTC, timed out at 14:10. Only about 10 of the 45 aws-node pods had upgraded, 5 were stuck in Terminating and the other 30 had not been attempted.

   Node NotReadyUpgrade stallIntermittent timeoutsIntermittent connection failures

   Trigger

   At 07:30 UTC on 2022-10-31 the daily node rollover replaced the existing nodes with nodes built from AMI v20221027, the latest AWS EKS node AMI, released on 2022-10-29 and later recalled because of a kernel issue.

   Root cause

   Software defect

   Component

   Node operating system imageLinux kernelkubeletAWS VPC CNINode launch templateTerraform

   Contributing factor

   No staged rolloutAutomation amplificationOverlapping failuresMonitoring blind spotNo health probes

   Detection

   The team noticed nodes flapping between NodeNotReady and NodeReady ("KubeletNotReady PLEG is not healthy") at 14:30 UTC while watching the stalled vpc-cni upgrade, about seven hours after the rollover. Time to detection was 7 hours. Alerting did not catch the NodeNotReady events or the socket growth.

   Remediation

   • cordoned, drained and deleted 15 stuck nodes one at a time to complete the vpc-cni upgrade
   • changed the Terraform infrastructure-modules so a specific AMI could be set
   • rolled the EC2 Auto Scaling group launch configuration back to the previous known good AMI through the pipeline

   Action items

   • Reach out to teams with suggestions about readiness and liveness probes
   • Create a dashboard for readiness and liveness probe coverage
   • Write a wiki article on readiness and liveness probes and their usefulness
   • Modify infrastructure-modules to allow specifying a particular AMI
   • Schedule a discussion on whether to take the latest AMI immediately and how to test new AMIs before they are deployed
   • Implement alerting on abnormal NodeNotReady events and on increased socket use
   • Create a learning path for Kubernetes within the team
   • Collect logs from nodes centrally
   • Create a Prometheus exporter that retrieves the latest available AMI, with a dashboard and alerts

   Lessons

   When a new node AMI has just been rolled out, upgrading other cluster components on the same day makes it hard to tell which change is causing trouble; here the vpc-cni upgrade on the same day confused matters. Taking the latest AMI automatically with no way to pin one meant a rollback first needed a Terraform change. The team also concluded that it needs better communication paths with application teams during incidents.

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2. IL-0461 Every rollout of Datadog's metrics query service on Kubernetes raised errors that the logs blamed on DNS

   Datadog2022

   Symptoms

   From September 2021, each rollout of an update to Datadog's metrics query service, which serves real-time and historical metric data to the web frontend and to monitor evaluation, came with a rise in errors. Clients retried failed queries, so few errors reached users, but the retries slowed dashboards and monitors. The service's logs showed DNS errors stopping it from connecting to the data stores it depends on.

   High error rateDNS resolution failuresHigh latencyOOMKilledPacket lossStale endpoint routing

   Trigger

   Rollouts of the metrics query service, which delete the old pods. The client behaviour behind the failures came from an August 2021 rollout of the metrics query clients that applied round_robin as the new default gRPC load balancing policy.

   Root cause

   Configuration change

   Component

   conntrack tableCiliumLinux kernelCoreDNSClient-side DNS resolver and cacheexternal-dnsHTTP and RPC client library

   Contributing factor

   Change with a delayed effectRetry stormUnknown limitMonitoring blind spot

   Detection

   Errors rose during rollouts of the metrics query service, and the service's logs showed DNS errors when connecting to its data stores.

   Remediation

   • Raised the memory of the node-local-dns pods from 64 MB to 256 MB, which stopped the OOM kills but not the DNS errors
   • Tested larger instance types and confirmed that scaling up the service's infrastructure resolved the errors
   • Removed the custom gRPC reconnect parameters from the clients to restore the defaults

   Action items

   • Contribute a change to Cilium that adds an unreachable route for a deleted pod's IP so clients get an ICMP error

   Lessons

   The errors looked like DNS but were not. ENA metrics and VPC Flow Logs gave the visibility into VPC connection tracking that host metrics did not, and Cilium, Kubernetes and AWS networking interact in ways that can make reverse path filtering drop packets it should allow. DNS propagation time depends on many settings. The causes were changes Datadog had made itself, to work around a dependency bug, to resolve earlier incidents and to override default reconnect parameters, which looked safe at the time and showed their effects much later, when the link was hard to see.

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3. 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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4. 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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5. IL-0176 Prometheus in a 235-node Kubernetes cluster crash-looped because over two million series exhausted host memory and the kernel OOM killer chose it first, as Burstable QoS gave it oom_score_adj 999

   LINE2020

   Symptoms

   One Monday morning the author opened the Prometheus dashboard to check a Kubernetes cluster for alerts and could not reach it. The Prometheus pod was in CrashLoopBackOff: kubectl get pods showed it 1/2 ready with 950 restarts over 3d20h on worker3.

   Container crash loopOOMKilledMonitoring outageProbe failures

   Trigger

   After start, the Prometheus time series count rose to 2,162,256 within five minutes and its memory use filled the 8GB host.

   Root cause

   Capacity exhaustion

   Component

   PrometheuskubeletLinux kernel

   Contributing factor

   No resource requests or limitsNo capacity planning

   Detection

   The author found it on a Monday morning when the Prometheus dashboard, opened to check the cluster for alerts, could not be reached.

   Remediation

   • removed most of the unnecessary settings from the Prometheus ConfigMap, after which the container stopped crashing

   Action items

   • Set appropriate resource requests and limits on the Prometheus pod
   • Reduce unneeded metrics by adjusting scrape targets or scrape interval
   • Estimate Prometheus memory needs, provide dedicated hosts with a node label such as deploy-topology: Prometheus, and pin the Prometheus pod to them with a nodeSelector

   Lessons

   Exit code 137 together with an OOM event in the kubelet log means the kernel killed the container, not kubelet. Under node memory pressure the kernel kills the process with the highest score, and kubelet derives each container's oom_score_adj from the pod's QoS class: a container without a memory request in a pod where another container has one ends up Burstable with a score near 1000, so it is killed first. In a large cluster, Prometheus memory needs to be estimated from the expected series count and requested explicitly.

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