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  1. IL-0075 Kubernetes API servers pegged on CPU when the cluster grew to about 290 nodes, traced to Datadog agents polling the API
    Civis Analytics2019
    Symptoms

    After Civis released its new script infrastructure on Kubernetes internally in September 2018, developers reported that kubectl commands were slow, and users intermittently could not start notebooks and services.

    Control plane lagControl plane unresponsiveHigh latencyHigh error rateDNS resolution failures
    Trigger

    Migrating clients' Python, R and container scripts from the in-house Bocce system to Kubernetes (the project called Croquet) pushed the cluster to about 290 EC2 instances under a large script load.

    Root cause
    Capacity exhaustion
    Component
    Kubernetes API serverTelemetry agentetcd
    Contributing factor
    Unknown limitUnverified assumptionMonitoring blind spotNo capacity planning
    Detection

    Developer reports of slow kubectl commands and user reports of notebooks and services failing to start, then high CPU on the master nodes.

    Remediation
    • moved internal users back to the old Bocce infrastructure
    • resized the three master nodes from m4.large to m4.4xlarge
    • changed the Datadog setup so per-node agents no longer polled the API server for service metadata
    • raised max-requests-inflight for non-mutating requests from 400 to 1200
    • grew the etcd EBS volumes from 20 to 100 GB (100 to 300 IOPS)
    • switched client scripts from the ClusterFirst DNS policy to Default
    Action items
    • Upgrade etcd from 2.2.1 to 3.x once Kops supports a safe migration
    • Solve the in-cluster DNS timeouts so client scripts can talk to other workloads in the cluster
    Lessons

    Kubernetes can reach thousands of nodes only after tuning, and third-party DaemonSets are a common cause of control plane load: an agent on every node that polls or watches the API server multiplies with the cluster size. Datadog, kube2iam and the fluentd metadata filter all showed this. A small configuration change often fixes it, but finding it took load testing and the API server access logs.

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By root cause1

Capacity exhaustion1 case

Component
etcdKubernetes API serverTelemetry agent
Contributing factor
Unverified assumptionUnknown limitMonitoring blind spotNo capacity planning
Organisation
Civis Analytics
  1. IL-0075 Kubernetes API servers pegged on CPU when the cluster grew to about 290 nodes, traced to Datadog agents polling the API
    Civis Analytics2019