Cases9 cases

4 to 8 of 9

1. IL-0016 Prometheus on the live cluster ran out of memory and was OOMKilled, and the monitoring node it ran on went NotReady

   UK Ministry of Justice2023

   Symptoms

   At 14:05 on 25 July 2023, a high-priority PagerDuty alert from Pingdom reported that the "Prometheus - live healthcheck" was DOWN. Prometheus on the live cluster was unavailable, and the Cloud Platform lost its monitoring for a while.

   Monitoring outageOOMKilledNode NotReady

   Trigger

   The growing number of namespaces and Prometheus rules raised Prometheus' memory needs beyond what its node instance size could hold.

   Root cause

   Capacity exhaustion

   Component

   PrometheusNode poolContainer memory limit

   Contributing factor

   No alert on limit

   Detection

   A Pingdom health check on Prometheus failed and raised a high-priority PagerDuty alert.

   Remediation

   • drained the monitoring node, moving Prometheus to another monitoring node
   • changed the node instance size to r6i.4xlarge
   • raised the Prometheus memory limit to 100Gi
   • set the Prometheus container limits to 12 CPU cores and 110Gi of memory

   Action items

   • Add an alert on node memory usage and on a pod using up most of a node's memory (issue #4538)

   View case
2. IL-0028 Temporal History service latency rose because its pods were CPU-throttled while CPU usage read below 60 percent

   Temporal2023

   Symptoms

   Request latency from the Temporal Server History service, the service that starts workflow executions and records their progress, was higher and less steady than it should be on a self-hosted Kubernetes deployment. The CPU dashboard showed the history pods using less than 60 percent of their CPU, yet the same pods were being throttled.

   CPU throttlingHigh latency

   Trigger

   Normal load on History pods that had a CPU limit of 2 cores on 8-core nodes, with the Go runtime's GOMAXPROCS left at its default of one per node core.

   Root cause

   Capacity exhaustion

   Component

   Container CPU limitLanguage runtime settingsPrometheus

   Contributing factor

   Unreviewed defaultsMonitoring blind spot

   Detection

   A Prometheus query for CPU throttling showed the history pods throttled although their CPU usage read under 60 percent.

   Remediation

   • set the GOMAXPROCS environment variable to 2 to match the 2-core CPU limit

   Action items

   • Set GOMAXPROCS automatically from the Kubernetes CPU limit, from Temporal release 1.21.0

   Lessons

   A CPU usage graph averaged over 15 seconds or more can sit far below 100 percent while a container is being throttled, so throttling needs its own metric. A Go program in a container should have GOMAXPROCS matched to its CPU limit, or to its CPU request when it has no limit. The author recommends not using CPU limits at all.

   View case
3. IL-0070 Critical pods on core nodes evicted when Prometheus began scraping about 200 nodes after a dask-gateway scale-up

   2i2c2023

   Symptoms

   The hub pod of the prod JupyterHub on the leap cluster (leap.2i2c.org) restarted unexpectedly during a large node scale-up, and a user opened a support ticket. The ingress-nginx and proxy pods kept running.

   Pod evictionPods Pending

   Trigger

   A user's dask-gateway workload added about 100 dask-worker nodes within a minute, and Prometheus started scraping the metrics exporters on about 200 nodes.

   Root cause

   Capacity exhaustion

   Component

   PrometheusNode pool

   Contributing factor

   No headroomExcessive blast radiusMonitoring blind spot

   Detection

   A user support ticket (2i2c Freshdesk ticket 414) about the leap hub; the engineer then looked at Grafana and the cluster's nodes and events.

   Action items

   • Configure CPU and memory requests for the hub and proxy pods (#2127; at least 100m CPU was proposed)
   • Make the Grafana OOMKiller dashboard work (#2213)
   • Move LEAP cloud infrastructure to shared nodes (#2209)
   • Update resource requests and limits, mainly for ingress-nginx and Prometheus (#2324)
   • Decide whether Prometheus should scrape dask worker pods (#2366)

   Lessons

   Prometheus load grows with the number of nodes, so a burst of autoscaled nodes can push a nearly full core node over the edge and evict the pods that matter most. Core pods that request 10m of CPU get a tenth of the CPU share of busy neighbours that request 100m. Kubernetes events expire after an hour, so evidence of OOM kills needs a dashboard that keeps it.

   View case
4. IL-0089 A test cluster deletion script run with the kube context pointing at the live-1 production cluster deleted its ingress controller, monitoring, logging, cert-manager, kiam and external-dns

   UK Ministry of Justice2020

   Symptoms

   At 18:27 on 21 September 2020 the Cloud Platform team detected that some services running on the live-1 production cluster had gone down, and some users could not reach them. The incident was declared at 18:40.

   Service outageResources deletedMonitoring outageStale endpoint routing

   Trigger

   A script for deleting a test cluster was triggered while the kube context was pointing at the live-1 production cluster instead of the test cluster.

   Root cause

   Operator error

   Component

   Ingress controllerCredential broker for podsexternal-dnsCloud load balancerPrometheus

   Contributing factor

   No safeguard on destructive change

   Detection

   The first detection was at 18:27, and the incident was declared 13 minutes later, at 18:40.

   Remediation

   • restored the default ingress controller together with external-dns and kiam, which it depends on
   • corrected the owner field in the Formbuilder Route 53 TXT records so external-dns pointed their A records at the new NLB
   • restored the remaining components with a targeted apply
   • ran the apply pipeline to restore all certificates, ServiceMonitors and Prometheus rules from the environment repository

   View case
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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