Kubelet process has high CPU usage over long time

Question

I have kubernetes cluster with weave CNI plugin consisting of 3 nodes:

1 master node (virtual machine)
2 worker baremetall nodes (4 cores xeon with hyperthreading - 8 logical nodes)

The trouble is that top shows that kubelet has 60-100% CPU usage on first worker. In journalctl -u kubelet I see a lot of messages (hundreds every minute)

May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.075243    3843 docker_sandbox.go:205] Failed to stop sandbox "011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640": Error response from daemon: {"message":"No such container: 011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640"}
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.075360    3843 remote_runtime.go:109] StopPodSandbox "011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640" from runtime service failed: rpc error: code = 2 desc = NetworkPlugin cni failed to teardown pod "cron-task-2533948c46c1-p6kwb_namespace" network: CNI failed to retrieve network namespace path: Error: No such container: 011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.075380    3843 kuberuntime_gc.go:138] Failed to stop sandbox "011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640" before removing: rpc error: code = 2 desc = NetworkPlugin cni failed to teardown pod "cron-task-2533948c46c1-p6kwb_namespace" network: CNI failed to retrieve network namespace path: Error: No such container: 011cf10cf46dbc6bf2e11d1cb562af478eee21eba0c40521bf7af51ee5399640
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.076549    3843 docker_sandbox.go:205] Failed to stop sandbox "0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf": Error response from daemon: {"message":"No such container: 0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf"}
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.076654    3843 remote_runtime.go:109] StopPodSandbox "0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf" from runtime service failed: rpc error: code = 2 desc = NetworkPlugin cni failed to teardown pod "cron-task-2533948c46c1-6g8jq_namespace" network: CNI failed to retrieve network namespace path: Error: No such container: 0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.076676    3843 kuberuntime_gc.go:138] Failed to stop sandbox "0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf" before removing: rpc error: code = 2 desc = NetworkPlugin cni failed to teardown pod "cron-task-2533948c46c1-6g8jq_namespace" network: CNI failed to retrieve network namespace path: Error: No such container: 0125de37634ef7f3aa852c999cfb5849750167b1e3d63293a085ceca416e4ebf
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.079585    3843 docker_sandbox.go:205] Failed to stop sandbox "014135ede46ee45c176528da02782a38ded36bd10566f864c147ccb66a617772": Error response from daemon: {"message":"No such container: 014135ede46ee45c176528da02782a38ded36bd10566f864c147ccb66a617772"}
May 19 09:57:38 kube-worker1 bash[3843]: E0519 09:57:38.079805    3843 remote_runtime.go:109] StopPodSandbox "014135ede46ee45c176528da02782a38ded36bd10566f864c147ccb66a617772" from runtime service failed: rpc error: code = 2 desc = NetworkPlugin cni failed to teardown pod "cron-task-2533948c46c1-r30cw_namespace" network: CNI failed to retrieve network namespace path: Error: No such container: 014135ede46ee45c176528da02782a38ded36bd10566f864c147ccb66a617772

It's happen after wrong cronetes tasks which failed during creation. I removed all pods with --forcebut kubelet still try to remove them. Also I restarted kubelet on that worker with no result. How can I talk to kubelet to forget them?

Version info

Kubernetes v1.6.1
Docker version 1.12.0, build 8eab29e
Linux kube-worker1 4.4.0-72-generic #93-Ubuntu SMP

Container manifest (without metadata)

  job:
    apiVersion: batch/v1
    kind: Job
    spec:
      template:
        spec:
          containers:
          - name: cron-task
            image: docker.company.ru/image:v2.3.2
            command: ["rake", "db:refresh_views"]
            env:
            - name: RAILS_ENV
              value: namespace
            - name: CONFIG_PATH
              value: /config
            volumeMounts:
            - name: config
              mountPath: /config
          volumes:
          - name: config
            configMap:
              name: task-conf
          restartPolicy: Never

Kalgi · Answer 1 · Sep 19, 2018

Kubelet stores information about all pods, running on it in

/var/lib/dockershim/sandbox

So when I ls in that folder I found files for all missing pods. Then I deleted these files and log messages disappeared and CPU usage returns to normal value (even without kubelet restart)