5

We have been experiencing an issue causing us pain for the last few months.

The issue appears to be that occasionally when we request a pod via the Kubernetes executor it fails to create.

For example, a spark pod may fail with the following error:

Events:
  Type     Reason                  Age                   From                                         Message
  ----     ------                  ----                  ----                                         -------
  Warning  FailedCreatePodSandBox  20m (x3 over 32m)     kubelet, k8s-agentpool1-123456789-vmss00000q  (combined from similar events): Failed create pod sandbox: rpc error: code = Unknown desc = failed to create a sandbox for pod "spark-worker-cc1d28bf3de8428a826c04471e58487c-8577d5d654-2jg89": operation timeout: context deadline exceeded
  Normal   SandboxChanged          16m (x150 over 159m)  kubelet, k8s-agentpool1-123456789-vmss00000q  Pod sandbox changed, it will be killed and re-created.
  Warning  FailedCreatePodSandBox  5m7s (x14 over 161m)  kubelet, k8s-agentpool1-123456789-vmss00000q  Failed create pod sandbox: rpc error: code = Unknown desc = failed to create a sandbox for pod "spark-worker-cc1d28bf3de8428a826c04471e58487c-8577d5d654-2jg89": operation timeout: context deadline exceeded

Looking at the logs we see "SyncLoop" from kubelet requsting a new pod.

Jul 16 16:33:58 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:33:58.001997    4797 kubelet.go:1908] SyncLoop (ADD, "api"): "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)

There are also some logs that indicate that volumes are mounted...

Jul 16 16:34:29 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:33:58.175573    4797 reconciler.go:252] operationExecutor.MountVolume started for volume "default-shared" (UniqueName: "kubernetes.io/glusterfs/8272d74f-a7e7-11e9-8f1c-000d3a7b202b-default-shared") pod "d9b3911585c4461c9728aefa39716c44" (UID: "8272d74f-a7e7-11e9-8f1c-000d3a7b202b")

We see a pod Sandbox going to be created:

Jul 16 16:34:29 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:34:29.627374    4797 kuberuntime_manager.go:397] No sandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" can be found. Need to start a new one

We don't seem to see anything else until we see this logged:

Jul 16 16:36:29 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:29.629252    4797 kuberuntime_manager.go:662] createPodSandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" failed: rpc error: code = Unknown desc = failed to create a sandbox for pod "d9b3911585c4461c9728aefa39716c44": operation timeout: context deadline exceeded
Jul 16 16:36:29 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:29.629301    4797 pod_workers.go:190] Error syncing pod 8272d74f-a7e7-11e9-8f1c-000d3a7b202b ("d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)"), skipping: failed to "CreatePodSandbox" for "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" with CreatePodSandboxError: "CreatePodSandbox for pod \"d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)\" failed: rpc error: code = Unknown desc = failed to create a sandbox for pod \"d9b3911585c4461c9728aefa39716c44\": operation timeout: context deadline exceeded"
Jul 16 16:36:43 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:36:43.937085    4797 kuberuntime_manager.go:397] No sandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" can be found. Need to start a new one
Jul 16 16:36:43 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:43.940691    4797 remote_runtime.go:96] RunPodSandbox from runtime service failed: rpc error: code = Unknown desc = failed to create a sandbox for pod "d9b3911585c4461c9728aefa39716c44": Error response from daemon: Conflict. The container name "/k8s_POD_d9b3911585c4461c9728aefa39716c44_default_8272d74f-a7e7-11e9-8f1c-000d3a7b202b_0" is already in use by container "2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27". You have to remove (or rename) that container to be able to reuse that name.
Jul 16 16:36:43 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:43.940731    4797 kuberuntime_sandbox.go:68] CreatePodSandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" failed: rpc error: code = Unknown desc = failed to create a sandbox for pod "d9b3911585c4461c9728aefa39716c44": Error response from daemon: Conflict. The container name "/k8s_POD_d9b3911585c4461c9728aefa39716c44_default_8272d74f-a7e7-11e9-8f1c-000d3a7b202b_0" is already in use by container "2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27". You have to remove (or rename) that container to be able to reuse that name.
Jul 16 16:36:43 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:43.940747    4797 kuberuntime_manager.go:662] createPodSandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" failed: rpc error: code = Unknown desc = failed to create a sandbox for pod "d9b3911585c4461c9728aefa39716c44": Error response from daemon: Conflict. The container name "/k8s_POD_d9b3911585c4461c9728aefa39716c44_default_8272d74f-a7e7-11e9-8f1c-000d3a7b202b_0" is already in use by container "2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27". You have to remove (or rename) that container to be able to reuse that name.
Jul 16 16:36:43 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: E0716 16:36:43.940805    4797 pod_workers.go:190] Error syncing pod 8272d74f-a7e7-11e9-8f1c-000d3a7b202b ("d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)"), skipping: failed to "CreatePodSandbox" for "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" with CreatePodSandboxError: "CreatePodSandbox for pod \"d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)\" failed: rpc error: code = Unknown desc = failed to create a sandbox for pod \"d9b3911585c4461c9728aefa39716c44\": Error response from daemon: Conflict. The container name \"/k8s_POD_d9b3911585c4461c9728aefa39716c44_default_8272d74f-a7e7-11e9-8f1c-000d3a7b202b_0\" is already in use by container \"2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27\". You have to remove (or rename) that container to be able to reuse that name."
Jul 16 16:36:44 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: W0716 16:36:44.221607    4797 docker_sandbox.go:384] failed to read pod IP from plugin/docker: NetworkPlugin cni failed on the status hook for pod "d9b3911585c4461c9728aefa39716c44_default": CNI failed to retrieve network namespace path: cannot find network namespace for the terminated container "2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27"
Jul 16 16:36:44 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:36:44.222749    4797 kubelet.go:1953] SyncLoop (PLEG): "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)", event: &pleg.PodLifecycleEvent{ID:"8272d74f-a7e7-11e9-8f1c-000d3a7b202b", Type:"ContainerDied", Data:"2a7ecfd3725bbe6604b3006abf6c59a36eb8a5d7142e71a3791f5f7378bf5e27"}
Jul 16 16:36:44 k8s-agentpool1-123456789-vmss00000T kubelet[4797]: I0716 16:36:44.739387    4797 kuberuntime_manager.go:415] No ready sandbox for pod "d9b3911585c4461c9728aefa39716c44_default(8272d74f-a7e7-11e9-8f1c-000d3a7b202b)" can be found. Need to start a new one

We thought that may be a CNI error, however we reviewed the Azure CNI logs and it doesn't appear to even get to the part where it starts to request an IP, only showing an error that the DEL command completed with err.

2019/07/16 16:23:06 [net] Deleting veth pair azv4ea5d9d9527 eth0.
2019/07/16 16:23:06 [net] Deleted endpoint &{Id:8e963d34-eth0 HnsId: SandboxKey: IfName:eth0 HostIfName:azv4ea5d9d9527 MacAddress:ce:93:bf:4d:e9:19 InfraVnetIP:{IP:<nil> Mask:<nil>} IPAddresses:[{IP:10.250.18.22
5 Mask:fffff800}] Gateways:[10.250.16.1] DNS:{Suffix: Servers:[168.63.129.16]} Routes:[{Dst:{IP:0.0.0.0 Mask:00000000} Src:<nil> Gw:10.250.16.1 Protocol:0 DevName: Scope:0}] VlanID:0 EnableSnatOnHost:false Enabl
eInfraVnet:false EnableMultitenancy:false NetworkNameSpace:/proc/10781/ns/net ContainerID:8e963d340597f1c9f789b93a7784e8d44ffb00687086de8ee6561338aab7c72d PODName:jupyter-some-person-10 PODNameSpace:defaul
t InfraVnetAddressSpace:}.
2019/07/16 16:23:06 [net] Save succeeded.
2019/07/16 16:23:06 [cni] Calling plugin azure-vnet-ipam DEL nwCfg:&{CNIVersion:0.3.0 Name:azure Type:azure-vnet Mode:bridge Master: Bridge:azure0 LogLevel: LogTarget: InfraVnetAddressSpace: PodNamespaceForDualN
etwork:[] MultiTenancy:false EnableSnatOnHost:false EnableExactMatchForPodName:false CNSUrl: Ipam:{Type:azure-vnet-ipam Environment: AddrSpace: Subnet:10.250.16.0/21 Address:10.250.18.225 QueryInterval:} DNS:{Na
meservers:[] Domain: Search:[] Options:[]} RuntimeConfig:{PortMappings:[] DNS:{Servers:[] Searches:[] Options:[]}} AdditionalArgs:[]}.
2019/07/16 16:23:06 [cni] Plugin azure-vnet-ipam returned err:<nil>.
2019/07/16 16:23:06 Get number of endpoints for ifname eth0 network azure
2019/07/16 16:23:06 [cni-net] DEL command completed with err:<nil>.
2019/07/16 16:23:06 [cni-net] Plugin stopped.
2019/07/16 16:36:38 [cni-net] Plugin azure-vnet version v1.0.18.
2019/07/16 16:36:38 [cni-net] Running on Linux version 4.15.0-1040-azure (buildd@lgw01-amd64-030) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.10)) #44-Ubuntu SMP Thu Feb 21 14:24:01 UTC 2019
Client:
 Version:           3.0.3
 API version:       1.40
 Go version:        go1.11.4
 Git commit:        48bd4c6d
 Built:             Wed Jan 23 16:17:56 2019
 OS/Arch:           linux/amd64
 Experimental:      false

Server:
 Engine:
  Version:          3.0.4
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.11.4
  Git commit:       8ecd530
  Built:            Fri Jan 25 01:45:38 2019
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          v1.2.2
  GitCommit:        9754871865f7fe2f4e74d43e2fc7ccd237edcbce
 runc:
  Version:          1.0.0-rc6+dev
  GitCommit:        96ec2177ae841256168fcf76954f7177af9446eb
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683

Here is the k8s version info:

Server Version: version.Info{Major:"1", Minor:"13", GitVersion:"v1.13.5", GitCommit:"2166946f41b36dea2c4626f90a77706f426cdea2", GitTreeState:"clean", BuildDate:"2019-03-25T15:19:22Z", GoVersion:"go1.11.5", Compiler:"gc", Platform:"linux/amd64"}

Here is our Node info - We are using AKS engine to create a Kubernetes cluster which uses Azure VMSS nodes.

 Kernel Version:             4.15.0-1050-azure
 OS Image:                   Ubuntu 16.04.6 LTS
 Operating System:           linux
 Architecture:               amd64
 Container Runtime Version:  docker://3.0.4
 Kubelet Version:            v1.13.5
 Kube-Proxy Version:         v1.13.5

I am kind of out of ideas as to what we can even do to troubleshoot this further, as we're unable to even re-create this issue.

I understand that this "Context deadline exceeded" alert is a generic gRPC timeout, but I'm not sure which gRPC transaction is getting hung up on.

1 Answer 1

3

The issue was a bug in Kubernetes / the Linux kernel discussed here with involved the cgroups growing exponentially and causing issues including high cpu / memory usage.

The issue is described here:

A workaround / fix is documented here: fix for cgroup leakage

The fix is is a daemonset which runs cleanup every hour.

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