my machine have enough memory, but the kubernetes can not schedule the pod and indicate that Insufficient memory

4/17/2020

I have a 1.16.2 version cluster of kubernetes. When I deploy all the service in the cluster with the replicas is 1, it works fine. Then i scale all the service's replicas to 2 And check out. found that some service are running Normal but But some states are pending. when I kubectl describe one of the Pending pod, I get the message like below

[root@runsdata-bj-01 society-training-service-v1-0]# kcd society-resident-service-v3-0-788446c49b-rzjsx
Name:           society-resident-service-v3-0-788446c49b-rzjsx
Namespace:      runsdata
Priority:       0
Node:           <none>
Labels:         app=society-resident-service-v3-0
                pod-template-hash=788446c49b
Annotations:    <none>
Status:         Pending
IP:             
IPs:            <none>
Controlled By:  ReplicaSet/society-resident-service-v3-0-788446c49b
Containers:
  society-resident-service-v3-0:
    Image:      docker.ssiid.com/society-resident-service:3.0.33
    Port:       8231/TCP
    Host Port:  0/TCP
    Limits:
      cpu:     1
      memory:  4Gi
    Requests:
      cpu:      200m
      memory:   2Gi
    Liveness:   http-get http://:8231/actuator/health delay=600s timeout=5s period=10s #success=1 #failure=3
    Readiness:  http-get http://:8231/actuator/health delay=30s timeout=5s period=10s #success=1 #failure=3
    Environment:
      spring_profiles_active:  production
      TZ:                      Asia/Hong_Kong
      JAVA_OPTS:               -Djgroups.use.jdk_logger=true -Xmx4000M  -Xms4000M  -Xmn600M  -XX:PermSize=500M  -XX:MaxPermSize=500M  -Xss384K  -XX:+DisableExplicitGC  -XX:SurvivorRatio=1 -XX:+UseConcMarkSweepGC  -XX:+UseParNewGC  -XX:+CMSParallelRemarkEnabled  -XX:+UseCMSCompactAtFullCollection  -XX:CMSFullGCsBeforeCompaction=0 -XX:+CMSClassUnloadingEnabled  -XX:LargePageSizeInBytes=128M  -XX:+UseFastAccessorMethods  -XX:+UseCMSInitiatingOccupancyOnly  -XX:CMSInitiatingOccupancyFraction=80 -XX:SoftRefLRUPolicyMSPerMB=0 -XX:+PrintClassHistogram  -XX:+PrintGCDetails  -XX:+PrintGCTimeStamps  -XX:+PrintHeapAtGC  -Xloggc:log/gc.log
    Mounts:
      /data/storage from nfs-data-storage (rw)
      /opt/security from security (rw)
      /var/log/runsdata from log (rw)
      /var/run/secrets/kubernetes.io/serviceaccount from application-token-vgcvb (ro)
Conditions:
  Type           Status
  PodScheduled   False 
Volumes:
  log:
    Type:          HostPath (bare host directory volume)
    Path:          /log/runsdata
    HostPathType:  
  security:
    Type:       PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
    ClaimName:  data-security-claim
    ReadOnly:   false
  nfs-data-storage:
    Type:       PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
    ClaimName:  data-storage-claim
    ReadOnly:   false
  application-token-vgcvb:
    Type:        Secret (a volume populated by a Secret)
    SecretName:  application-token-vgcvb
    Optional:    false
QoS Class:       Burstable
Node-Selectors:  <none>
Tolerations:     node.kubernetes.io/not-ready:NoExecute for 300s
                 node.kubernetes.io/unreachable:NoExecute for 300s
Events:
  Type     Reason            Age        From               Message
  ----     ------            ----       ----               -------
  Warning  FailedScheduling  <unknown>  default-scheduler  0/4 nodes are available: 4 Insufficient memory.

And from below, you can see that my machine have more than 2G memory left .

[root@runsdata-bj-01 society-training-service-v1-0]# kcp |grep Pending
society-insurance-foundation-service-v2-0-7697b9bd5b-7btq6      0/1     Pending            0          60m
society-notice-service-v1-0-548b8d5946-c5gzm                    0/1     Pending            0          60m
society-online-business-service-v2-1-7f897f564-phqjs            0/1     Pending            0          60m
society-operation-gateway-7cf86b77bd-lmswm                      0/1     Pending            0          60m
society-operation-user-service-v1-1-755dcff964-dr9mj            0/1     Pending            0          60m
society-resident-service-v3-0-788446c49b-rzjsx                  0/1     Pending            0          60m
society-training-service-v1-0-774f8c5d98-tl7vq                  0/1     Pending            0          60m
society-user-service-v3-0-74865dd9d7-t9fwz                      0/1     Pending            0          60m
traefik-ingress-controller-8688cccf79-5gkjg                     0/1     Pending            0          60m
[root@runsdata-bj-01 society-training-service-v1-0]# kubectl top nodes
NAME           CPU(cores)   CPU%   MEMORY(bytes)   MEMORY%   
192.168.0.94   384m         9%     11482Mi         73%       
192.168.0.95   399m         9%     11833Mi         76%       
192.168.0.96   399m         9%     11023Mi         71%       
192.168.0.97   457m         11%    10782Mi         69%       
[root@runsdata-bj-01 society-training-service-v1-0]# kubectl get nodes
NAME           STATUS   ROLES    AGE   VERSION
192.168.0.94   Ready    <none>   8d    v1.16.2
192.168.0.95   Ready    <none>   8d    v1.16.2
192.168.0.96   Ready    <none>   8d    v1.16.2
192.168.0.97   Ready    <none>   8d    v1.16.2
[root@runsdata-bj-01 society-training-service-v1-0]#

here is the description of all 4 node

[root@runsdata-bj-01 frontend]#kubectl describe node 192.168.0.94
Allocated resources:
  (Total limits may be over 100 percent, i.e., overcommitted.)
  Resource           Requests      Limits
  --------           --------      ------
  cpu                1930m (48%)   7600m (190%)
  memory             9846Mi (63%)  32901376Ki (207%)
  ephemeral-storage  0 (0%)        0 (0%)
Events:              <none>
[root@runsdata-bj-01 frontend]#kubectl describe node 192.168.0.95
    Allocated resources:
  (Total limits may be over 100 percent, i.e., overcommitted.)
  Resource           Requests      Limits
  --------           --------      ------
  cpu                1670m (41%)   6600m (165%)
  memory             7196Mi (46%)  21380Mi (137%)
  ephemeral-storage  0 (0%)        0 (0%)
Events:              <none>
[root@runsdata-bj-01 frontend]# kubectl describe node 192.168.0.96
Allocated resources:
  (Total limits may be over 100 percent, i.e., overcommitted.)
  Resource           Requests      Limits
  --------           --------      ------
  cpu                2610m (65%)   7 (175%)
  memory             9612Mi (61%)  19960Mi (128%)
  ephemeral-storage  0 (0%)        0 (0%)
Events:              <none>
[root@runsdata-bj-01 frontend]# kubectl describe node 192.168.0.97  
Allocated resources:
  (Total limits may be over 100 percent, i.e., overcommitted.)
  Resource           Requests       Limits
  --------           --------       ------
  cpu                2250m (56%)    508200m (12705%)
  memory             10940Mi (70%)  28092672Ki (176%)
  ephemeral-storage  0 (0%)         0 (0%)
Events:              <none>

And the memory of all the 4 node:

[root@runsdata-bj-00 ~]# free -h
              total        used        free      shared  buff/cache   available
Mem:            15G        2.8G        6.7G        2.1M        5.7G         11G
Swap:            0B          0B          0B
[root@runsdata-bj-01 frontend]# free -h
              total        used        free      shared  buff/cache   available
Mem:            15G        7.9G        3.7G        2.4M        3.6G        6.8G
Swap:            0B          0B          0B
[root@runsdata-bj-02 ~]# free -h
              total        used        free      shared  buff/cache   available
Mem:            15G        5.0G        2.9G        3.9M        7.4G        9.5G
Swap:            0B          0B          0B
[root@runsdata-bj-03 ~]# free -h
              total        used        free      shared  buff/cache   available
Mem:            15G        6.5G        2.2G        2.3M        6.6G        8.2G
Swap:            0B          0B          0B

here is the kube-scheduler log:

[root@runsdata-bj-01 log]# cat messages|tail -n 5000|grep kube-scheduler
Apr 17 14:31:24 runsdata-bj-01 kube-scheduler: E0417 14:31:24.404442   12740 factory.go:585] pod is already present in the activeQ
Apr 17 14:31:25 runsdata-bj-01 kube-scheduler: E0417 14:31:25.490310   12740 factory.go:585] pod is already present in the backoffQ
Apr 17 14:31:25 runsdata-bj-01 kube-scheduler: E0417 14:31:25.873292   12740 factory.go:585] pod is already present in the backoffQ
Apr 18 21:44:18 runsdata-bj-01 etcd: read-only range request "key:\"/registry/services/endpoints/kube-system/kube-scheduler\" " with result "range_response_count:1 size:440" took too long (100.521269ms) to execute
Apr 18 21:59:40 runsdata-bj-01 kube-scheduler: E0418 21:59:40.050852   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:03:07 runsdata-bj-01 kube-scheduler: E0418 22:03:07.069465   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:03:07 runsdata-bj-01 kube-scheduler: E0418 22:03:07.950254   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:03:08 runsdata-bj-01 kube-scheduler: E0418 22:03:08.567290   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:03:09 runsdata-bj-01 kube-scheduler: E0418 22:03:09.152812   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:03:09 runsdata-bj-01 kube-scheduler: E0418 22:03:09.344902   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:04:32 runsdata-bj-01 kube-scheduler: E0418 22:04:32.969606   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:09:51 runsdata-bj-01 kube-scheduler: E0418 22:09:51.366877   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:32:16 runsdata-bj-01 kube-scheduler: E0418 22:32:16.430976   12740 factory.go:585] pod is already present in the activeQ
Apr 18 22:32:16 runsdata-bj-01 kube-scheduler: E0418 22:32:16.441182   12740 factory.go:585] pod is already present in the activeQ

I searched google and stackoverflow and can not found the solution. who can help me ?

-- Esc
kube-scheduler
kubelet
kubernetes
memory
memory-management

1 Answer

4/23/2020

Kubernetes preserves the node stability instead the resource provisioning, the memory available is not calculate based on free -m command, as the documentation mention:

The value for memory.available is derived from the cgroupfs instead of tools like free -m. This is important because free -m does not work in a container, and if users use the node allocatable feature, out of resource decisions are made local to the end user Pod part of the cgroup hierarchy as well as the root node. This script reproduces the same set of steps that the kubelet performs to calculate memory.available. The kubelet excludes inactive_file (i.e. # of bytes of file-backed memory on inactive LRU list) from its calculation as it assumes that memory is reclaimable under pressure.

You could use the script mentioned above to check your memory available in the nodes and if there's no available resource you will need to increase the cluster size adding a new node.

Additionally, you can check the documenation page for more information about resources limits

-- KoopaKiller
Source: StackOverflow