calico: Pod calico-node Hit error connecting to datastore - i/o timeout
Expected Behavior
Pod calico-node-xxx up and running on each node
Current Behavior
Pods calico-node on worker nodes are in state ‘CrashLoopBackOff’ This is output from one of the pod
~$ kubectl logs -n kube-system calico-node-92lqd
2019-12-26 10:49:12.798 [INFO][8] startup.go 259: Early log level set to info
2019-12-26 10:49:12.798 [INFO][8] startup.go 275: Using NODENAME environment for node name
2019-12-26 10:49:12.798 [INFO][8] startup.go 287: Determined node name: ip-10-10-20-38.ap-southeast-1.compute.internal
2019-12-26 10:49:12.799 [INFO][8] k8s.go 228: Using Calico IPAM
2019-12-26 10:49:12.799 [INFO][8] startup.go 319: Checking datastore connection
2019-12-26 10:49:42.800 [INFO][8] startup.go 334: Hit error connecting to datastore - retry error=Get https://172.20.0.1:443/api/v1/nodes/foo: dial tcp 172.20.0.1:443: i/o timeout
2019-12-26 10:50:13.800 [INFO][8] startup.go 334: Hit error connecting to datastore - retry error=Get https://172.20.0.1:443/api/v1/nodes/foo: dial tcp 172.20.0.1:443: i/o timeout
Steps to Reproduce (for bugs)
- I followed step-by-step from this medium article and official calico docs here and here
- Create new nodegroup deprived from aws-node using nodeAffinity
kubectl apply -f calico.yaml
on that new nodegroup also using nodeAffinity- Error
This is my edited calico.yaml
---
# Source: calico/templates/calico-config.yaml
# This ConfigMap is used to configure a self-hosted Calico installation.
kind: ConfigMap
apiVersion: v1
metadata:
name: calico-config
namespace: kube-system
data:
# Typha is disabled.
typha_service_name: "none"
# Configure the backend to use.
calico_backend: "bird"
# Configure the MTU to use
veth_mtu: "1440"
# The CNI network configuration to install on each node. The special
# values in this config will be automatically populated.
cni_network_config: |-
{
"name": "k8s-pod-network",
"cniVersion": "0.3.1",
"plugins": [
{
"type": "calico",
"log_level": "info",
"datastore_type": "kubernetes",
"nodename": "__KUBERNETES_NODE_NAME__",
"mtu": __CNI_MTU__,
"ipam": {
"type": "calico-ipam"
},
"policy": {
"type": "k8s"
},
"kubernetes": {
"kubeconfig": "__KUBECONFIG_FILEPATH__"
}
},
{
"type": "portmap",
"snat": true,
"capabilities": {"portMappings": true}
}
]
}
---
# Source: calico/templates/kdd-crds.yaml
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: felixconfigurations.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: FelixConfiguration
plural: felixconfigurations
singular: felixconfiguration
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: ipamblocks.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: IPAMBlock
plural: ipamblocks
singular: ipamblock
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: blockaffinities.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: BlockAffinity
plural: blockaffinities
singular: blockaffinity
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: ipamhandles.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: IPAMHandle
plural: ipamhandles
singular: ipamhandle
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: ipamconfigs.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: IPAMConfig
plural: ipamconfigs
singular: ipamconfig
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: bgppeers.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: BGPPeer
plural: bgppeers
singular: bgppeer
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: bgpconfigurations.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: BGPConfiguration
plural: bgpconfigurations
singular: bgpconfiguration
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: ippools.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: IPPool
plural: ippools
singular: ippool
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: hostendpoints.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: HostEndpoint
plural: hostendpoints
singular: hostendpoint
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: clusterinformations.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: ClusterInformation
plural: clusterinformations
singular: clusterinformation
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: globalnetworkpolicies.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: GlobalNetworkPolicy
plural: globalnetworkpolicies
singular: globalnetworkpolicy
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: globalnetworksets.crd.projectcalico.org
spec:
scope: Cluster
group: crd.projectcalico.org
version: v1
names:
kind: GlobalNetworkSet
plural: globalnetworksets
singular: globalnetworkset
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: networkpolicies.crd.projectcalico.org
spec:
scope: Namespaced
group: crd.projectcalico.org
version: v1
names:
kind: NetworkPolicy
plural: networkpolicies
singular: networkpolicy
---
apiVersion: apiextensions.k8s.io/v1beta1
kind: CustomResourceDefinition
metadata:
name: networksets.crd.projectcalico.org
spec:
scope: Namespaced
group: crd.projectcalico.org
version: v1
names:
kind: NetworkSet
plural: networksets
singular: networkset
---
# Source: calico/templates/rbac.yaml
# Include a clusterrole for the kube-controllers component,
# and bind it to the calico-kube-controllers serviceaccount.
kind: ClusterRole
apiVersion: rbac.authorization.k8s.io/v1
metadata:
name: calico-kube-controllers
rules:
# Nodes are watched to monitor for deletions.
- apiGroups: [""]
resources:
- nodes
verbs:
- watch
- list
- get
# Pods are queried to check for existence.
- apiGroups: [""]
resources:
- pods
verbs:
- get
# IPAM resources are manipulated when nodes are deleted.
- apiGroups: ["crd.projectcalico.org"]
resources:
- ippools
verbs:
- list
- apiGroups: ["crd.projectcalico.org"]
resources:
- blockaffinities
- ipamblocks
- ipamhandles
verbs:
- get
- list
- create
- update
- delete
# Needs access to update clusterinformations.
- apiGroups: ["crd.projectcalico.org"]
resources:
- clusterinformations
verbs:
- get
- create
- update
---
kind: ClusterRoleBinding
apiVersion: rbac.authorization.k8s.io/v1
metadata:
name: calico-kube-controllers
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: ClusterRole
name: calico-kube-controllers
subjects:
- kind: ServiceAccount
name: calico-kube-controllers
namespace: kube-system
---
# Include a clusterrole for the calico-node DaemonSet,
# and bind it to the calico-node serviceaccount.
kind: ClusterRole
apiVersion: rbac.authorization.k8s.io/v1
metadata:
name: calico-node
rules:
# The CNI plugin needs to get pods, nodes, and namespaces.
- apiGroups: [""]
resources:
- pods
- nodes
- namespaces
verbs:
- get
- apiGroups: [""]
resources:
- endpoints
- services
verbs:
# Used to discover service IPs for advertisement.
- watch
- list
# Used to discover Typhas.
- get
- apiGroups: [""]
resources:
- nodes/status
verbs:
# Needed for clearing NodeNetworkUnavailable flag.
- patch
# Calico stores some configuration information in node annotations.
- update
# Watch for changes to Kubernetes NetworkPolicies.
- apiGroups: ["networking.k8s.io"]
resources:
- networkpolicies
verbs:
- watch
- list
# Used by Calico for policy information.
- apiGroups: [""]
resources:
- pods
- namespaces
- serviceaccounts
verbs:
- list
- watch
# The CNI plugin patches pods/status.
- apiGroups: [""]
resources:
- pods/status
verbs:
- patch
# Calico monitors various CRDs for config.
- apiGroups: ["crd.projectcalico.org"]
resources:
- globalfelixconfigs
- felixconfigurations
- bgppeers
- globalbgpconfigs
- bgpconfigurations
- ippools
- ipamblocks
- globalnetworkpolicies
- globalnetworksets
- networkpolicies
- networksets
- clusterinformations
- hostendpoints
- blockaffinities
verbs:
- get
- list
- watch
# Calico must create and update some CRDs on startup.
- apiGroups: ["crd.projectcalico.org"]
resources:
- ippools
- felixconfigurations
- clusterinformations
verbs:
- create
- update
# Calico stores some configuration information on the node.
- apiGroups: [""]
resources:
- nodes
verbs:
- get
- list
- watch
# These permissions are only requried for upgrade from v2.6, and can
# be removed after upgrade or on fresh installations.
- apiGroups: ["crd.projectcalico.org"]
resources:
- bgpconfigurations
- bgppeers
verbs:
- create
- update
# These permissions are required for Calico CNI to perform IPAM allocations.
- apiGroups: ["crd.projectcalico.org"]
resources:
- blockaffinities
- ipamblocks
- ipamhandles
verbs:
- get
- list
- create
- update
- delete
- apiGroups: ["crd.projectcalico.org"]
resources:
- ipamconfigs
verbs:
- get
# Block affinities must also be watchable by confd for route aggregation.
- apiGroups: ["crd.projectcalico.org"]
resources:
- blockaffinities
verbs:
- watch
# The Calico IPAM migration needs to get daemonsets. These permissions can be
# removed if not upgrading from an installation using host-local IPAM.
- apiGroups: ["apps"]
resources:
- daemonsets
verbs:
- get
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:
name: calico-node
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: ClusterRole
name: calico-node
subjects:
- kind: ServiceAccount
name: calico-node
namespace: kube-system
---
# Source: calico/templates/calico-node.yaml
# This manifest installs the calico-node container, as well
# as the CNI plugins and network config on
# each master and worker node in a Kubernetes cluster.
kind: DaemonSet
apiVersion: apps/v1
metadata:
name: calico-node
namespace: kube-system
labels:
k8s-app: calico-node
spec:
selector:
matchLabels:
k8s-app: calico-node
updateStrategy:
type: RollingUpdate
rollingUpdate:
maxUnavailable: 1
template:
metadata:
labels:
k8s-app: calico-node
annotations:
# This, along with the CriticalAddonsOnly toleration below,
# marks the pod as a critical add-on, ensuring it gets
# priority scheduling and that its resources are reserved
# if it ever gets evicted.
scheduler.alpha.kubernetes.io/critical-pod: ''
spec:
nodeSelector:
beta.kubernetes.io/os: linux
affinity:
nodeAffinity:
requiredDuringSchedulingIgnoredDuringExecution:
nodeSelectorTerms:
- matchExpressions:
- key: app.kubernetes.io/purpose
operator: In
values:
- calico
hostNetwork: true
tolerations:
# Make sure calico-node gets scheduled on all nodes.
- effect: NoSchedule
operator: Exists
# Mark the pod as a critical add-on for rescheduling.
- key: CriticalAddonsOnly
operator: Exists
- effect: NoExecute
operator: Exists
serviceAccountName: calico-node
# Minimize downtime during a rolling upgrade or deletion; tell Kubernetes to do a "force
# deletion": https://kubernetes.io/docs/concepts/workloads/pods/pod/#termination-of-pods.
terminationGracePeriodSeconds: 0
priorityClassName: system-node-critical
initContainers:
# This container performs upgrade from host-local IPAM to calico-ipam.
# It can be deleted if this is a fresh installation, or if you have already
# upgraded to use calico-ipam.
- name: upgrade-ipam
image: calico/cni:v3.11.1
command: ["/opt/cni/bin/calico-ipam", "-upgrade"]
env:
- name: KUBERNETES_NODE_NAME
valueFrom:
fieldRef:
fieldPath: spec.nodeName
- name: CALICO_NETWORKING_BACKEND
valueFrom:
configMapKeyRef:
name: calico-config
key: calico_backend
volumeMounts:
- mountPath: /var/lib/cni/networks
name: host-local-net-dir
- mountPath: /host/opt/cni/bin
name: cni-bin-dir
securityContext:
privileged: true
# This container installs the CNI binaries
# and CNI network config file on each node.
- name: install-cni
image: calico/cni:v3.11.1
command: ["/install-cni.sh"]
env:
# Name of the CNI config file to create.
- name: CNI_CONF_NAME
value: "10-calico.conflist"
# The CNI network config to install on each node.
- name: CNI_NETWORK_CONFIG
valueFrom:
configMapKeyRef:
name: calico-config
key: cni_network_config
# Set the hostname based on the k8s node name.
- name: KUBERNETES_NODE_NAME
valueFrom:
fieldRef:
fieldPath: spec.nodeName
# CNI MTU Config variable
- name: CNI_MTU
valueFrom:
configMapKeyRef:
name: calico-config
key: veth_mtu
# Prevents the container from sleeping forever.
- name: SLEEP
value: "false"
volumeMounts:
- mountPath: /host/opt/cni/bin
name: cni-bin-dir
- mountPath: /host/etc/cni/net.d
name: cni-net-dir
securityContext:
privileged: true
# Adds a Flex Volume Driver that creates a per-pod Unix Domain Socket to allow Dikastes
# to communicate with Felix over the Policy Sync API.
- name: flexvol-driver
image: calico/pod2daemon-flexvol:v3.11.1
volumeMounts:
- name: flexvol-driver-host
mountPath: /host/driver
securityContext:
privileged: true
containers:
# Runs calico-node container on each Kubernetes node. This
# container programs network policy and routes on each
# host.
- name: calico-node
image: calico/node:v3.11.1
env:
# Use Kubernetes API as the backing datastore.
- name: DATASTORE_TYPE
value: "kubernetes"
# Wait for the datastore.
- name: WAIT_FOR_DATASTORE
value: "true"
# Set based on the k8s node name.
- name: NODENAME
valueFrom:
fieldRef:
fieldPath: spec.nodeName
# Choose the backend to use.
- name: CALICO_NETWORKING_BACKEND
valueFrom:
configMapKeyRef:
name: calico-config
key: calico_backend
# Cluster type to identify the deployment type
- name: CLUSTER_TYPE
value: "k8s,bgp"
# Auto-detect the BGP IP address.
- name: IP
value: "autodetect"
- name: IP_AUTODETECTION_METHOD
value: "interface=eth.*"
# Enable IPIP
- name: CALICO_IPV4POOL_IPIP
value: "CrossSubnet"
# Set MTU for tunnel device used if ipip is enabled
- name: FELIX_IPINIPMTU
valueFrom:
configMapKeyRef:
name: calico-config
key: veth_mtu
# The default IPv4 pool to create on startup if none exists. Pod IPs will be
# chosen from this range. Changing this value after installation will have
# no effect. This should fall within `--cluster-cidr`.
- name: CALICO_IPV4POOL_CIDR
value: "10.11.0.0/16"
# Disable file logging so `kubectl logs` works.
- name: CALICO_DISABLE_FILE_LOGGING
value: "true"
# Set Felix endpoint to host default action to ACCEPT.
- name: FELIX_DEFAULTENDPOINTTOHOSTACTION
value: "ACCEPT"
# Disable IPv6 on Kubernetes.
- name: FELIX_IPV6SUPPORT
value: "false"
# Set Felix logging to "info"
- name: FELIX_LOGSEVERITYSCREEN
value: "info"
- name: FELIX_HEALTHENABLED
value: "true"
- name: CALICO_IPV4POOL_NAT_OUTGOING
value: "true"
securityContext:
privileged: true
resources:
requests:
cpu: 250m
livenessProbe:
exec:
command:
- /bin/calico-node
- -felix-live
- -bird-live
periodSeconds: 10
initialDelaySeconds: 10
failureThreshold: 6
readinessProbe:
exec:
command:
- /bin/calico-node
- -felix-ready
- -bird-ready
periodSeconds: 10
volumeMounts:
- mountPath: /lib/modules
name: lib-modules
readOnly: true
- mountPath: /run/xtables.lock
name: xtables-lock
readOnly: false
- mountPath: /var/run/calico
name: var-run-calico
readOnly: false
- mountPath: /var/lib/calico
name: var-lib-calico
readOnly: false
- name: policysync
mountPath: /var/run/nodeagent
volumes:
# Used by calico-node.
- name: lib-modules
hostPath:
path: /lib/modules
- name: var-run-calico
hostPath:
path: /var/run/calico
- name: var-lib-calico
hostPath:
path: /var/lib/calico
- name: xtables-lock
hostPath:
path: /run/xtables.lock
type: FileOrCreate
# Used to install CNI.
- name: cni-bin-dir
hostPath:
path: /opt/cni/bin
- name: cni-net-dir
hostPath:
path: /etc/cni/net.d
# Mount in the directory for host-local IPAM allocations. This is
# used when upgrading from host-local to calico-ipam, and can be removed
# if not using the upgrade-ipam init container.
- name: host-local-net-dir
hostPath:
path: /var/lib/cni/networks
# Used to create per-pod Unix Domain Sockets
- name: policysync
hostPath:
type: DirectoryOrCreate
path: /var/run/nodeagent
# Used to install Flex Volume Driver
- name: flexvol-driver-host
hostPath:
type: DirectoryOrCreate
path: /usr/libexec/kubernetes/kubelet-plugins/volume/exec/nodeagent~uds
---
apiVersion: v1
kind: ServiceAccount
metadata:
name: calico-node
namespace: kube-system
---
# Source: calico/templates/calico-kube-controllers.yaml
# See https://github.com/projectcalico/kube-controllers
apiVersion: apps/v1
kind: Deployment
metadata:
name: calico-kube-controllers
namespace: kube-system
labels:
k8s-app: calico-kube-controllers
spec:
# The controllers can only have a single active instance.
replicas: 1
selector:
matchLabels:
k8s-app: calico-kube-controllers
strategy:
type: Recreate
template:
metadata:
name: calico-kube-controllers
namespace: kube-system
labels:
k8s-app: calico-kube-controllers
annotations:
scheduler.alpha.kubernetes.io/critical-pod: ''
spec:
nodeSelector:
beta.kubernetes.io/os: linux
tolerations:
# Mark the pod as a critical add-on for rescheduling.
- key: CriticalAddonsOnly
operator: Exists
- key: node-role.kubernetes.io/master
effect: NoSchedule
serviceAccountName: calico-kube-controllers
priorityClassName: system-cluster-critical
containers:
- name: calico-kube-controllers
image: calico/kube-controllers:v3.11.1
env:
# Choose which controllers to run.
- name: ENABLED_CONTROLLERS
value: node
- name: DATASTORE_TYPE
value: kubernetes
readinessProbe:
exec:
command:
- /usr/bin/check-status
- -r
---
apiVersion: v1
kind: ServiceAccount
metadata:
name: calico-kube-controllers
namespace: kube-system
---
# Source: calico/templates/calico-etcd-secrets.yaml
---
# Source: calico/templates/calico-typha.yaml
---
# Source: calico/templates/configure-canal.yaml
This is customization I perform on the manifest:
- Add nodeAffinity on calico-node DaemonSet
- Add env IP_AUTODETECTION_METHOD=“interface=eth.*”
- Change env CALICO_IPV4POOL_IPIP=“CrossSubnet”
- Change env CALICO_IPV4POOL_CIDR=“10.11.0.0/16”
- Add env CALICO_IPV4POOL_NAT_OUTGOING=“true”
Context
I try to bypass AWS EKS maximum pod limitation by disabling AWS CNI and use Calico CNI as IP pool.
Your Environment
- Calico version: v3.11
- Orchestrator version: k8s 1.14.7
- Operating System and version: Amazon Linux 2 (Linux 4.14.146-119.123.amzn2.x86_64)
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 25 (5 by maintainers)
@Goeldeepesh your issue seems to be quite different. From your kube-proxy logs it looks to be a problem there. Please resolve the issue with kube-proxy before you try to fix any problems with Calico. It looks like your certificates are not setup correctly for kube-proxy. I can’t offer any help on that.
Reviewing my old notes… at the end, the problem is: no comunication between elements (master and nodes…)
During configuration of VM (in my case with KVM) i setup 3 (master, 2 nodes)
Each vm need… swap / bridge / ipforward (https://kubernetes.io/docs/setup/production-environment/tools/kubeadm/install-kubeadm/)
And the “trick” came here: https://wiki.debian.org/KVM
If you use libvirt to manage your VMs, libvirt provides a NATed bridged network named “default” that allows the host to communicate with the guests. This network is available only for the system domains (that is VMs created by root or using the qemu:///system connection URI). … In order for things to work this way you need to have the recommended packages dnsmasq-base, bridge-utils and iptables installed.
Hope it’s help @usersina
In my case, after reading a lot about it… my principal problem was the need of bridge-utils (https://wiki.debian.org/es/KVM)
I know this ticket is closed but just to help people who find this post i solved the problem when i changed my pod-network-cidr to pod-network-cidr=10.244.0.0/16