How to deploy Mongodb replicaset on microk8s cluster - mongodb

Question

I'm trying to deploy a Mongodb ReplicaSet on microk8s cluster. I have installed a VM running on Ubuntu 20.04. After the deployment, the mongo pods do not run but crash. I've enabled microk8s storage, dns and rbac add-ons but still the same problem persists. Can any one help me find the reason behind it? Below is my manifest file:
apiVersion: v1
kind: Service
metadata:
name: mongodb-service
labels:
name: mongo
spec:
ports:
- port: 27017
targetPort: 27017
clusterIP: None
selector:
role: mongo
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: mongo
spec:
selector:
matchLabels:
role: mongo
environment: test
serviceName: mongodb-service
replicas: 3
template:
metadata:
labels:
role: mongo
environment: test
replicaset: MainRepSet
spec:
affinity:
podAntiAffinity:
preferredDuringSchedulingIgnoredDuringExecution:
- weight: 100
podAffinityTerm:
labelSelector:
matchExpressions:
- key: replicaset
operator: In
values:
- MainRepSet
topologyKey: kubernetes.io/hostname
terminationGracePeriodSeconds: 10
volumes:
- name: secrets-volume
secret:
secretName: shared-bootstrap-data
defaultMode: 256
containers:
- name: mongod-container
#image: pkdone/mongo-ent:3.4
image: mongo
command:
- "numactl"
- "--interleave=all"
- "mongod"
- "--wiredTigerCacheSizeGB"
- "0.1"
- "--bind_ip"
- "0.0.0.0"
- "--replSet"
- "MainRepSet"
- "--auth"
- "--clusterAuthMode"
- "keyFile"
- "--keyFile"
- "/etc/secrets-volume/internal-auth-mongodb-keyfile"
- "--setParameter"
- "authenticationMechanisms=SCRAM-SHA-1"
resources:
requests:
cpu: 0.2
memory: 200Mi
ports:
- containerPort: 27017
volumeMounts:
- name: secrets-volume
readOnly: true
mountPath: /etc/secrets-volume
- name: mongodb-persistent-storage-claim
mountPath: /data/db
volumeClaimTemplates:
- metadata:
name: mongodb-persistent-storage-claim
spec:
storageClassName: microk8s-hostpath
accessModes: [ "ReadWriteOnce" ]
resources:
requests:
storage: 5Gi
Also, here are the pv, pvc and sc outputs:
yyy#xxx:$ kubectl get pvc
NAME STATUS VOLUME CAPACITY ACCESS MODES STORAGECLASS AGE
mongodb-persistent-storage-claim-mongo-0 Bound pvc-1b3de8f7-e416-4a1a-9c44-44a0422e0413 5Gi RWO microk8s-hostpath 13m
yyy#xxx:$ kubectl get pv
NAME CAPACITY ACCESS MODES RECLAIM POLICY STATUS CLAIM STORAGECLASS REASON AGE
pvc-5b75ddf6-abbd-4ff3-a135-0312df1e6703 20Gi RWX Delete Bound container-registry/registry-claim microk8s-hostpath 38m
pvc-1b3de8f7-e416-4a1a-9c44-44a0422e0413 5Gi RWO Delete Bound default/mongodb-persistent-storage-claim-mongo-0 microk8s-hostpath 13m
yyy#xxx:$ kubectl get sc
NAME PROVISIONER RECLAIMPOLICY VOLUMEBINDINGMODE ALLOWVOLUMEEXPANSION AGE
microk8s-hostpath (default) microk8s.io/hostpath Delete Immediate false 108m
yyy#xxx:$ kubectl get pods -n kube-system
NAME READY STATUS RESTARTS AGE
metrics-server-8bbfb4bdb-xvwcw 1/1 Running 1 148m
dashboard-metrics-scraper-78d7698477-4qdhj 1/1 Running 0 146m
kubernetes-dashboard-85fd7f45cb-6t7xr 1/1 Running 0 146m
hostpath-provisioner-5c65fbdb4f-ff7cl 1/1 Running 0 113m
coredns-7f9c69c78c-dr5kt 1/1 Running 0 65m
calico-kube-controllers-f7868dd95-wtf8j 1/1 Running 0 150m
calico-node-knzc2 1/1 Running 0 150m
I have installed the cluster using this command:
sudo snap install microk8s --classic --channel=1.21
Output of mongodb deployment:
yyy#xxx:$ kubectl get all
NAME READY STATUS RESTARTS AGE
pod/mongo-0 0/1 CrashLoopBackOff 5 4m18s
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
service/kubernetes ClusterIP 10.152.183.1 <none> 443/TCP 109m
service/mongodb-service ClusterIP None <none> 27017/TCP 4m19s
NAME READY AGE
statefulset.apps/mongo 0/3 4m19s
Pod logs:
yyy#xxx:$ kubectl logs pod/mongo-0
{"t":{"$date":"2021-09-07T16:21:13.191Z"},"s":"F", "c":"CONTROL", "id":20574, "ctx":"-","msg":"Error during global initialization","attr":{"error":{"code":2,"codeName":"BadValue","errmsg":"storage.wiredTiger.engineConfig.cacheSizeGB must be greater than or equal to 0.25"}}}
yyy#xxx:$ kubectl describe pod/mongo-0
Name: mongo-0
Namespace: default
Priority: 0
Node: citest1/192.168.9.105
Start Time: Tue, 07 Sep 2021 16:17:38 +0000
Labels: controller-revision-hash=mongo-66bd776569
environment=test
replicaset=MainRepSet
role=mongo
statefulset.kubernetes.io/pod-name=mongo-0
Annotations: cni.projectcalico.org/podIP: 10.1.150.136/32
cni.projectcalico.org/podIPs: 10.1.150.136/32
Status: Running
IP: 10.1.150.136
IPs:
IP: 10.1.150.136
Controlled By: StatefulSet/mongo
Containers:
mongod-container:
Container ID: containerd://458e21fac3e87dcf304a9701da0eb827b2646efe94cabce7f283cd49f740c15d
Image: mongo
Image ID: docker.io/library/mongo#sha256:58ea1bc09f269a9b85b7e1fae83b7505952aaa521afaaca4131f558955743842
Port: 27017/TCP
Host Port: 0/TCP
Command:
numactl
--interleave=all
mongod
--wiredTigerCacheSizeGB
0.1
--bind_ip
0.0.0.0
--replSet
MainRepSet
--auth
--clusterAuthMode
keyFile
--keyFile
/etc/secrets-volume/internal-auth-mongodb-keyfile
--setParameter
authenticationMechanisms=SCRAM-SHA-1
State: Waiting
Reason: CrashLoopBackOff
Last State: Terminated
Reason: Error
Exit Code: 1
Started: Tue, 07 Sep 2021 16:24:03 +0000
Finished: Tue, 07 Sep 2021 16:24:03 +0000
Ready: False
Restart Count: 6
Requests:
cpu: 200m
memory: 200Mi
Environment: <none>
Mounts:
/data/db from mongodb-persistent-storage-claim (rw)
/etc/secrets-volume from secrets-volume (ro)
/var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-b7nf8 (ro)
Conditions:
Type Status
Initialized True
Ready False
ContainersReady False
PodScheduled True
Volumes:
mongodb-persistent-storage-claim:
Type: PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
ClaimName: mongodb-persistent-storage-claim-mongo-0
ReadOnly: false
secrets-volume:
Type: Secret (a volume populated by a Secret)
SecretName: shared-bootstrap-data
Optional: false
kube-api-access-b7nf8:
Type: Projected (a volume that contains injected data from multiple sources)
TokenExpirationSeconds: 3607
ConfigMapName: kube-root-ca.crt
ConfigMapOptional: <nil>
DownwardAPI: true
QoS Class: Burstable
Node-Selectors: <none>
Tolerations: node.kubernetes.io/not-ready:NoExecute op=Exists for 300s
node.kubernetes.io/unreachable:NoExecute op=Exists for 300s
Events:
Type Reason Age From Message
---- ------ ---- ---- -------
Warning FailedScheduling 7m53s default-scheduler 0/1 nodes are available: 1 pod has unbound immediate PersistentVolumeClaims.
Warning FailedScheduling 7m52s default-scheduler 0/1 nodes are available: 1 pod has unbound immediate PersistentVolumeClaims.
Normal Scheduled 7m50s default-scheduler Successfully assigned default/mongo-0 to citest1
Normal Pulled 7m25s kubelet Successfully pulled image "mongo" in 25.215669443s
Normal Pulled 7m21s kubelet Successfully pulled image "mongo" in 1.192994197s
Normal Pulled 7m6s kubelet Successfully pulled image "mongo" in 1.203239709s
Normal Pulled 6m38s kubelet Successfully pulled image "mongo" in 1.213451175s
Normal Created 6m38s (x4 over 7m23s) kubelet Created container mongod-container
Normal Started 6m37s (x4 over 7m23s) kubelet Started container mongod-container
Normal Pulling 5m47s (x5 over 7m50s) kubelet Pulling image "mongo"
Warning BackOff 2m49s (x23 over 7m20s) kubelet Back-off restarting failed container

Answer 1

The logs you provided show that you have an incorrectly set parameter wiredTigerCacheSizeGB. In your case it is 0.1, and according to the message
"code":2,"codeName":"BadValue","errmsg":"storage.wiredTiger.engineConfig.cacheSizeGB must be greater than or equal to 0.25"
it should be at least 0.25.
In the section containers:
containers:
- name: mongod-container
#image: pkdone/mongo-ent:3.4
image: mongo
command:
- "numactl"
- "--interleave=all"
- "mongod"
- "--wiredTigerCacheSizeGB"
- "0.1"
- "--bind_ip"
- "0.0.0.0"
- "--replSet"
- "MainRepSet"
- "--auth"
- "--clusterAuthMode"
- "keyFile"
- "--keyFile"
- "/etc/secrets-volume/internal-auth-mongodb-keyfile"
- "--setParameter"
- "authenticationMechanisms=SCRAM-SHA-1"
you should change in this place
- "--wiredTigerCacheSizeGB"
- "0.1"
the value "0.1" to any other greather or equal "0.25".
Additionally I have seen another error:
1 pod has unbound immediate PersistentVolumeClaims
It should related to what I wrote earlier. However, you may find alternative ways to solve it here, here and here.