How to change or increase the size of PVC/storage in Mongodb deployed in kubernetes using Kubedb

Question

I have deployed a sharded cluster of Mongodb in my kubernetes cluster as you can see in the yml configuration file below and is working just fine. I followed this doc/article for the setup. Now the issue is that I have to increase the size of my Mongodb storage but I am getting some error. Any help is highly appreciated. Thanks.

apiVersion: kubedb.com/v1alpha1
kind: MongoDB
metadata:
  name: mongo-sh
  namespace: mongo
spec:
  version: 4.1.7
  shardTopology:
    configServer:
      replicas: 3
      storage:
        resources:
          requests:
            storage: 1Gi #I tried to change this to 2Gi
        storageClassName: fast
    mongos:
      replicas: 2
      strategy:
        type: RollingUpdate
    shard:
      replicas: 3
      shards: 3
      storage:
        resources:
          requests:
            storage: 1Gi #I tried to change this to 2Gi
        storageClassName: fast
  monitor:
    agent: prometheus.io/builtin

In the above yaml Kubedb Mongodb deployment file I changed the storage from 1 Gi to 2 Gi and tried to reapply it again: kubectl apply -f kubedb-mongodb-deployment.yaml

but i am getting this error:

Error from server (BadRequest): error when applying patch:
{"metadata":{"annotations":{"kubectl.kubernetes.io/last-applied-configuration":"{\"apiVersion\":\"kubedb.com/v1alpha1\",\"kind\":\"MongoDB\",\"metadata\":{\"annotations\":{},\"name\":\"mongo-sh\",\"namespace\":\"mongo\"},\"spec\":{\"monitor\":{\"agent\":\"prometheus.io/builtin\"},\"shardTopology\":{\"configServer\":{\"replicas\":3,\"storage\":{\"resources\":{\"requests\":{\"storage\":\"2Gi\"}},\"storageClassName\":\"fast\"}},\"mongos\":{\"replicas\":2,\"strategy\":{\"type\":\"RollingUpdate\"}},\"shard\":{\"replicas\":3,\"shards\":3,\"storage\":{\"resources\":{\"requests\":{\"storage\":\"2Gi\"}},\"storageClassName\":\"fast\"}}},\"version\":\"4.1.7\"}}\n"}},"spec":{"shardTopology":{"configServer":{"storage":{"resources":{"requests":{"storage":"2Gi"}}}},"shard":{"storage":{"resources":{"requests":{"storage":"2Gi"}}}}}}}
to:
Resource: "kubedb.com/v1alpha1, Resource=mongodbs", GroupVersionKind: "kubedb.com/v1alpha1, Kind=MongoDB"
Name: "mongo-sh", Namespace: "mongo"
Object: &{map["apiVersion":"kubedb.com/v1alpha1" "kind":"MongoDB" "metadata":map["annotations":map["kubectl.kubernetes.io/last-applied-configuration":"{\"apiVersion\":\"kubedb.com/v1alpha1\",\"kind\":\"MongoDB\",\"metadata\":{\"annotations\":{},\"name\":\"mongo-sh\",\"namespace\":\"mongo\"},\"spec\":{\"monitor\":{\"agent\":\"prometheus.io/builtin\"},\"shardTopology\":{\"configServer\":{\"replicas\":3,\"storage\":{\"resources\":{\"requests\":{\"storage\":\"1Gi\"}},\"storageClassName\":\"fast\"}},\"mongos\":{\"replicas\":2,\"strategy\":{\"type\":\"RollingUpdate\"}},\"shard\":{\"replicas\":3,\"shards\":3,\"storage\":{\"resources\":{\"requests\":{\"storage\":\"1Gi\"}},\"storageClassName\":\"fast\"}}},\"version\":\"4.1.7\"}}\n"] "creationTimestamp":"2020-01-31T09:14:24Z" "finalizers":["kubedb.com"] "generation":'\x05' "name":"mongo-sh" "namespace":"mongo" "resourceVersion":"200611174" "selfLink":"/apis/kubedb.com/v1alpha1/namespaces/mongo/mongodbs/mongo-sh" "uid":"12f07f14-440a-11ea-92d9-42010a9c0fd3"] "spec":map["certificateSecret":map["secretName":"mongo-sh-keyfile"] "databaseSecret":map["secretName":"mongo-sh-auth"] "monitor":map["agent":"prometheus.io/builtin" "prometheus":map["port":'\ufffd'] "resources":map[]] "serviceTemplate":map["metadata":map[] "spec":map[]] "shardTopology":map["configServer":map["podTemplate":map["controller":map[] "metadata":map[] "spec":map["livenessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x05'] "readinessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x01'] "resources":map[] "securityContext":map["fsGroup":'\u03e7' "runAsNonRoot":%!q(bool=true) "runAsUser":'\u03e7']]] "replicas":'\x03' "storage":map["dataSource":<nil> "resources":map["requests":map["storage":"1Gi"]] "storageClassName":"fast"]] "mongos":map["podTemplate":map["controller":map[] "metadata":map[] "spec":map["livenessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x05'] "readinessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x01'] "resources":map[] "securityContext":map["fsGroup":'\u03e7' "runAsNonRoot":%!q(bool=true) "runAsUser":'\u03e7']]] "replicas":'\x02' "strategy":map["type":"RollingUpdate"]] "shard":map["podTemplate":map["controller":map[] "metadata":map[] "spec":map["livenessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x05'] "readinessProbe":map["exec":map["command":["mongo" "--eval" "db.adminCommand('ping')"]] "failureThreshold":'\x03' "periodSeconds":'\n' "successThreshold":'\x01' "timeoutSeconds":'\x01'] "resources":map[] "securityContext":map["fsGroup":'\u03e7' "runAsNonRoot":%!q(bool=true) "runAsUser":'\u03e7']]] "replicas":'\x03' "shards":'\x03' "storage":map["dataSource":<nil> "resources":map["requests":map["storage":"1Gi"]] "storageClassName":"fast"]]] "storageType":"Durable" "terminationPolicy":"Pause" "updateStrategy":map["type":"RollingUpdate"] "version":"4.1.7"] "status":map["observedGeneration":"4$6211945921239001045" "phase":"Running"]]}
for: "mongodb.yaml": admission webhook "mongodb.validators.kubedb.com" denied the request: precondition failed for: map[metadata:map[annotations:map[kubectl.kubernetes.io/last-applied-configuration:{"apiVersion":"kubedb.com/v1alpha1","kind":"MongoDB","metadata":{"annotations":{},"name":"mongo-sh","namespace":"mongo"},"spec":{"monitor":{"agent":"prometheus.io/builtin"},"shardTopology":{"configServer":{"replicas":3,"storage":{"resources":{"requests":{"storage":"2Gi"}},"storageClassName":"fast"}},"mongos":{"replicas":2,"strategy":{"type":"RollingUpdate"}},"shard":{"replicas":3,"shards":3,"storage":{"resources":{"requests":{"storage":"2Gi"}},"storageClassName":"fast"}}},"version":"4.1.7"}}
] generation:6] spec:map[shardTopology:map[configServer:map[storage:map[resources:map[requests:map[storage:2Gi]]]] shard:map[storage:map[resources:map[requests:map[storage:2Gi]]]]]]].At least one of the following was changed:
    apiVersion
    kind
    name
    namespace
    spec.storageType
    spec.storage
    spec.databaseSecret
    spec.certificateSecret
    spec.init
    spec.replicaSet.name
    spec.shardTopology.*.storage
    spec.shardTopology.*.prefix

Where is your cluster located and which Kubernetes version are you running? — Wytrzymały Wiktor, Feb 07 '20 at 09:50

score 0 · Answer 1 · answered Feb 07 '20 at 14:01

The error you experience here is because you try to rescale by editing the mongodb-deployment.yaml which is kind: MongoDB and not the PVC itself. As stated in the official documentation:

Note: spec.storage section is used to create PVC for database pod. It will create PVC with storage size specified instorage.resources.requests field. Don’t specify limits here. PVC does not get resized automatically.

What you should do is to edit the PVC .yaml file with the desired values. Check out this blog to find out how to do that in more detail.

Please let me know if that helped.

How to change or increase the size of PVC/storage in Mongodb deployed in kubernetes using Kubedb

1 Answers1