K
Q

How to deploy a single instance mongodb with persistant volume using NFS

1/12/2021

I have a microservice that is working on my laptop. However, I am using docker compose. I am working to deploy to a kubernetes cluster which I have already set up. I am stuck on making data persistent. E.g here is my mongodb in docker-compose

systemdb:
    container_name: system-db
    image: mongo:4.4.1
    restart: always
    ports:
      - '9000:27017'
    volumes:
      - ./system_db:/data/db
    networks:
      - backend

Since it is an on premise solution, I went with an NFS server. I have created a Persistent Volume and Persistent Volume Claim (pvc-nfs-pv1) which seem to work well when testing with nginx. However, I don't know how to deploy a mongodb statefulset to use the pvc. I am not implementing a replicaset.

Here is my yaml: 

apiVersion: apps/v1
kind: StatefulSet
metadata:
  name: mongod
spec:
  serviceName: mongodb-service
  replicas: 1
  selector:
    matchLabels:
      role: mongo
  template:
    metadata:
      labels:
        role: mongo
        environment: test
    spec:
      terminationGracePeriodSeconds: 10
      containers:
        - name: mongod-container
          image: mongo
          resources:
            requests:
              cpu: "0.2"
              memory: 200Mi
          ports:
            - containerPort: 27017
          volumeMounts:
            - name: pvc-nfs-pv1
              mountPath: /data/db
  volumeClaimTemplates:
  - metadata:
      name: pvc-nfs-pv1
       annotations:
         volume.beta.kubernetes.io/storage-class: "standard"
    spec:
      accessModes: [ "ReadWriteOnce" ]
      resources:
        requests:
          storage: 500Mi

How do i do it?

-- Denn
docker-compose
kubernetes
mongodb
persistent-storage

Similar Questions

How to check kubelet configurations currently in use?
Limit access to Kubernetes secret by RBAC
how does kubernetes service decide which backend pod to route to
How to check a particular script execution is completed by a Kubernetes pod
Logstash with helm in Kubernetes : grok filter not working

4 Answers

1/12/2021

Your question is how the mongo StatefulSet is going to use the pvc u have created ? By default It wont . It will create numbers of new pvc (depending of number of replicaset) automatically via the volumeClaimTemplates and it will be named like so : pvc-nfs-pv1-mongod-0 , pvc-nfs-pv1-mongod-1 etc .. So if you want to use the pvc you created change the name to match pvc-nfs-pv1-mongod-0 something like this 

apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  labels:
    role: mongo
  name: pvc-nfs-pv1-mongod-0
  namespace: default
spec:
...
  volumeName: nfs-pv1
  accessModes:
  - ReadWriteOnce
  resources:
    requests:
      storage: 500Mi
...

However I dont recommend using this method (issue: when you have many other replicasets .. do you have to create all the pvcs manually and the correspondent pv ).. Here is similar questions is asked in here and also in here , I recommend using Dynamic NFS Provisioning.

Hope I helped

-- Shay
Source: StackOverflow
5/12/2021

I do not use NFS but volumes at hetzner.com where my dev server is running. But I have exactly the same problem: As it is my dev system I destroy and rebuild it regularly. And by doing so I want the data on my volumes survive the deletion of the whole cluster. And when I rebuild it, all the volumes shall be mounted to the right pod.

For my postgres this works just fine. But using the mongodb kubernetes operator I am not able to get this running. The one mongodb pod stays forever in the state "Pending" because the PVC I created and bound manually to the volume is already bound to a volume. Or so it seems to me.

I am thankful for any help, Tobias

The exact message I can see is:

0/1 nodes are available: 1 pod has unbound immediate PersistentVolumeClaims

PVC and PV:

apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: data-volume-system-mongodb-0
  labels:
    app: moderetic
    type: mongodb
spec:
  storageClassName: hcloud-volumes
  volumeName: mongodb-data-volume
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 10Gi
---
apiVersion: v1
kind: PersistentVolume
metadata:
  name: mongodb-data-volume
  labels:
    app: moderetic
    type: mongodb
spec:
  storageClassName: hcloud-volumes
  claimRef:
    name: data-volume-system-mongodb-0
  capacity:
    storage: 10Gi
  accessModes:
    - ReadWriteOnce
  csi:
    volumeHandle: "11099996"
    driver: csi.hetzner.cloud
    fsType: ext4

And the mongodb StatefulSet:

apiVersion: mongodbcommunity.mongodb.com/v1
kind: MongoDBCommunity
metadata:
  name: system-mongodb
  labels:
    app: moderetic
    type: mongodb
spec:
  members: 1
  type: ReplicaSet
  version: "4.2.6"
  security:
    authentication:
      modes: ["SCRAM"]
  users:
    - name: moderetic
      db: moderetic
      passwordSecretRef:
        name: mongodb-secret
      roles:
        - name: clusterAdmin
          db: moderetic
        - name: userAdminAnyDatabase
          db: moderetic
      scramCredentialsSecretName: moderetic-scram-secret
  additionalMongodConfig:
    storage.wiredTiger.engineConfig.journalCompressor: zlib
  persistent: true
  statefulSet:
    spec:
      template:
        spec:
          containers:
            - name: mongod
              resources:
                requests:
                  cpu: 1
                  memory: 1Gi
                limits:
                  memory: 8Gi
            - name: mongodb-agent
              resources:
                requests:
                  memory: 50Mi
                limits:
                  cpu: 500m
                  memory: 256Mi
      volumeClaimTemplates:
        - metadata:
            name: data-volume
          spec:
            accessModes: ["ReadWriteOnce"]
            storageClassName: hcloud-volumes
            resources:
              requests:
                storage: 10Gi
        - metadata:
            name: logs-volume
          spec:
            accessModes: ["ReadWriteOnce"]
            storageClassName: hcloud-volumes
            resources:
              requests:
                storage: 10Gi
-- Tobias Neubert
Source: StackOverflow
5/13/2021

Ok, I have a solution. It works simply by selecting the volume by using the matchLabels selector.

apiVersion: v1
kind: PersistentVolume
metadata:
  name: mongodb-data-volume
  labels:
    app: moderetic
    type: mongodb
    role: data
spec:
  storageClassName: hcloud-volumes
  capacity:
    storage: 10Gi
  accessModes:
    - ReadWriteOnce
  csi:
    volumeHandle: "11099996"
    driver: csi.hetzner.cloud
    fsType: ext4

---

---
apiVersion: mongodbcommunity.mongodb.com/v1
kind: MongoDBCommunity
metadata:
  name: system-mongodb
  labels:
    app: moderetic
    type: mongodb
spec:
  members: 1
  type: ReplicaSet
  version: "4.2.6"
  logLevel: INFO
  security:
    authentication:
      modes: ["SCRAM"]
  users:
    - name: moderetic
      db: moderetic
      passwordSecretRef:
        name: mongodb-secret
      roles:
        - name: clusterAdmin
          db: moderetic
        - name: userAdminAnyDatabase
          db: moderetic
      scramCredentialsSecretName: moderetic-scram-secret
  additionalMongodConfig:
    storage.wiredTiger.engineConfig.journalCompressor: zlib
  persistent: true
  statefulSet:
    spec:
      template:
        spec:
          containers:
            - name: mongod
              resources:
                requests:
                  cpu: 1
                  memory: 1Gi
                limits:
                  memory: 8Gi
            - name: mongodb-agent
              resources:
                requests:
                  memory: 50Mi
                limits:
                  cpu: 500m
                  memory: 256Mi
      volumeClaimTemplates:
        - metadata:
            name: data-volume
          spec:
            accessModes: ["ReadWriteOnce"]
            storageClassName: hcloud-volumes
            resources:
              requests:
                storage: 10Gi
            selector:
              matchLabels:
                app: moderetic
                type: mongodb
                role: data
        - metadata:
            name: logs-volume
          spec:
            accessModes: ["ReadWriteOnce"]
            storageClassName: hcloud-volumes
            resources:
              requests:
                storage: 10Gi
            selector:
              matchLabels:
                app: moderetic
                type: mongodb
                role: logs
-- Tobias Neubert
Source: StackOverflow
1/12/2021

volumeClaimTemplates are used for dynamic volume provisioning. So you're defining one volume claim template which will be used to create a PersistentVolumeClaim for each pod.

The volumeClaimTemplates will provide stable storage using PersistentVolumes provisioned by a PersistentVolume Provisioner

So for your use case you would need to create storageclass with nfs provisioner. NFS Subdir external provisioner is an automatic provisioner that use your existing and already configured NFS server to support dynamic provisioning of Kubernetes Persistent Volumes via Persistent Volume Claims. Persistent volumes are provisioned as ${namespace}-${pvcName}-${pvName}.

Here`s an example how to define storage class: 

apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
  name: managed-nfs-storage
provisioner: fuseim.pri/ifs # or choose another name, must match deployment's env PROVISIONER_NAME'
parameters:
  pathPattern: "${.PVC.namespace}/${.PVC.annotations.nfs.io/storage-path}" # waits for nfs.io/storage-path annotation, if not specified will accept as empty string.
  onDelete: delete
-- acid_fuji
Source: StackOverflow