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

Question

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?

Answer 1

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

Answer 2

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

Answer 3

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

Answer 4

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