Question

How to configure postgresql using do-block-storage in K8

I have the following configuration

kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: postgres-pvc-v1  # Sets name of PVC
  labels:
    app: postgres
spec:
  storageClassName: do-block-storage
  accessModes:
    - ReadWriteOnce  # Sets read and write access
  resources:
    requests:
      storage: 10Gi  # Sets volume size
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: postgres
spec:
  replicas: 1
  selector:
    matchLabels:
      app: postgres
  template:
    metadata:
      labels:
        app: postgres
    spec:
      containers:
        - name: postgres
          image: postgis/postgis # Sets Image
          imagePullPolicy: "IfNotPresent"
          ports:
            - containerPort: 5432  # Exposes container port
          envFrom:
            - configMapRef:
                name: postgres-cfg
          volumeMounts:
            - mountPath: /var/lib/postgresql/data
              name: postgredb
      volumes:
        - name: postgredb
          persistentVolumeClaim:
            claimName: postgres-pvc-v1
---

but in the pod log I have the following error

Data page checksums are disabled.

initdb: error: directory "/var/lib/postgresql/data" exists but is not empty
initdb: detail: It contains a lost+found directory, perhaps due to it being a mount point.
initdb: hint: Using a mount point directly as the data directory is not recommended.
Create a subdirectory under the mount point.

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Bobby Iliev
Site Moderator
Site Moderator badge
April 5, 2023

Hi there,

To resolve this issue, you can create a subdirectory under the mount point and use that as the PostgreSQL data directory. Modify your Deployment configuration to include the subPath field for the volumeMounts. Here’s an updated configuration:

apiVersion: apps/v1
kind: Deployment
metadata:
  name: postgres
spec:
  replicas: 1
  selector:
    matchLabels:
      app: postgres
  template:
    metadata:
      labels:
        app: postgres
    spec:
      containers:
        - name: postgres
          image: postgis/postgis # Sets Image
          imagePullPolicy: "IfNotPresent"
          ports:
            - containerPort: 5432  # Exposes container port
          envFrom:
            - configMapRef:
                name: postgres-cfg
          volumeMounts:
            - mountPath: /var/lib/postgresql/data
              subPath: pgdata
              name: postgredb
      volumes:
        - name: postgredb
          persistentVolumeClaim:
            claimName: postgres-pvc-v1

For more info on subPath, you can check out the docs here:

https://kubernetes.io/docs/concepts/storage/volumes/#using-subpath

With this change, PostgreSQL will store its data in the pgdata subdirectory of the mounted volume, avoiding the issue with the lost+found directory.

However, on another note, I would personally use a managed Postgres database instead of running it on the Kubernetes cluster directly:

https://docs.digitalocean.com/products/databases/postgresql/

Hope that this helps!

Best,

Bobby

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