Cannot deploy MySQL pod. --initialize specified but the data directory has files in it

Question

I'm trying to setup a MySQL pod on Digital Ocean with Kubernetes.

I kept getting this error:

Initializing database
2019-03-05T14:32:58.707421Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2019-03-05T14:32:58.708753Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2019-03-05T14:32:58.711746Z 0 [ERROR] Aborting

My yaml as a lot of stuff but the lines that interest this part of the config are the following.

# ------------------- Persistent Volume Claim ------------------- #

kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: test-mysql-volume-claim
  ...
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 2Gi
  storageClassName: do-block-storage

---

# ------------------- Deployment ------------------- #

kind: Deployment
apiVersion: apps/v1 # for versions before 1.9.0 use apps/v1beta2
...
spec:
      ...
    spec:
      containers:
        - image: mysql:5.7
          ...
          volumeMounts:
            - name: test-mysql-volume
              mountPath: "/var/lib/mysql"
      volumes:
        - name: test-mysql-volume
          persistentVolumeClaim:
            claimName: test-mysql-volume-claim

---

If I comment out the PVC and the lines relative to PVC in the deployment config, everything works.

Also, if I change

mountPath: "/var/lib/mysql"

to

mountPath: "/data"

it works. But I obviously need /var/lib/mysql...

It happens also on brand new clusters.

Any idea?

Answer 1

I had this issue with Kubernetes and MySQL 5.7 as well.

Adding the suggestion from yosifki to my container's definition got things working.

A new ext4 disk partition is not usually empty; there is a lost+found directory, which mysql is known to choke on. You could try adding --ignore-db-dir=lost+found to the CMD to know for sure (from mysql docs)

Here's an extract of my working YAML definition:

name: mysql-master
image: mysql:5.7
args:
  - "--ignore-db-dir=lost+found"

Answer 2

I had a similar problem.

Using mysql:5.6 fixed it.

For more information refer to:

https://github.com/docker-library/mysql/issues/69

https://github.com/docker-library/mysql/issues/186