Kubernetes MySql image persistent volume is non empty during init - mysql

Question

I am working through the persistent disks tutorial found here while also creating it as a StatefulSet instead of a deployment.
When I run the yaml file into GKE the database fails to start, looking at the logs it has the following error.
[ERROR] --initialize specified but the data directory has files in it. Aborting.
Is it possible to inspect the volume created to see what is in the directory? Otherwise, what am I doing wrong that is causing the disk to be non empty?
Thanks
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: datalayer-pvc
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 100Gi
---
apiVersion: v1
kind: Service
metadata:
name: datalayer-svc
labels:
app: myapplication
spec:
ports:
- port: 80
name: dbadmin
clusterIP: None
selector:
app: database
---
apiVersion: apps/v1beta2
kind: StatefulSet
metadata:
name: datalayer
spec:
selector:
matchLabels:
app: myapplication
serviceName: "datalayer-svc"
replicas: 1
template:
metadata:
labels:
app: myapplication
spec:
terminationGracePeriodSeconds: 10
containers:
- name: database
image: mysql:5.7.22
env:
- name: "MYSQL_ROOT_PASSWORD"
valueFrom:
secretKeyRef:
name: mysql-root-password
key: password
- name: "MYSQL_DATABASE"
value: "appdatabase"
- name: "MYSQL_USER"
value: "app_user"
- name: "MYSQL_PASSWORD"
value: "app_password"
ports:
- containerPort: 3306
name: mysql
volumeMounts:
- name: datalayer-pv
mountPath: /var/lib/mysql
volumes:
- name: datalayer-pv
persistentVolumeClaim:
claimName: datalayer-pvc

Answer 1

This issue could be caused by the lost+found directory on the filesystem of the PersistentVolume.
I was able to verify this by adding a k8s.gcr.io/busybox container (in PVC set accessModes: [ReadWriteMany], OR comment out the database container):
- name: init
image: "k8s.gcr.io/busybox"
command: ["/bin/sh","-c","ls -l /var/lib/mysql"]
volumeMounts:
- name: database
mountPath: "/var/lib/mysql"
There are a few potential workarounds...
Most preferable is to use a subPath on the volumeMounts object. This uses a subdirectory of the PersistentVolume, which should be empty at creation time, instead of the volume root:
volumeMounts:
- name: database
mountPath: "/var/lib/mysql"
subPath: mysql
Less preferable workarounds include:
Use a one-time container to rm -rf /var/lib/mysql/lost+found (not a great solution, because the directory is managed by the filesystem and is likely to re-appear)
Use mysql:5 image, and add args: ["--ignore-db-dir=lost+found"] to the container (this option was removed in mysql 8)
Use mariadb image instead of mysql
More details might be available at docker-library/mysql issues: #69 and #186

Answer 2

You would usually see if your volumes were mounted with:
kubectl get pods # gets you all the pods on the default namespace
# and
kubectl describe pod <pod-created-by-your-statefulset>
Then you can these commands to check on your PVs and PVCs
kubectl get pv # gets all the PVs on the default namespace
kubectl get pvc # same for PVCs
kubectl describe pv <pv-name>
kubectl describe pvc <pvc-name>
Then you can to the GCP console on disks and see if your disks got created:

Answer 3

You can add the ignore dir lost+found
containers:
- image: mysql:5.7
name: mysql
args:
- "--ignore-db-dir=lost+found"

Answer 4

I use a init container to remove that file (I'm using postgres in my case):
initContainers:
- name: busybox
image: busybox:latest
args: ["rm", "-rf", "/var/lib/postgresql/data/lost+found"]
volumeMounts:
- name: nfsv-db
mountPath: /var/lib/postgresql/data