Error while creating persistanceVolume with mysql on kubernetes - mysql

Question

I'm trying to create a kubernetes persistence volume to connect it with a spring boot application, but I found this error on a pod of the persistance volume:
mysqld: Table 'mysql.plugin' doesn't exist.
A secret file is created for both user and admin and a configMap file also to map the spring boot image to the service of mysql. Here is my deployment file:
# Define a 'Service' To Expose mysql to Other Services
apiVersion: v1
kind: Service
metadata:
name: mysql # DNS name
labels:
app: mysql
tier: database
spec:
ports:
- port: 3306
targetPort: 3306
selector: # mysql Pod Should contain same labels
app: mysql
tier: database
clusterIP: None # We Use DNS, Thus ClusterIP is not relevant
---
# Define a 'Persistent Volume Claim'(PVC) for Mysql Storage, dynamically provisioned by cluster
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: mysql-pv-claim # name of PVC essential for identifying the storage data
labels:
app: mysql
tier: database
spec:
accessModes:
- ReadWriteOnce #This specifies the mode of the claim that we are trying to create.
resources:
requests:
storage: 1Gi #This will tell kubernetes about the amount of space we are trying to claim.
---
apiVersion: v1
kind: PersistentVolume
metadata:
name: task-pv-volume
labels:
type: local
spec:
capacity:
storage: 1Gi
accessModes:
- ReadWriteOnce
hostPath:
path: "/mnt/data"
---
# Configure 'Deployment' of mysql server
apiVersion: apps/v1
kind: Deployment
metadata:
name: mysql
labels:
app: mysql
tier: database
spec:
selector: # mysql Pod Should contain same labels
matchLabels:
app: mysql
tier: database
strategy:
type: Recreate
template:
metadata:
labels: # Must match 'Service' and 'Deployment' selectors
app: mysql
tier: database
spec:
containers:
- image: mysql:latest # image from docker-hub
args:
- "--ignore-db-dir"
- "lost+found" # Workaround for https://github.com/docker-library/mysql/issues/186
name: mysql
env:
- name: MYSQL_ROOT_PASSWORD # Setting Root Password of mysql From a 'Secret'
valueFrom:
secretKeyRef:
name: db-admin # Name of the 'Secret'
key: password # 'key' inside the Secret which contains required 'value'
- name: MYSQL_USER # Setting USER username on mysql From a 'Secret'
valueFrom:
secretKeyRef:
name: db-user
key: username
- name: MYSQL_PASSWORD # Setting USER Password on mysql From a 'Secret'
valueFrom:
secretKeyRef:
name: db-user
key: password
- name: MYSQL_DATABASE # Setting Database Name from a 'ConfigMap'
valueFrom:
configMapKeyRef:
name: db-config
key: name
ports:
- containerPort: 3306
name: mysql
volumeMounts: # Mounting volume obtained from Persistent Volume Claim
- name: mysql-persistent-storage
mountPath: /var/lib/mysql #This is the path in the container on which the mounting will take place.
volumes:
- name: mysql-persistent-storage # Obtaining 'volume' from PVC
persistentVolumeClaim:
claimName: mysql-pv-claim
I'm using the latest image of mysql with docker. Is there any configuration in my file that I must change ?

Answer 1

First of all, using lastest mysql container you are using mysql:8.
--ignore-db-dir flag does not exist in version 8 so you should see in logs this error:
2020-09-21 0 [ERROR] [MY-000068] [Server] unknown option '--ignore-db-dir'.
2020-09-21 0 [ERROR] [MY-010119] [Server] Aborting
After removing this flag, mysql stops crashing, but there appears to be other problem.
The hostPath volume does not work as expected. When I runned:
$ kubectl get pvc
NAME STATUS VOLUME CAPACITY ACCESS MODES STORAGECLASS AGE
mysql-pv-claim Bound pvc-xxxx 1Gi RWO standard 4m16s
you can see that STORAGECLASS is set to standard, and its causing k8s to provision a pv, instead of using already created one.
# kubectl get pv
NAME CAPACITY ACCESS MODES RECLAIM POLICY STATUS CLAIM STORAGECLASS REASON AGE
pvc-xxxx 1Gi RWO Delete Bound default/mysql-pv-claim standard 6m31s
task-pv-volume 1Gi RWO Retain Available 6m31s
As you probably see the task-pv-volume status is Available and that means that nothing is using it.
To use it you you need to set storageClassName for Persistent Volume Claim to empty string: "" and maybe add volumeName like following:
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: mysql-pv-claim
labels:
app: mysql
tier: database
spec:
storageClassName: ""
volumeName: task-pv-volume
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 1Gi
After doing this hostPath volume will work as expected, but there is still a problem with lost+found directory.
My solution would be to create another directory in /mnt/data/ dir e.g. /mnt/data/mysqldata/ and use /mnt/data/mysqldata/ as hostPath in PersistentVolume object.
Other solution would be using older version of mysql that supports --ignore-db-dir flag.