MySQL statefulset 与 minikube 上的持久存储

Question

I am trying to have a scalable mysql DB whith persistent memory. I thought it was something common, but it seems like online no one really explains it. I am using minikube for my single node cluster. I started off from the kubernetes guide on how to run replicated stateful applications but it does not really get into the persistent volume creation. I have created the configmap like the one in the guide:

apiVersion: v1
kind: ConfigMap
metadata:
  name: mysql
  labels:
    app: mysql
data:
  primary.cnf: |
    # Apply this config only on the primary.
    [mysqld]
    log-bin
  replica.cnf: |
    # Apply this config only on replicas.
    [mysqld]
    super-read-only

And the two serivces:

# Headless service for stable DNS entries of StatefulSet members.
apiVersion: v1
kind: Service
metadata:
  name: mysql
  labels:
    app: mysql
spec:
  ports:
  - name: mysql
    port: 3306
  clusterIP: None
  selector:
    app: mysql
---
# Client service for connecting to any MySQL instance for reads.
# For writes, you must instead connect to the primary: mysql-0.mysql.
apiVersion: v1
kind: Service
metadata:
  name: mysql-read
  labels:
    app: mysql
spec:
  ports:
  - name: mysql
    port: 3306
  selector:
    app: mysql

I needed to initialize the schema of my database, so I made this configmap to pass inside the statefulset:

apiVersion: v1
kind: ConfigMap
metadata:
  name: mysql-initdb-config
data:
  initdb.sql: |
    CREATE DATABASE football;
    CREATE TABLE `squadra` (
        `name` varchar(15) PRIMARY KEY NOT NULL
    );
    USE football;
    ...

I created a storageclass and a persistent volume, thanks to this answer.

apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
  name: local-storage
provisioner: kubernetes.io/no-provisioner
volumeBindingMode: WaitForFirstConsumer
---
apiVersion: v1
kind: PersistentVolume
metadata:
  name: pv-volume
spec:
  storageClassName: local-storage
  accessModes:
    - ReadWriteOnce
  capacity:
    storage: 5Gi
  hostPath:
    path: /data/mysql_data/

And made a secret containing the password to the root user of my db:

apiVersion: v1
kind: Secret
metadata:
  name: mysql-pass-root
type: kubernetes.io/basic-auth
stringData:
  username: root
  password: password

My statefulset I have was substantially taken from some answer on stackoverflow I am not finding anymore. It was basically a modification of the one on the kubernetes website. What I added is the database schema initialization, the volumeclaimtemplate and the password from the secret:

apiVersion: apps/v1
kind: StatefulSet
metadata:
  name: mysql
spec:
  selector:
    matchLabels:
      app: mysql
  serviceName: mysql
  replicas: 2
  template:
    metadata:
      labels:
        app: mysql
    spec:
      initContainers:
      - name: init-mysql
        image: mysql:5.7
        command:
        - bash
        - "-c"
        - |
          set -ex
          # Generate mysql server-id from pod ordinal index.
          [[ `hostname` =~ -([0-9]+)$ ]] || exit 1
          ordinal=${BASH_REMATCH[1]}
          echo [mysqld] > /mnt/conf.d/server-id.cnf
          # Add an offset to avoid reserved server-id=0 value.
          echo server-id=$((100 + $ordinal)) >> /mnt/conf.d/server-id.cnf
          # Copy appropriate conf.d files from config-map to emptyDir.
          if [[ $ordinal -eq 0 ]]; then
            cp /mnt/config-map/primary.cnf /mnt/conf.d/
          else
            cp /mnt/config-map/replica.cnf /mnt/conf.d/
          fi
        volumeMounts:
        - name: conf
          mountPath: /mnt/conf.d
        - name: config-map
          mountPath: /mnt/config-map
      - name: clone-mysql
        image: gcr.io/google-samples/xtrabackup:1.0
        command:
        - bash
        - "-c"
        - |
          set -ex
          # Skip the clone if data already exists.
          [[ -d /var/lib/mysql/mysql ]] && exit 0
          # Skip the clone on master (ordinal index 0).
          [[ `hostname` =~ -([0-9]+)$ ]] || exit 1
          ordinal=${BASH_REMATCH[1]}
          [[ $ordinal -eq 0 ]] && exit 0
          # Clone data from previous peer.
          ncat --recv-only mysql-$(($ordinal-1)).mysql 3307 | xbstream -x -C /var/lib/mysql
          # Prepare the backup.
          xtrabackup --prepare --target-dir=/var/lib/mysql
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
      containers:
      - name: mysql
        image: mysql:5.7
        env:
        - name: MYSQL_ROOT_PASSWORD
          valueFrom:
            secretKeyRef:
              name: mysql-pass-root
              key: password
        - name: MYSQL_USER
          value: server
        - name: MYSQL_DATABASE
          value: medlor
        ports:
        - name: mysql
          containerPort: 3306
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
        - name: mysql-initdb
          mountPath: /docker-entrypoint-initdb.d
        resources:
          requests:
            cpu: 500m
            memory: 100Mi
        livenessProbe:
          exec:
            command: ["mysqladmin", "-uroot", "-p$MYSQL_ROOT_PASSWORD", "ping"]
          initialDelaySeconds: 30
          periodSeconds: 10
          timeoutSeconds: 5
        readinessProbe:
          exec:
            # Check we can execute queries over TCP (skip-networking is off).
            command:
            - /bin/sh
            - -ec
            - >-
              mysql -hlocalhost -uroot -p$MYSQL_ROOT_PASSWORD -e'SELECT 1'
          initialDelaySeconds: 5
          periodSeconds: 2
          timeoutSeconds: 1
      - name: xtrabackup
        image: gcr.io/google-samples/xtrabackup:1.0
        env:
        - name: MYSQL_ROOT_PASSWORD
          valueFrom:
            secretKeyRef:
              name: mysql-pass-root
              key: password
        ports:
        - name: xtrabackup
          containerPort: 3307
        command:
        - bash
        - "-c"
        - |
          set -ex
          cd /var/lib/mysql

          # Determine binlog position of cloned data, if any.
          if [[ -f xtrabackup_slave_info ]]; then
            # XtraBackup already generated a partial "CHANGE MASTER TO" query
            # because we're cloning from an existing slave.
            mv xtrabackup_slave_info change_master_to.sql.in
            # Ignore xtrabackup_binlog_info in this case (it's useless).
            rm -f xtrabackup_binlog_info
          elif [[ -f xtrabackup_binlog_info ]]; then
            # We're cloning directly from master. Parse binlog position.
            [[ `cat xtrabackup_binlog_info` =~ ^(.*?)[[:space:]]+(.*?)$ ]] || exit 1
            rm xtrabackup_binlog_info
            echo "CHANGE MASTER TO MASTER_LOG_FILE='${BASH_REMATCH[1]}',\
                  MASTER_LOG_POS=${BASH_REMATCH[2]}" > change_master_to.sql.in
          fi

          # Check if we need to complete a clone by starting replication.
          if [[ -f change_master_to.sql.in ]]; then
            echo "Waiting for mysqld to be ready (accepting connections)"
            until mysql -h localhost -uroot -p$MYSQL_ROOT_PASSWORD -e "SELECT 1"; do sleep 1; done

            echo "Initializing replication from clone position"
            # In case of container restart, attempt this at-most-once.
            mv change_master_to.sql.in change_master_to.sql.orig
            mysql -h localhost -uroot -p$MYSQL_ROOT_PASSWORD <<EOF
          $(<change_master_to.sql.orig),
            MASTER_HOST='mysql-0.mysql',
            MASTER_USER='root',
            MASTER_PASSWORD='$MYSQL_ROOT_PASSWORD',
            MASTER_CONNECT_RETRY=10;
          START SLAVE USER='root' PASSWORD='$MYSQL_ROOT_PASSWORD';
          EOF
          fi

          # Start a server to send backups when requested by peers.
          exec ncat --listen --keep-open --send-only --max-conns=1 3307 -c \
            "xtrabackup --backup --slave-info --stream=xbstream --host=127.0.0.1 --user=root --password=$MYSQL_ROOT_PASSWORD"
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
        resources:
          requests:
            cpu: 100m
            memory: 500Mi
      volumes:
      - name: conf
        emptyDir: {}
      - name: config-map
        configMap:
          name: mysql
      - name: mysql-initdb
        configMap:
          name: mysql-initdb-config
  volumeClaimTemplates:
  - metadata:
      name: data
    spec:
      accessModes: [ "ReadWriteOnce" ]
      storageClassName: "local-storage"
      resources:
        requests:
          storage: 1Gi

When I start up minikube, I run the following commands:

docker exec minikube mkdir data/mysql_data ->in order to create the folder where mysql saves the data inside the minikube container
minikube mount local_path_to_a_folder:/data/mysql_data -> to keep the mysql data in my physical storage too.
kubectl apply -f pv-volume.yaml (the volume I showed before)
kubectl apply -f database\mysql\mysql-configmap.yaml (the configmap from the guide)
kubectl apply -f database\mysql\mysql-initdb-config.yaml (my configmap with the db schema)
kubectl apply -f database\mysql\mysql-secret.yaml (the secret containing the db password)
kubectl apply -f %root%\database\mysql\mysql-services.yaml (the two services)

Now, when I run all these commands my MySql pod fails, and this is what I can see from the dashboard:

Although in the persistent volumes section I can see my volume has been claimed:

I must have understood something wrong and there must be a logic error in all of this, but I can't figure out what it is. Any help would be extremely appreciated.

Answer 1

The storage size of PV and the requested PVC is not matching. You created the PV of size 5Gi and you are requesting for 1Gi using the PVC.