Kubernetes mysql statefulset with root password

Question

I followed the example in here https://kubernetes.io/docs/tasks/run-application/run-replicated-stateful-application/ to create a 3 replica mysql statefulset in kubernetes and everything works fine.

However, after I added root password, and modified the deploy yaml to include the password, mysql-1 always fail.

Here is how I add the password:

1. I create a secret mysql-root-pass
2. I remove the MYSQL_ALLOW_EMPTY_PASSWORD and replace it with MYSQL_ROOT_PASSWORD read from the secret
3. Add -p$MYSQL_ROOT_PASSWORD to everywhere mysql is called in the yaml file.
4. Still, mysql-0 is created and runs, but mysql-1 crashed:

mysql-1 0/2 Init:CrashLoopBackOff

Anyone has a working example on how to add password?

Edit: Add yaml file

apiVersion: apps/v1
kind: StatefulSet
metadata:
  name: mysql
  labels:
    app: mysql
spec:
  selector:
    matchLabels:
      app: mysql
  serviceName: mysql
  replicas: 3
  template:
    metadata:
      labels:
        app: mysql
    spec:
      initContainers:
      - name: init-mysql
        image: mysql:5.7
        command:
        # initContainer is used to setup config according to config-map
        - 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 [[ $ordinal -eq 0 ]]; then
            cp /mnt/config-map/master.cnf /mnt/conf.d/
          else
            cp /mnt/config-map/slave.cnf /mnt/conf.d/
          fi
        volumeMounts:
        - name: conf
          mountPath: /mnt/conf.d
        - name: config-map
          mountPath: /mnt/config-map
      - name: clone-mysql
        image: gcr.io/google-samples/xtrabackup:1.0
        command:
        - bash
        - "-c"
        - |
          set -ex
          # Skip the clone if data already exists.
          [[ -d /var/lib/mysql/mysql ]] && exit 0
          # Skip the clone on master (ordinal index 0).
          [[ `hostname` =~ -([0-9]+)$ ]] || exit 1
          ordinal=${BASH_REMATCH[1]}
          [[ $ordinal -eq 0 ]] && exit 0
          # Clone data from previous peer.
          ncat --recv-only mysql-$(($ordinal-1)).mysql 3307 | xbstream -x -C /var/lib/mysql
          # Prepare the backup.
          xtrabackup --prepare --user=root --password=$MYSQL_ROOT_PASSWORD --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-root-pass
              key: password
        ports:
        - name: mysql
          containerPort: 3306
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
        resources:
          requests:
            cpu: 500m
            memory: 1Gi
        livenessProbe:
          exec:
            command:
            - bash
            - "-c"
            - |
              set -ex
              mysqladmin -p$MYSQL_ROOT_PASSWORD ping &> /dev/null
          initialDelaySeconds: 30
          periodSeconds: 10
          timeoutSeconds: 5
        readinessProbe:
          exec:
            # Check we can execute queries over TCP (skip-networking is off).
            command:
            - bash
            - "-c"
            - |
              set -ex
              mysql -h 127.0.0.1 -p$MYSQL_ROOT_PASSWORD -e "SELECT 1" &> /dev/null
          initialDelaySeconds: 5
          periodSeconds: 2
          timeoutSeconds: 1
      - name: xtrabackup
        image: gcr.io/google-samples/xtrabackup:1.0
        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 127.0.0.1 -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 127.0.0.1 -p$MYSQL_ROOT_PASSWORD <<EOF
          $(<change_master_to.sql.orig),
            MASTER_HOST='mysql-0.mysql',
            MASTER_USER='root',
            MASTER_PASSWORD='',
            MASTER_CONNECT_RETRY=10;
          START SLAVE;
          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"
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
        resources:
          requests:
            cpu: 100m
            memory: 100Mi

      volumes:
      - name: conf
        emptyDir: {}
      - name: config-map
        configMap:
          name: mysql
  volumeClaimTemplates:
  - metadata:
      name: data
    spec:
      accessModes: ["ReadWriteOnce"]
      storageClassName: dynamic-nfs
      resources:
        requests:
          storage: 10Gi

Answer 1

The answer provided by Nicola Ben is close, but there were a few mistakes in the StatefulSet declaration.

The main problem is that the environment variable is declared in the mysql image but not in the xtrabackup where it is also referenced. Secondly the START SLAVE and xtrabackup commands should take the user and password as well.

Here is a working version of the StatefulSet yaml declaration:

---

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 [[ $ordinal -eq 0 ]]; then
            cp /mnt/config-map/master.cnf /mnt/conf.d/
          else
            cp /mnt/config-map/slave.cnf /mnt/conf.d/
          fi
        volumeMounts:
        - name: conf
          mountPath: /mnt/conf.d
        - name: config-map
          mountPath: /mnt/config-map
      - name: clone-mysql
        image: gcr.io/google-samples/xtrabackup:1.0
        command:
        - bash
        - "-c"
        - |
          set -ex
          # Skip the clone if data already exists.
          [[ -d /var/lib/mysql/mysql ]] && exit 0
          # Skip the clone on master (ordinal index 0).
          [[ `hostname` =~ -([0-9]+)$ ]] || exit 1
          ordinal=${BASH_REMATCH[1]}
          [[ $ordinal -eq 0 ]] && exit 0
          # Clone data from previous peer.
          ncat --recv-only mysql-$(($ordinal-1)).mysql 3307 | xbstream -x -C /var/lib/mysql
          # Prepare the backup.
          xtrabackup --prepare --target-dir=/var/lib/mysql
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
      containers:
      - name: mysql
        image: mysql:5.7
        env:
        - name: MYSQL_ROOT_PASSWORD
          valueFrom:
            secretKeyRef:
              name: mysql-pass-root
              key: password
        - name: MYSQL_USER
          value: server
        - name: MYSQL_PASSWORD
          valueFrom:
            secretKeyRef:
              name: mysql-pass-user
              key: password
        - name: MYSQL_DATABASE
          value: medlor
        ports:
        - name: mysql
          containerPort: 3306
        volumeMounts:
        - name: data
          mountPath: /var/lib/mysql
          subPath: mysql
        - name: conf
          mountPath: /etc/mysql/conf.d
        resources:
          requests:
            cpu: 500m
            memory: 1Gi
        livenessProbe:
          exec:
            command: ["mysqladmin", "-uroot", "-p$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 -h127.0.0.1 -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 127.0.0.1 -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 127.0.0.1 -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: 100Mi
      volumes:
      - name: conf
        emptyDir: {}
      - name: config-map
        configMap:
          name: mysql
  volumeClaimTemplates:
  - metadata:
      name: data
    spec:
      accessModes: ["ReadWriteOnce"]
      resources:
        requests:
          storage: 10Gi

I also noticed that in his file he has the replicas set to 1 which would only start the master and no slaves, so that might explain why some were getting startup failure on the slaves.