Run MySQL in Amazon Elastic Kubernetes Service (Amazon EKS) Using KubeDB

16-Aug-2022

Overview

KubeDB is the Kubernetes Native Database Management Solution which simplifies and automates routine database tasks such as Provisioning, Monitoring, Upgrading, Patching, Scaling, Volume Expansion, Backup, Recovery, Failure detection, and Repair for various popular databases on private and public clouds. The databases that KubeDB supports are MySQL, MongoDB, MariaDB, Elasticsearch, Redis, PostgreSQL, ProxySQL, Percona XtraDB, Memcached and PgBouncer. You can find the guides to all the supported databases here. In this tutorial we will deploy MySQL database in Amazon Elastic Kubernetes Service (Amazon EKS). We will cover the following steps:

  1. Install KubeDB
  2. Deploy MySQL Clustered Database
  3. Install Stash
  4. Backup MySQL Database Using Stash
  5. Recover MySQL Database Using Stash

Install KubeDB

We will follow the steps to install KubeDB.

Get Cluster ID

We need the cluster ID to get the KubeDB License. To get cluster ID we can run the following command:

$ kubectl get ns kube-system -o jsonpath='{.metadata.uid}'
250a26e3-2413-4ed2-99dc-57b0548407ff

Get License

Go to Appscode License Server to get the license.txt file. For this tutorial we will use KubeDB Enterprise Edition.

License Server

Install KubeDB

We will use helm to install KubeDB. Please install helm here if it is not already installed. Now, let’s install KubeDB.

$ helm repo add appscode https://charts.appscode.com/stable/
$ helm repo update

$ helm search repo appscode/kubedb
NAME                              	CHART VERSION	APP VERSION	DESCRIPTION                                       
appscode/kubedb                   	v2022.08.08  	v2022.08.08	KubeDB by AppsCode - Production ready databases...
appscode/kubedb-autoscaler        	v0.13.0      	v0.13.0    	KubeDB Autoscaler by AppsCode - Autoscale KubeD...
appscode/kubedb-catalog           	v2022.08.08  	v2022.08.08	KubeDB Catalog by AppsCode - Catalog for databa...
appscode/kubedb-community         	v0.24.2      	v0.24.2    	KubeDB Community by AppsCode - Community featur...
appscode/kubedb-crds              	v2022.08.08  	v2022.08.08	KubeDB Custom Resource Definitions                
appscode/kubedb-dashboard         	v0.4.0       	v0.4.0     	KubeDB Dashboard by AppsCode                      
appscode/kubedb-enterprise        	v0.11.2      	v0.11.2    	KubeDB Enterprise by AppsCode - Enterprise feat...
appscode/kubedb-grafana-dashboards	v2022.08.08  	v2022.08.08	A Helm chart for kubedb-grafana-dashboards by A...
appscode/kubedb-metrics           	v2022.08.08  	v2022.08.08	KubeDB State Metrics                              
appscode/kubedb-ops-manager       	v0.15.0      	v0.15.1    	KubeDB Ops Manager by AppsCode - Enterprise fea...
appscode/kubedb-opscenter         	v2022.08.08  	v2022.08.08	KubeDB Opscenter by AppsCode                      
appscode/kubedb-provisioner       	v0.28.0      	v0.28.1    	KubeDB Provisioner by AppsCode - Community feat...
appscode/kubedb-schema-manager    	v0.4.0       	v0.4.0     	KubeDB Schema Manager by AppsCode                 
appscode/kubedb-ui                	v2022.06.14  	0.3.9      	A Helm chart for Kubernetes                       
appscode/kubedb-ui-server         	v2021.12.21  	v2021.12.21	A Helm chart for kubedb-ui-server by AppsCode     
appscode/kubedb-webhook-server    	v0.4.0       	v0.4.1     	KubeDB Webhook Server by AppsCode    

# Install KubeDB Enterprise operator chart
$ helm install kubedb appscode/kubedb \
  --version v2022.08.08 \
  --namespace kubedb --create-namespace \
  --set kubedb-provisioner.enabled=true \
  --set kubedb-ops-manager.enabled=true \
  --set kubedb-autoscaler.enabled=true \
  --set kubedb-dashboard.enabled=true \
  --set kubedb-schema-manager.enabled=true \
  --set-file global.license=/path/to/the/license.txt

Let’s verify the installation:

$ watch kubectl get pods --all-namespaces -l "app.kubernetes.io/instance=kubedb"
NAMESPACE   NAME                                            READY   STATUS    RESTARTS   AGE
kubedb      kubedb-kubedb-autoscaler-799757d78d-sp2xl       1/1     Running   0          2m4s
kubedb      kubedb-kubedb-dashboard-77c6bb64ff-7m6rn        1/1     Running   0          2m4s
kubedb      kubedb-kubedb-ops-manager-6cdff67966-xdn6j      1/1     Running   0          2m4s
kubedb      kubedb-kubedb-provisioner-667d7fd79b-9b2sv      1/1     Running   0          2m4s
kubedb      kubedb-kubedb-schema-manager-76c68d984-gl7xn    1/1     Running   0          2m4s
kubedb      kubedb-kubedb-webhook-server-7ffd5bc579-rvghn   1/1     Running   0          2m4s

We can list the CRD Groups that have been registered by the operator by running the following command:

$ kubectl get crd -l app.kubernetes.io/name=kubedb
NAME                                              CREATED AT
elasticsearchautoscalers.autoscaling.kubedb.com   2022-08-11T11:08:01Z
elasticsearchdashboards.dashboard.kubedb.com      2022-08-11T11:07:59Z
elasticsearches.kubedb.com                        2022-08-11T11:07:59Z
elasticsearchopsrequests.ops.kubedb.com           2022-08-11T11:08:07Z
elasticsearchversions.catalog.kubedb.com          2022-08-11T10:46:46Z
etcds.kubedb.com                                  2022-08-11T11:08:07Z
etcdversions.catalog.kubedb.com                   2022-08-11T10:46:49Z
mariadbautoscalers.autoscaling.kubedb.com         2022-08-11T11:08:01Z
mariadbdatabases.schema.kubedb.com                2022-08-11T11:08:04Z
mariadbopsrequests.ops.kubedb.com                 2022-08-11T11:08:28Z
mariadbs.kubedb.com                               2022-08-11T11:08:05Z
mariadbversions.catalog.kubedb.com                2022-08-11T10:46:50Z
memcacheds.kubedb.com                             2022-08-11T11:08:11Z
memcachedversions.catalog.kubedb.com              2022-08-11T10:46:51Z
mongodbautoscalers.autoscaling.kubedb.com         2022-08-11T11:08:01Z
mongodbdatabases.schema.kubedb.com                2022-08-11T11:08:01Z
mongodbopsrequests.ops.kubedb.com                 2022-08-11T11:08:11Z
mongodbs.kubedb.com                               2022-08-11T11:08:01Z
mongodbversions.catalog.kubedb.com                2022-08-11T10:46:52Z
mysqldatabases.schema.kubedb.com                  2022-08-11T11:07:59Z
mysqlopsrequests.ops.kubedb.com                   2022-08-11T11:08:25Z
mysqls.kubedb.com                                 2022-08-11T11:08:00Z
mysqlversions.catalog.kubedb.com                  2022-08-11T10:46:53Z
perconaxtradbopsrequests.ops.kubedb.com           2022-08-11T11:08:44Z
perconaxtradbs.kubedb.com                         2022-08-11T11:08:16Z
perconaxtradbversions.catalog.kubedb.com          2022-08-11T10:46:54Z
pgbouncers.kubedb.com                             2022-08-11T11:08:17Z
pgbouncerversions.catalog.kubedb.com              2022-08-11T10:46:55Z
postgresdatabases.schema.kubedb.com               2022-08-11T11:08:03Z
postgreses.kubedb.com                             2022-08-11T11:08:03Z
postgresopsrequests.ops.kubedb.com                2022-08-11T11:08:36Z
postgresversions.catalog.kubedb.com               2022-08-11T10:46:57Z
proxysqlopsrequests.ops.kubedb.com                2022-08-11T11:08:40Z
proxysqls.kubedb.com                              2022-08-11T11:08:18Z
proxysqlversions.catalog.kubedb.com               2022-08-11T10:46:58Z
redises.kubedb.com                                2022-08-11T11:08:18Z
redisopsrequests.ops.kubedb.com                   2022-08-11T11:08:31Z
redissentinels.kubedb.com                         2022-08-11T11:08:19Z
redisversions.catalog.kubedb.com                  2022-08-11T10:46:59Z

Deploy MySQL Clustered Database

Now, we are going to Deploy MySQL with the help of KubeDB. At first, let’s create a Namespace in which we will deploy the database.

$ kubectl create ns demo
namespace/demo created

Here is the yaml of the MySQL CRO we are going to use:

apiVersion: kubedb.com/v1alpha2
kind: MySQL
metadata:
  name: sample-mysql
  namespace: demo
spec:
  version: "8.0.29"
  replicas: 3
  topology:
    mode: GroupReplication
  storageType: Durable
  storage:
    storageClassName: "gp2"
    accessModes:
      - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  terminationPolicy: WipeOut

Let’s save this yaml configuration into sample-mysql.yaml Then create the above MySQL CRO

$ kubectl create -f sample-mysql.yaml
mysql.kubedb.com/sample-mysql created
  • In this yaml we can see in the spec.version field specifies the version of MySQL. Here, we are using MySQL version 8.0.29. You can list the KubeDB supported versions of MySQL by running $ kubectl get mysqlversions command.
  • spec.storage specifies PVC spec that will be dynamically allocated to store data for this database. This storage spec will be passed to the StatefulSet created by KubeDB operator to run database pods. You can specify any StorageClass available in your cluster with appropriate resource requests.
  • And the spec.terminationPolicy field is Wipeout means that the database will be deleted without restrictions. It can also be “Halt”, “Delete” and “DoNotTerminate”. Learn More about these HERE.

Once these are handled correctly and the MySQL object is deployed, you will see that the following objects are created:

$ kubectl get all -n demo
NAME                 READY   STATUS    RESTARTS   AGE
pod/sample-mysql-0   2/2     Running   0          2m34s
pod/sample-mysql-1   2/2     Running   0          2m3s
pod/sample-mysql-2   2/2     Running   0          85s

NAME                           TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)    AGE
service/sample-mysql           ClusterIP   10.100.24.208   <none>        3306/TCP   2m38s
service/sample-mysql-pods      ClusterIP   None            <none>        3306/TCP   2m38s
service/sample-mysql-standby   ClusterIP   10.100.11.2     <none>        3306/TCP   2m38s

NAME                            READY   AGE
statefulset.apps/sample-mysql   3/3     2m41s

NAME                                              TYPE               VERSION   AGE
appbinding.appcatalog.appscode.com/sample-mysql   kubedb.com/mysql   8.0.29    2m44s

NAME                            VERSION   STATUS   AGE
mysql.kubedb.com/sample-mysql   8.0.29    Ready    2m59s

Let’s check if the database is ready to use,

$ kubectl get mysql -n demo sample-mysql
NAME           VERSION   STATUS   AGE
sample-mysql   8.0.29    Ready    3m37s

We have successfully deployed MySQL in EKS. Now we can exec into the container to use the database.

Accessing Database Through CLI

To access the database through CLI, we have to get the credentials to access. KubeDB will create Secret and Service for the database sample-mysql that we have deployed. Let’s check them using the following commands,

$ kubectl get secret -n demo -l=app.kubernetes.io/instance=sample-mysql
NAME                TYPE                       DATA   AGE
sample-mysql-auth   kubernetes.io/basic-auth   2      3m57s

$ kubectl get service -n demo -l=app.kubernetes.io/instance=sample-mysql
NAME                   TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)    AGE
sample-mysql           ClusterIP   10.100.24.208   <none>        3306/TCP   4m10s
sample-mysql-pods      ClusterIP   None            <none>        3306/TCP   4m10s
sample-mysql-standby   ClusterIP   10.100.11.2     <none>        3306/TCP   4m10s

Now, we are going to use sample-mysql-auth to get the credentials.

$ kubectl get secrets -n demo sample-mysql-auth -o jsonpath='{.data.username}' | base64 -d
root

$ kubectl get secrets -n demo sample-mysql-auth -o jsonpath='{.data.password}' | base64 -d
R9etGyj4v(KP6URi

$ kubectl exec -it sample-mysql-0 -n demo -c mysql -- bash

Insert Sample Data

In this section, we are going to login into our MySQL database pod and insert some sample data.

bash-4.4# mysql --user=root --password='R9etGyj4v(KP6URi'

Welcome to the MySQL monitor.  Commands end with ; or \g.


mysql> CREATE DATABASE Music;
Query OK, 1 row affected (0.02 sec)

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| Music              |
| information_schema |
| kubedb_system      |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
6 rows in set (0.00 sec)

mysql> CREATE TABLE Music.Artist (id INT(6) UNSIGNED AUTO_INCREMENT PRIMARY KEY, Name VARCHAR(50), Song VARCHAR(25));
Query OK, 0 rows affected (0.05 sec)

mysql> INSERT INTO Music.Artist (Name, Song) VALUES ("John Denver", "Country Roads");
Query OK, 1 row affected (0.01 sec)

mysql> SELECT * FROM Music.Artist;
+----+-------------+---------------+
| id | Name        | Song          |
+----+-------------+---------------+
|  1 | John Denver | Country Roads |
+----+-------------+---------------+
1 row in set (0.00 sec)

mysql> exit
Bye

We’ve successfully inserted some sample data to our database. And this was just an example of our MySQL Clustered database deployment. More information about Run & Manage Production-Grade MySQL Database on Kubernetes can be found HERE

Backup MySQL Database Using Stash

Here, we are going to use Stash to backup the MySQL database that we have just deployed.

Install Stash

Kubedb Enterprise License works for Stash too. So, we will use the Enterprise license that we have already obtained.

$ helm install stash appscode/stash             \
  --version v2022.07.09                  \
  --namespace kube-system                       \
  --set features.enterprise=true                \
  --set-file global.license=/path/to/the/license.txt

Let’s verify the installation:

$ watch kubectl get pods --all-namespaces -l app.kubernetes.io/name=stash-enterprise
NAMESPACE     NAME                                      READY   STATUS    RESTARTS   AGE
kube-system   stash-stash-enterprise-795bd94d64-5lbl6   2/2     Running   0          39s

Now, to confirm CRD groups have been registered by the operator, run the following command:

$ kubectl get crd -l app.kubernetes.io/name=stash
NAME                                      CREATED AT
backupbatches.stash.appscode.com          2022-08-11T11:40:34Z
backupblueprints.stash.appscode.com       2022-08-11T11:40:34Z
backupconfigurations.stash.appscode.com   2022-08-11T11:40:32Z
backupsessions.stash.appscode.com         2022-08-11T11:40:32Z
functions.stash.appscode.com              2022-08-11T11:35:53Z
repositories.stash.appscode.com           2022-08-11T11:08:07Z
restorebatches.stash.appscode.com         2022-08-11T11:40:34Z
restoresessions.stash.appscode.com        2022-08-11T11:08:08Z
tasks.stash.appscode.com                  2022-08-11T11:35:55Z

Prepare Backend

Stash supports various backends for storing data snapshots. It can be a cloud storage like GCS bucket, AWS S3, Azure Blob Storage etc. or a Kubernetes persistent volume like HostPath, PersistentVolumeClaim, NFS etc.

For this tutorial we are going to use AWS S3 storage. You can find other setups here.

My Empty AWS storage

At first we need to create a secret so that we can access the AWS S3 storage bucket. We can do that by the following code:

$ echo -n 'changeit' > RESTIC_PASSWORD
$ echo -n '<your-aws-access-key-id-here>' > AWS_ACCESS_KEY_ID
$ echo -n '<your-aws-secret-access-key-here>' > AWS_SECRET_ACCESS_KEY
$ kubectl create secret generic -n demo s3-secret \
    --from-file=./RESTIC_PASSWORD \
    --from-file=./AWS_ACCESS_KEY_ID \
    --from-file=./AWS_SECRET_ACCESS_KEY
secret/s3-secret created

Create Repository

apiVersion: stash.appscode.com/v1alpha1
kind: Repository
metadata:
  name: s3-repo
  namespace: demo
spec:
  backend:
    s3:
      endpoint: s3.amazonaws.com
      bucket: stash-qa
      region: us-east-1
      prefix: /backup/sample-mysql
    storageSecretName: s3-secret

This repository CRO specifies the s3-secret we created before and stores the name and path to the AWS storage bucket. It also specifies the location to the container where we want to backup our database.

Here, My bucket name is stash-qa. Don’t forget to change spec.backend.s3.bucket to your bucket name and For S3, use s3.amazonaws.com as endpoint.

Lets create this repository,

$ kubectl create -f s3-repo.yaml 
repository.stash.appscode.com/s3-repo created

Create BackupConfiguration

Now, we need to create a BackupConfiguration file that specifies what to backup, where to backup and when to backup.

apiVersion: stash.appscode.com/v1beta1
kind: BackupConfiguration
metadata:
  name: sample-mysql-backup
  namespace: demo
spec:
  schedule: "*/5 * * * *"
  repository:
    name: s3-repo
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: sample-mysql
  retentionPolicy:
    name: keep-last-5
    keepLast: 5
    prune: true

Create this BackupConfiguration by following command,

$ kubectl apply -f sample-mysql-backup.yaml
backupconfiguration.stash.appscode.com/sample-mysql-backup created
  • BackupConfiguration creates a cronjob that backs up the specified database (spec.target) every 5 minutes.
  • spec.repository contains the repository name that we have created before called s3-repo.
  • spec.target.ref contains the reference to the appbinding that we want to backup.
  • spec.schedule specifies that we want to backup the database at 5 minutes interval.
  • spec.retentionPolicy specifies the policy to follow for cleaning old snapshots.
  • To learn more about AppBinding, click here AppBinding. So, after 5 minutes we can see the following status:
$ kubectl get backupsession -n demo
NAME                             INVOKER-TYPE          INVOKER-NAME          PHASE       DURATION   AGE
sample-mysql-backup-1660219804   BackupConfiguration   sample-mysql-backup   Succeeded   26s        42s

$ kubectl get repository -n demo
NAME      INTEGRITY   SIZE        SNAPSHOT-COUNT   LAST-SUCCESSFUL-BACKUP   AGE
s3-repo   true        3.681 MiB   1                59s                      7m7s

Now if we check our Amazon S3 bucket, we can see that the backup has been successful.

AWSSuccess

If you have reached here, CONGRATULATIONS!! 🎊 🎊 🎊 You have successfully backed up MySQL Database using Stash. If you had any problem during the backup process, you can reach out to us via EMAIL.

Recover MySQL Database Using Stash

Let’s think of a scenario in which the database has been accidentally deleted or there was an error in the database causing it to crash.

Temporarily pause backup

At first, let’s stop taking any further backup of the database so that no backup runs after we delete the sample data. We are going to pause the BackupConfiguration object. Stash will stop taking any further backup when the BackupConfiguration is paused.

$ kubectl patch backupconfiguration -n demo sample-mysql-backup --type="merge" --patch='{"spec": {"paused": true}}'
backupconfiguration.stash.appscode.com/sample-mysql-backup patched

Now, we are going to delete database to simulate accidental database deletion.

$ kubectl exec -it sample-mysql-0 -n demo -c mysql -- bash
bash-4.4# mysql --user=root --password='R9etGyj4v(KP6URi'

Welcome to the MySQL monitor.  Commands end with ; or \g.

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| Music              |
| information_schema |
| kubedb_system      |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
6 rows in set (0.00 sec)

mysql> DROP DATABASE Music;
Query OK, 1 row affected (0.03 sec)

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| kubedb_system      |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
5 rows in set (0.00 sec)

mysql> exit
Bye

Create a RestoreSession

Below, is the contents of YAML file of the RestoreSession object that we are going to create.

apiVersion: stash.appscode.com/v1beta1
kind: RestoreSession
metadata:
  name: sample-mysql-restore
  namespace: demo
spec:
  repository:
    name: s3-repo
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: sample-mysql
  rules:
    - snapshots: [latest]

Now, let’s create RestoreSession that will initiate restoring from the cloud.

$ kubectl create -f sample-mysql-restore.yaml
restoresession.stash.appscode.com/sample-mysql-restore created

This RestoreSession specifies where the data will be restored. Once this is applied, a RestoreSession will be created. Once it has succeeded, the database has been successfully recovered as you can see below:

$ kubectl get restoresession -n demo
NAME                   REPOSITORY   PHASE       DURATION   AGE
sample-mysql-restore   s3-repo      Succeeded   18s        43s

Now, let’s check whether the database has been correctly restored:

$ kubectl exec -it sample-mysql-0 -n demo -c mysql -- bash
bash-4.4# mysql --user=root --password='R9etGyj4v(KP6URi'

Welcome to the MySQL monitor.  Commands end with ; or \g.

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| Music              |
| information_schema |
| kubedb_system      |
| mysql              |
| performance_schema |
| sys                |
+--------------------+
6 rows in set (0.00 sec)

mysql> SELECT * FROM Music.Artist;
+----+-------------+---------------+
| id | Name        | Song          |
+----+-------------+---------------+
|  1 | John Denver | Country Roads |
+----+-------------+---------------+
1 row in set (0.00 sec)

mysql> exit
Bye

You can see the database has been restored. The recovery of MySQL Database has been successful. If you faced any difficulties in the recovery process, you can reach out to us through EMAIL.

We have made an in depth video on Managing Semi-synchronous MySQL Cluster Using KubeDB in Kubernetes. You can have a look into the video below:

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More about MySQL in Kubernetes

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