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Storage Autoscaling of a PerconaXtraDB Cluster

This guide will show you how to use KubeDB to autoscale the storage of a PerconaXtraDB Replicaset database.

Before You Begin

At first, you need to have a Kubernetes cluster, and the kubectl command-line tool must be configured to communicate with your cluster.
Install KubeDB Community, Enterprise and Autoscaler operator in your cluster following the steps here.
Install Metrics Server from here
Install Prometheus from here
You must have a StorageClass that supports volume expansion.
You should be familiar with the following KubeDB concepts:

To keep everything isolated, we are going to use a separate namespace called demo throughout this tutorial.

$ kubectl create ns demo
namespace/demo created

Storage Autoscaling of Cluster Database

At first verify that your cluster has a storage class, that supports volume expansion. Let’s check,

$ kubectl get storageclass
NAME                  PROVISIONER             RECLAIMPOLICY   VOLUMEBINDINGMODE      ALLOWVOLUMEEXPANSION   AGE
standard (default)    rancher.io/local-path   Delete          WaitForFirstConsumer   false                  79m
topolvm-provisioner   topolvm.cybozu.com      Delete          WaitForFirstConsumer   true                   78m

We can see from the output the topolvm-provisioner storage class has ALLOWVOLUMEEXPANSION field as true. So, this storage class supports volume expansion. We can use it. You can install topolvm from here

Now, we are going to deploy a PerconaXtraDB replicaset using a supported version by KubeDB operator. Then we are going to apply PerconaXtraDBAutoscaler to set up autoscaling.

Deploy PerconaXtraDB Cluster

In this section, we are going to deploy a PerconaXtraDB replicaset database with version 8.0.26. Then, in the next section we will set up autoscaling for this database using PerconaXtraDBAutoscaler CRD. Below is the YAML of the PerconaXtraDB CR that we are going to create,

If you want to autoscale PerconaXtraDB Standalone, Just remove the spec.Replicas from the below yaml and rest of the steps are same.

apiVersion: kubedb.com/v1
kind: PerconaXtraDB
metadata:
  name: sample-pxc
  namespace: demo
spec:
  version: "8.0.26"
  replicas: 3
  storageType: Durable
  storage:
    storageClassName: "topolvm-provisioner"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  deletionPolicy: WipeOut

Let’s create the PerconaXtraDB CRO we have shown above,

$ kubectl create -f https://github.com/kubedb/docs/raw/v2024.8.2-rc.2/docs/guides/percona-xtradb/autoscaler/storage/cluster/examples/sample-pxc.yaml
perconaxtradb.kubedb.com/sample-pxc created

Now, wait until sample-pxc has status Ready. i.e,

$ kubectl get perconaxtradb -n demo
NAME             VERSION   STATUS   AGE
sample-pxc      8.0.26    Ready    3m46s

Let’s check volume size from petset, and from the persistent volume,

$ kubectl get sts -n demo sample-pxc -o json | jq '.spec.volumeClaimTemplates[].spec.resources.requests.storage'
"1Gi"

$ kubectl get pv -n demo
NAME                                       CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                        STORAGECLASS          REASON   AGE
pvc-43266d76-f280-4cca-bd78-d13660a84db9   1Gi        RWO            Delete           Bound    demo/data-sample-pxc-2   topolvm-provisioner            57s
pvc-4a509b05-774b-42d9-b36d-599c9056af37   1Gi        RWO            Delete           Bound    demo/data-sample-pxc-0   topolvm-provisioner            58s
pvc-c27eee12-cd86-4410-b39e-b1dd735fc14d   1Gi        RWO            Delete           Bound    demo/data-sample-pxc-1   topolvm-provisioner            57s

You can see the petset has 1GB storage, and the capacity of all the persistent volume is also 1GB.

We are now ready to apply the PerconaXtraDBAutoscaler CRO to set up storage autoscaling for this database.

Storage Autoscaling

Here, we are going to set up storage autoscaling using a PerconaXtraDBAutoscaler Object.

Create PerconaXtraDBAutoscaler Object

In order to set up vertical autoscaling for this replicaset database, we have to create a PerconaXtraDBAutoscaler CRO with our desired configuration. Below is the YAML of the PerconaXtraDBAutoscaler object that we are going to create,

apiVersion: autoscaling.kubedb.com/v1alpha1
kind: PerconaXtraDBAutoscaler
metadata:
  name: px-as-st
  namespace: demo
spec:
  databaseRef:
    name: sample-pxc
  storage:
    perconaxtradb:
      trigger: "On"
      usageThreshold: 20
      scalingThreshold: 20
      expansionMode: "Online"

Here,

spec.databaseRef.name specifies that we are performing vertical scaling operation on sample-pxc database.
spec.storage.perconaxtradb.trigger specifies that storage autoscaling is enabled for this database.
spec.storage.perconaxtradb.usageThreshold specifies storage usage threshold, if storage usage exceeds 20% then storage autoscaling will be triggered.
spec.storage.perconaxtradb.scalingThreshold specifies the scaling threshold. Storage will be scaled to 20% of the current amount.
spec.storage.perconaxtradb.expansionMode specifies the expansion mode of volume expansion PerconaXtraDBOpsRequest created by PerconaXtraDBAutoscaler. topolvm-provisioner supports online volume expansion so here expansionMode is set as “Online”.

Let’s create the PerconaXtraDBAutoscaler CR we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.8.2-rc.2/docs/guides/percona-xtradb/autoscaler/storage/cluster/examples/pxas-storage.yaml
perconaxtradbautoscaler.autoscaling.kubedb.com/px-as-st created

Storage Autoscaling is set up successfully

Let’s check that the perconaxtradbautoscaler resource is created successfully,

$ kubectl get perconaxtradbautoscaler -n demo
NAME           AGE
px-as-st   33s

$ kubectl describe perconaxtradbautoscaler px-as-st -n demo
Name:         px-as-st
Namespace:    demo
Labels:       <none>
Annotations:  API Version:  autoscaling.kubedb.com/v1alpha1
Kind:         PerconaXtraDBAutoscaler
Metadata:
  Creation Timestamp:  2022-01-14T06:08:02Z
  Generation:          1
  Managed Fields:
    ...
  Resource Version:  24009
  UID:               4f45a3b3-fc72-4d04-b52c-a770944311f6
Spec:
  Database Ref:
    Name:  sample-pxc
  Storage:
    Mariadb:
      Scaling Threshold:  20
      Trigger:            On
      Usage Threshold:    20
Events:                   <none>

So, the perconaxtradbautoscaler resource is created successfully.

Now, for this demo, we are going to manually fill up the persistent volume to exceed the usageThreshold using dd command to see if storage autoscaling is working or not.

Let’s exec into the database pod and fill the database volume(var/lib/mysql) using the following commands:

$ kubectl exec -it -n demo sample-pxc-0 -- bash
root@sample-pxc-0:/ df -h /var/lib/mysql
Filesystem                                         Size  Used Avail Use% Mounted on
/dev/topolvm/57cd4330-784f-42c1-bf8e-e743241df164 1014M  357M  658M  36% /var/lib/mysql
root@sample-pxc-0:/ dd if=/dev/zero of=/var/lib/mysql/file.img bs=500M count=1
1+0 records in
1+0 records out
524288000 bytes (524 MB, 500 MiB) copied, 0.340877 s, 1.5 GB/s
root@sample-pxc-0:/ df -h /var/lib/mysql
Filesystem                                         Size  Used Avail Use% Mounted on
/dev/topolvm/57cd4330-784f-42c1-bf8e-e743241df164 1014M  857M  158M  85% /var/lib/mysql

So, from the above output we can see that the storage usage is 83%, which exceeded the usageThreshold 20%.

Let’s watch the perconaxtradbopsrequest in the demo namespace to see if any perconaxtradbopsrequest object is created. After some time you’ll see that a perconaxtradbopsrequest of type VolumeExpansion will be created based on the scalingThreshold.

$ kubectl get perconaxtradbopsrequest -n demo
NAME                         TYPE              STATUS        AGE
mops-sample-pxc-xojkua   VolumeExpansion   Progressing   15s

Let’s wait for the ops request to become successful.

$ kubectl get perconaxtradbopsrequest -n demo
NAME                         TYPE              STATUS       AGE
mops-sample-pxc-xojkua   VolumeExpansion   Successful   97s

We can see from the above output that the PerconaXtraDBOpsRequest has succeeded. If we describe the PerconaXtraDBOpsRequest we will get an overview of the steps that were followed to expand the volume of the database.

$ kubectl describe perconaxtradbopsrequest -n demo mops-sample-pxc-xojkua
Name:         mops-sample-pxc-xojkua
Namespace:    demo
Labels:       app.kubernetes.io/component=database
              app.kubernetes.io/instance=sample-pxc
              app.kubernetes.io/managed-by=kubedb.com
              app.kubernetes.io/name=perconaxtradbs.kubedb.com
Annotations:  <none>
API Version:  ops.kubedb.com/v1alpha1
Kind:         PerconaXtraDBOpsRequest
Metadata:
  Creation Timestamp:  2022-01-14T06:13:10Z
  Generation:          1
  Managed Fields: ...
  Owner References:
    API Version:           autoscaling.kubedb.com/v1alpha1
    Block Owner Deletion:  true
    Controller:            true
    Kind:                  PerconaXtraDBAutoscaler
    Name:                  px-as-st
    UID:                   4f45a3b3-fc72-4d04-b52c-a770944311f6
  Resource Version:        25557
  UID:                     90763a49-a03f-407c-a233-fb20c4ab57d7
Spec:
  Database Ref:
    Name:  sample-pxc
  Type:    VolumeExpansion
  Volume Expansion:
    Mariadb:  1594884096
Status:
  Conditions:
    Last Transition Time:  2022-01-14T06:13:10Z
    Message:               Controller has started to Progress the PerconaXtraDBOpsRequest: demo/mops-sample-pxc-xojkua
    Observed Generation:   1
    Reason:                OpsRequestProgressingStarted
    Status:                True
    Type:                  Progressing
    Last Transition Time:  2022-01-14T06:14:25Z
    Message:               Volume Expansion performed successfully in PerconaXtraDB pod for PerconaXtraDBOpsRequest: demo/mops-sample-pxc-xojkua
    Observed Generation:   1
    Reason:                SuccessfullyVolumeExpanded
    Status:                True
    Type:                  VolumeExpansion
    Last Transition Time:  2022-01-14T06:14:25Z
    Message:               Controller has successfully expand the volume of PerconaXtraDB demo/mops-sample-pxc-xojkua
    Observed Generation:   1
    Reason:                OpsRequestProcessedSuccessfully
    Status:                True
    Type:                  Successful
  Observed Generation:     3
  Phase:                   Successful
Events:
  Type    Reason      Age    From                        Message
  ----    ------      ----   ----                        -------
  Normal  Starting    2m58s  KubeDB Enterprise Operator  Start processing for PerconaXtraDBOpsRequest: demo/mops-sample-pxc-xojkua
  Normal  Starting    2m58s  KubeDB Enterprise Operator  Pausing PerconaXtraDB databse: demo/sample-pxc
  Normal  Successful  2m58s  KubeDB Enterprise Operator  Successfully paused PerconaXtraDB database: demo/sample-pxc for PerconaXtraDBOpsRequest: mops-sample-pxc-xojkua
  Normal  Successful  103s   KubeDB Enterprise Operator  Volume Expansion performed successfully in PerconaXtraDB pod for PerconaXtraDBOpsRequest: demo/mops-sample-pxc-xojkua
  Normal  Starting    103s   KubeDB Enterprise Operator  Updating PerconaXtraDB storage
  Normal  Successful  103s   KubeDB Enterprise Operator  Successfully Updated PerconaXtraDB storage
  Normal  Starting    103s   KubeDB Enterprise Operator  Resuming PerconaXtraDB database: demo/sample-pxc
  Normal  Successful  103s   KubeDB Enterprise Operator  Successfully resumed PerconaXtraDB database: demo/sample-pxc
  Normal  Successful  103s   KubeDB Enterprise Operator  Controller has Successfully expand the volume of PerconaXtraDB: demo/sample-pxc

Now, we are going to verify from the Petset, and the Persistent Volume whether the volume of the replicaset database has expanded to meet the desired state, Let’s check,

$ kubectl get sts -n demo sample-pxc -o json | jq '.spec.volumeClaimTemplates[].spec.resources.requests.storage'
"1594884096"
$ kubectl get pv -n demo
NAME                                       CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                        STORAGECLASS          REASON   AGE
pvc-43266d76-f280-4cca-bd78-d13660a84db9   2Gi        RWO            Delete           Bound    demo/data-sample-pxc-2   topolvm-provisioner            23m
pvc-4a509b05-774b-42d9-b36d-599c9056af37   2Gi        RWO            Delete           Bound    demo/data-sample-pxc-0   topolvm-provisioner            24m
pvc-c27eee12-cd86-4410-b39e-b1dd735fc14d   2Gi        RWO            Delete           Bound    demo/data-sample-pxc-1   topolvm-provisioner            23m

The above output verifies that we have successfully autoscaled the volume of the PerconaXtraDB replicaset database.

Cleaning Up

To clean up the Kubernetes resources created by this tutorial, run:

kubectl delete perconaxtradb -n demo sample-pxc
kubectl delete perconaxtradbautoscaler -n demo px-as-st
kubectl delete ns demo

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