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Monitoring PerconaXtraDB Using Prometheus operator

Prometheus operator provides simple and Kubernetes native way to deploy and configure Prometheus server. This tutorial will show you how to use Prometheus operator to monitor PerconaXtraDB deployed with KubeDB.

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. If you do not already have a cluster, you can create one by using kind.
To learn how Prometheus monitoring works with KubeDB in general, please visit here.
To keep Prometheus resources isolated, we are going to use a separate namespace called monitoring to deploy respective monitoring resources. We are going to deploy database in demo namespace.
```
$ kubectl create ns monitoring
namespace/monitoring created

$ kubectl create ns demo
namespace/demo created
```
We need a Prometheus operator instance running. If you don’t already have a running instance, deploy one following the docs from here.
If you already don’t have a Prometheus server running, deploy one following tutorial from here.

Note: YAML files used in this tutorial are stored in docs/examples/percona-xtradb folder in GitHub repository kubedb/docs.

Find out required labels for ServiceMonitor

We need to know the labels used to select ServiceMonitor by a Prometheus resource. We are going to provide these labels in .spec.monitor.prometheus.labels field of PerconaXtraDB object so that KubeDB creates ServiceMonitor object accordingly.

At first, let’s find out the available Prometheus server in our cluster.

$ kubectl get prometheus --all-namespaces
NAMESPACE    NAME         AGE
monitoring   prometheus   18m

If you don’t have any Prometheus server running in your cluster, deploy one following the guide specified in Before You Begin section.

Now, let’s view the YAML of the available Prometheus server prometheus in monitoring namespace.

$ kubectl get prometheus -n monitoring prometheus -o yaml
apiVersion: monitoring.coreos.com/v1
kind: Prometheus
metadata:
  annotations:
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"monitoring.coreos.com/v1","kind":"Prometheus","metadata":{"annotations":{},"labels":{"prometheus":"prometheus"},"name":"prometheus","namespace":"monitoring"},"spec":{"replicas":1,"resources":{"requests":{"memory":"400Mi"}},"serviceAccountName":"prometheus","serviceMonitorSelector":{"matchLabels":{"k8s-app":"prometheus"}}}}      
  creationTimestamp: 2019-01-03T13:41:51Z
  generation: 1
  labels:
    prometheus: prometheus
  name: prometheus
  namespace: monitoring
  resourceVersion: "44402"
  selfLink: /apis/monitoring.coreos.com/v1/namespaces/monitoring/prometheuses/prometheus
  uid: 5324ad98-0f5d-11e9-b230-080027f306f3
spec:
  replicas: 1
  resources:
    requests:
      memory: 400Mi
  serviceAccountName: prometheus
  serviceMonitorSelector:
    matchLabels:
      k8s-app: prometheus

Notice the .spec.serviceMonitorSelector section. Here, k8s-app: prometheus label is used to select ServiceMonitor resource. So, we are going to use this label in .spec.monitor.prometheus.labels field of PerconaXtraDB resource.

Deploy PerconaXtraDB with Monitoring Enabled

At first, let’s deploy a sample PerconaXtraDB with monitoring enabled. Below is the PerconaXtraDB object that we are going to create.

apiVersion: kubedb.com/v1alpha2
kind: PerconaXtraDB
metadata:
  name: px-coreos-prom
  namespace: demo
spec:
  version: "5.7-cluster"
  replicas: 3
  storageType: Durable
  storage:
    storageClassName: "standard"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 50Mi
  terminationPolicy: WipeOut
  monitor:
    agent: prometheus.io/operator
    prometheus:
      serviceMonitor:
        labels:
          k8s-app: prometheus
        interval: 10s

Here,

.spec.monitor.agent: prometheus.io/operator indicates that we are going to monitor this server using Prometheus operator.
.spec.monitor.prometheus.namespace: monitoring specifies that KubeDB should create ServiceMonitor in monitoring namespace.
.spec.monitor.prometheus.labels specifies that KubeDB should create ServiceMonitor with these labels.
.spec.monitor.prometheus.interval indicates that the Prometheus server should scrape metrics from this database with 10 seconds interval.

Let’s create the PerconaXtraDB object that we have shown above,

$ kubectl create -f https://github.com/kubedb/docs/raw/v2021.04.16/docs/examples/percona-xtradb/px-coreos-prom.yaml
perconaxtradb.kubedb.com/px-coreos-prom created

Now, wait for the database to go into Running state.

$ kubectl get px -n demo px-coreos-prom
NAME             VERSION       STATUS    AGE
px-coreos-prom   5.7-cluster   Running   5m4s

KubeDB will create a separate stats service with name {PerconaXtraDB_obj_name}-stats for monitoring purpose.

$ kubectl get svc -n demo --selector="app.kubernetes.io/instance=px-coreos-prom"
NAME                   TYPE        CLUSTER-IP       EXTERNAL-IP   PORT(S)     AGE
px-coreos-prom         ClusterIP   10.107.58.214    <none>        3306/TCP    5m25s
px-coreos-prom-gvr     ClusterIP   None             <none>        3306/TCP    5m25s
px-coreos-prom-stats   ClusterIP   10.106.130.209   <none>        56790/TCP   48s

Here, px-coreos-prom-stats service has been created for monitoring purpose.

Let’s describe this stats service.

$ kubectl describe svc -n demo px-coreos-prom-stats
Name:              px-coreos-prom-stats
Namespace:         demo
Labels:            app.kubernetes.io/name=perconaxtradbs.kubedb.com
                   app.kubernetes.io/instance=px-coreos-prom
                   kubedb.com/role=stats
Annotations:       monitoring.appscode.com/agent: prometheus.io/operator
Selector:          app.kubernetes.io/name=perconaxtradbs.kubedb.com,app.kubernetes.io/instance=px-coreos-prom
Type:              ClusterIP
IP:                10.106.130.209
Port:              prom-http  56790/TCP
TargetPort:        prom-http/TCP
Endpoints:         10.244.1.7:56790,10.244.2.11:56790,10.244.2.9:56790
Session Affinity:  None
Events:            <none>

Notice the Labels and Port fields. ServiceMonitor will use these information to target its endpoints.

KubeDB will also create a ServiceMonitor resource in monitoring namespace that select the endpoints of px-coreos-prom-stats service. Verify that the ServiceMonitor resource has been created.

$ kubectl get servicemonitor -n monitoring
NAME                         AGE
kubedb-demo-px-coreos-prom   2m45s

Let’s verify that the ServiceMonitor has the label that we had specified in .spec.monitor section of PerconaXtraDB object.

$ kubectl get servicemonitor -n monitoring kubedb-demo-px-coreos-prom -o yaml
apiVersion: monitoring.coreos.com/v1
kind: ServiceMonitor
metadata:
  creationTimestamp: "2019-12-19T07:17:11Z"
  generation: 1
  labels:
    k8s-app: prometheus
    monitoring.appscode.com/service: px-coreos-prom-stats.demo
  name: kubedb-demo-px-coreos-prom
  namespace: monitoring
  ownerReferences:
  - apiVersion: v1
    blockOwnerDeletion: true
    kind: Service
    name: px-coreos-prom-stats
    uid: fb353fac-9945-48ca-ad81-f79dcf5e8e24
  resourceVersion: "13989"
  selfLink: /apis/monitoring.coreos.com/v1/namespaces/monitoring/servicemonitors/kubedb-demo-px-coreos-prom
  uid: 07fd2ae4-d294-4e7f-88d8-960ca3a63a40
spec:
  endpoints:
  - honorLabels: true
    interval: 10s
    path: /metrics
    port: prom-http
  namespaceSelector:
    matchNames:
    - demo
  selector:
    matchLabels:
      app.kubernetes.io/name: perconaxtradbs.kubedb.com
      app.kubernetes.io/instance: px-coreos-prom
      kubedb.com/role: stats

Notice that the ServiceMonitor has label k8s-app: prometheus that we had specified in PerconaXtraDB object.

Also notice that the ServiceMonitor has selector which match the labels we have seen in the px-coreos-prom-stats service. It also, target the prom-http port that we have seen in the stats service.

Verify Monitoring Metrics

At first, let’s find out the respective Prometheus Pod for prometheus Prometheus server.

$ kubectl get pod -n monitoring -l=app=prometheus
NAME                      READY   STATUS    RESTARTS   AGE
prometheus-prometheus-0   3/3     Running   1          51m

Prometheus server is listening to port 9090 of prometheus-prometheus-0 Pod. We are going to use port forwarding to access Prometheus dashboard.

Run the following command on a separate terminal to forward the port 9090 of prometheus-prometheus-0 Pod,

$ kubectl port-forward -n monitoring prometheus-prometheus-0 9090
Forwarding from 127.0.0.1:9090 -> 9090
Forwarding from [::1]:9090 -> 9090

Now, we can access the dashboard at localhost:9090. Open http://localhost:9090 in your browser. You should see prom-http endpoint of px-coreos-prom-stats service as one of the targets.

Prometheus Target

Check the followings:

Endpoint URLs of backend servers marked by green rectangles
endpoint, pod, and service labels marked by red rectangles

They all indicate that the target is our expected database.

Now, you can view the collected metrics and create a graph from homepage of this Prometheus dashboard. You can also use this Prometheus server as data source for Grafana and create beautiful dashboard with collected metrics.

Cleaning up

To cleanup the Kubernetes resources created by this tutorial, run following commands

# cleanup database
$ kubectl delete -n demo px/px-coreos-prom

# cleanup prometheus resources
$ kubectl delete -n monitoring prometheus prometheus
$ kubectl delete clusterrolebinding prometheus
$ kubectl delete clusterrole prometheus
$ kubectl delete -n monitoring serviceaccount prometheus
$ kubectl delete -n monitoring service prometheus-operated

# cleanup prometheus operator resources
$ kubectl delete -n monitoring deployment prometheus-operator
$ kubectl delete clusterrolebinding prometheus-operator
$ kubectl delete clusterrole prometheus-operator
$ kubectl delete -n monitoring serviceaccount prometheus-operator

# delete namespace
$ kubectl delete ns monitoring
$ kubectl delete ns demo

Next Steps

Monitor your PerconaXtraDB database with KubeDB using out-of-the-box builtin-Prometheus.
Initialize PerconaXtraDB with Script.
Use private Docker registry to deploy PerconaXtraDB with KubeDB.
How to use custom configuration.
How to use custom rbac resource for PerconaXtraDB.
Use Stash to Backup PerconaXtraDB.
Detail concepts of PerconaXtraDB object.
Detail concepts of PerconaXtraDBVersion object.
Want to hack on KubeDB? Check our contribution guidelines.

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