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Monitoring the Kubernetes cluster

Dgraph exposes Prometheus metrics to monitor the state of various components involved in the cluster, including Dgraph Alpha and Zero nodes. You can setup Prometheus monitoring for your cluster.

You can use Helm to install kube-prometheus-stack chart. This Helm chart is a collection of Kubernetes manifests, Grafana dashboards, Prometheus rules combined with scripts to provide monitoring with Prometheus using the Prometheus Operator. This Helm chart also installs Grafana, node_exporter, kube-state-metrics.

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Before you begin

  • Install the Kubernetes command line tool.
  • Ensure that you have a production-ready Kubernetes cluster with at least three worker nodes running in a cloud provider of your choice.
  • Install Helm

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Install using Helm chart

  1. Create a YAML file named dgraph-prometheus-operator.yaml and edit the values as appropriate for adding endpoints, adding alert rules, adjusting alert manager configuration, adding Grafana dashboard, and others. For more information see, Dgraph Helm chart values.

    prometheusOperator:
  createCustomResource: true

grafana:
  enabled: true
  persistence:
    enabled: true
    accessModes: ["ReadWriteOnce"]
    size: 5Gi
  defaultDashboardsEnabled: true
  service:
    type: ClusterIP

alertmanager:
  service:
    labels:
      app: dgraph-io
  alertmanagerSpec:
    storage:
      volumeClaimTemplate:
        spec:
          accessModes: ["ReadWriteOnce"]
          resources:
            requests:
              storage: 5Gi
    replicas: 1
    logLevel: debug
  config:
    global:
      resolve_timeout: 2m
    route:
      group_by: ['job']
      group_wait: 30s
      group_interval: 5m
      repeat_interval: 12h
      receiver: 'null'
      routes:
      - match:
          alertname: Watchdog
           receiver: 'null'
    receivers:
    - name: 'null'

prometheus:
  service:
      type: ClusterIP
  serviceAccount:
    create: true
    name: prometheus-dgraph-io

  prometheusSpec:
    storageSpec:
      volumeClaimTemplate:
        spec:
          accessModes: ["ReadWriteOnce"]
          resources:
            requests:
              storage: 25Gi
    resources:
      requests:
        memory: 400Mi
    enableAdminAPI: false

  additionalServiceMonitors:
    - name: zero-dgraph-io
      endpoints:
        - port: http-zero
          path: /debug/prometheus_metrics
      namespaceSelector:
        any: true
      selector:
        matchLabels:
          monitor: zero-dgraph-io
    - name: alpha-dgraph-io
      endpoints:
        - port: http-alpha
          path: /debug/prometheus_metrics
      namespaceSelector:
        any: true
      selector:
        matchLabels:
          monitor: alpha-dgraph-io

  2. Create a YAML file named secrets.yaml that has the credentials for Grafana.

    grafana:
  adminPassword: <GRAFANA-PASSWORD>

  3. Add the prometheus-operator Helm chart:

    helm repo add stable https://charts.helm.sh/stable
helm repo add prometheus-community https://prometheus-community.github.io/helm-charts
helm repo update

  4. Install kube-prometheus-stack with the <MY-RELEASE-NAME> in the namespace named monitoring:

    helm install <MY-RELEASE-NAME>\
  --values dgraph-prometheus-operator.yaml \
  --values secrets.yaml \
  prometheus-community/kube-prometheus-stack --namespace monitoring

    An output similar to the following appears:

    NAME: dgraph-prometheus-release
LAST DEPLOYED: Sun Feb  5 21:35:45 2023
NAMESPACE: monitoring
STATUS: deployed
REVISION: 1
NOTES:
kube-prometheus-stack has been installed. Check its status by running:
  kubectl --namespace monitoring get pods -l "release=dgraph-prometheus-release"

Visit https://github.com/prometheus-operator/kube-prometheus instructions on how to create & configure Alertmanager and Prometheus instances using the Operator.

  5. Check the list of services in the monitoring namespace using kubectl get svc -n monitoring:

    NAME                                                 TYPE        CLUSTER-IP       EXTERNAL-IP   PORT(S)                      AGE
alertmanager-operated                                ClusterIP   None             <none>        9093/TCP,9094/TCP,9094/UDP   29s
dgraph-prometheus-release-alertmanager               ClusterIP   10.128.239.240   <none>        9093/TCP                     32s
dgraph-prometheus-release-grafana                    ClusterIP   10.128.213.70    <none>        80/TCP                       32s
dgraph-prometheus-release-kube-state-metrics         ClusterIP   10.128.139.145   <none>        8080/TCP                     32s
dgraph-prometheus-release-operator                   ClusterIP   10.128.6.5       <none>        443/TCP                      32s
dgraph-prometheus-release-prometheus                 ClusterIP   10.128.255.88    <none>        9090/TCP                     32s
dgraph-prometheus-release-prometheus-node-exporter   ClusterIP   10.128.103.131   <none>        9100/TCP                     32s
prometheus-operated                                  ClusterIP   None             <none>        9090/TCP                     29s

  6. Use kubectl port-forward svc/dgraph-prometheus-release-prometheus -n monitoring 9090 to access Prometheus at localhost:9090.

  7. Use kubectl --namespace monitoring port-forward svc/grafana 3000:80 to access Grafana at localhost:3000.

  8. Log in to Grafana using the password that you had set in the secrets.yaml file.

  9. In the Dashboards menu of Grafana, select Import.

  10. In the Dashboards/Import dashboard page copy the contents of the dgraph-kubernetes-grafana-dashboard.json file in Import via panel JSON and click Load.

    You can visualize all Dgraph Alpha and Zero Kubernetes Pods, using the regular expression pattern "/dgraph-.*-[0-9]*$/. You can change this in the dashboard configuration and select the variable Pod. For example, if you have multiple releases, and only want to visualize the current release named my-release-3, change the regular expression pattern to "/my-release-3.*dgraph-.*-[0-9]*$/" in the Pod variable of the dashboard configuration. By default, the Prometheus that you installed is configured as the Datasource in Grafana.

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Kubernetes storage

The Kubernetes configurations in the previous sections were configured to run Dgraph with any storage type (storage-class: anything). On the common cloud environments like AWS, Google Cloud, and Azure, the default storage type are slow disks like hard disks or low IOPS SSDs. We highly recommend using faster disks for ideal performance when running Dgraph.

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Local storage

The AWS storage-optimized i-class instances provide locally attached NVMe-based SSD storage which provide consistent very high IOPS. The Dgraph team uses i3.large instances on AWS to test Dgraph.

You can create a Kubernetes StorageClass object to provision a specific type of storage volume which you can then attach to your Dgraph Pods. You can set up your cluster with local SSDs by using Local Persistent Volumes. This Kubernetes feature is in beta at the time of this writing (Kubernetes v1.13.1). You can first set up an EC2 instance with locally attached storage. Once it’s formatted and mounted properly, then you can create a StorageClass to access it.:

apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
  name: <your-local-storage-class-name>
provisioner: kubernetes.io/no-provisioner
volumeBindingMode: WaitForFirstConsumer

Currently, Kubernetes doesn’t allow automatic provisioning of local storage. So a PersistentVolume with a specific mount path should be created:

apiVersion: v1
kind: PersistentVolume
metadata:
  name: <your-local-pv-name>
spec:
  capacity:
    storage: 475Gi
  volumeMode: Filesystem
  accessModes:
    - ReadWriteOnce
  persistentVolumeReclaimPolicy: Delete
  storageClassName: <your-local-storage-class-name>
  local:
    path: /data
  nodeAffinity:
    required:
      nodeSelectorTerms:
        - matchExpressions:
            - key: kubernetes.io/hostname
              operator: In
              values:
                - <node-name>

Then, in the StatefulSet configuration you can claim this local storage in .spec.volumeClaimTemplate:

kind: StatefulSet
---
volumeClaimTemplates:
  - metadata:
      name: datadir
    spec:
      accessModes:
        - ReadWriteOnce
      storageClassName: <your-local-storage-class-name>
      resources:
        requests:
          storage: 500Gi

You can repeat these steps for each instance that’s configured with local node storage.

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Non-local persistent disks

EBS volumes on AWS and PDs on Google Cloud are persistent disks that can be configured with Dgraph. The disk performance is much lower than locally attached storage but can be sufficient for your workload such as testing environments.

When using EBS volumes on AWS, we recommend using Provisioned IOPS SSD EBS volumes (the io1 disk type) which provide consistent IOPS. The available IOPS for AWS EBS volumes is based on the total disk size. With Kubernetes, you can request io1 disks to be provisioned with this configuration with 50 IOPS/GB using the iopsPerGB parameter:

kind: StorageClass
apiVersion: storage.k8s.io/v1
metadata:
  name: <your-storage-class-name>
provisioner: kubernetes.io/aws-ebs
parameters:
  type: io1
  iopsPerGB: "50"
  fsType: ext4

Example: requesting a disk size of 250Gi with this storage class would provide 12.5K IOPS.

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Removing a Dgraph pod

In the event that you need to completely remove a Pod (for example, the disk became corrupted and data can’t be recovered), you can use the /removeNode API to remove the node from the cluster. With a Kubernetes StatefulSet, you’ll need to remove the node in this order:

  1. On the Zero leader, call /removeNode to remove the Dgraph instance from the cluster (see More about Dgraph Zero). The removed instance will immediately stop running. Any further attempts to join the cluster fails for that instance since it has been removed.
  2. Remove the PersistentVolumeClaim associated with the Pod to delete its data. This prepares the Pod to join with a clean state.
  3. Restart the Pod. This creates a new PersistentVolumeClaim to create new data directories.

When an Alpha Pod restarts in a replicated cluster, it joins as a new member of the cluster, be assigned a group and an unused index from Zero, and receive the latest snapshot from the Alpha leader of the group.

When a Zero Pod restarts, it must join the existing group with an unused index ID. You set the index ID with the --raft superflag’s idx option. This might require you to update the StatefulSet configuration.

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Kubernetes and Bulk Loader

You may want to initialize a new cluster with an existing data set such as data from the Dgraph Bulk Loader. You can use Init Containers to copy the data to the Pod volume before the Alpha process runs.

See the initContainers configuration in dgraph-ha.yaml to learn more.

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