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Kubernetes: Spinning up a Neo4j 3.1 Causal Cluster

Photo of Mark Needham Mark NeedhamNovember 28th, 2016Last Updated: November 28th, 2016
0 16 5 minutes read

A couple of weeks ago I wrote a blog post explaining how I’d created a Neo4j causal cluster using docker containers directly and for my next pet project I wanted to use Kubernetes as an orchestration layer so that I could declaratively change the number of servers in my cluster.

I’d never used Kubernetes before but I saw a presentation showing how to use it to create an Elastic cluster at the GDG Cloud meetup a couple of months ago.

In that presentation I was introduced to the idea of a PetSet which is an abstraction exposed by Kubernetes which allows us to manage a set of pods (containers) which have a fixed identity. The documentation explains it better:

A PetSet ensures that a specified number of “pets” with unique identities are running at any given time. The identity of a Pet is comprised of:

  • a stable hostname, available in DNS
  • an ordinal index
  • stable storage: linked to the ordinal & hostname

In my case I need to have a stable hostname because each member of a Neo4j cluster is given a list of other cluster members with which it can create a new cluster or join an already existing one. This is the first use case described in the documentation:

PetSet also helps with the 2 most common problems encountered managing such clustered applications:

  • discovery of peers for quorum
  • startup/teardown ordering

So the first thing we need to do is create some stable storage for our pods to use.

We’ll create a cluster of 3 members so we need to create one PersistentVolume for each of them. The following script does the job:

volumes.sh

for i in $(seq 0 2); do
  cat <<EOF | kubectl create -f -
kind: PersistentVolume
apiVersion: v1
metadata:
  name: pv${i}
  labels:
    type: local
    app: neo4j
spec:
  capacity:
    storage: 1Gi
  accessModes:
    - ReadWriteOnce
  hostPath:
    path: "/tmp/${i}"
EOF
 
  cat <<EOF | kubectl create -f -
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: datadir-neo4j-${i}
  labels:
    app: neo4j
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 1Gi
EOF
done;

If we run this script it’ll create 3 volumes which we can see by running the following command:

$ kubectl get pv
NAME      CAPACITY   ACCESSMODES   STATUS    CLAIM                     REASON    AGE
pv0       1Gi        RWO           Bound     default/datadir-neo4j-0             7s
pv1       1Gi        RWO           Bound     default/datadir-neo4j-1             7s
pv2       1Gi        RWO           Bound     default/datadir-neo4j-2             7s
$ kubectl get pvc
NAME              STATUS    VOLUME    CAPACITY   ACCESSMODES   AGE
datadir-neo4j-0   Bound     pv0       1Gi        RWO           26s
datadir-neo4j-1   Bound     pv1       1Gi        RWO           26s
datadir-neo4j-2   Bound     pv2       1Gi        RWO           25s

Next we need to create a PetSet template. After a lot of iterations I ended up with the following:

# Headless service to provide DNS lookup
apiVersion: v1
kind: Service
metadata:
  labels:
    app: neo4j
  name: neo4j
spec:
  clusterIP: None
  ports:
    - port: 7474
  selector:
    app: neo4j
----
# new API name
apiVersion: "apps/v1alpha1"
kind: PetSet
metadata:
  name: neo4j
spec:
  serviceName: neo4j
  replicas: 3
  template:
    metadata:
      annotations:
        pod.alpha.kubernetes.io/initialized: "true"
        pod.beta.kubernetes.io/init-containers: '[
            {
                "name": "install",
                "image": "gcr.io/google_containers/busybox:1.24",
                "command": ["/bin/sh", "-c", "echo \"
                unsupported.dbms.edition=enterprise\n
                dbms.mode=CORE\n
                dbms.connectors.default_advertised_address=$HOSTNAME.neo4j.default.svc.cluster.local\n
                dbms.connectors.default_listen_address=0.0.0.0\n
                dbms.connector.bolt.type=BOLT\n
                dbms.connector.bolt.enabled=true\n
                dbms.connector.bolt.listen_address=0.0.0.0:7687\n
                dbms.connector.http.type=HTTP\n
                dbms.connector.http.enabled=true\n
                dbms.connector.http.listen_address=0.0.0.0:7474\n
                causal_clustering.raft_messages_log_enable=true\n
                causal_clustering.initial_discovery_members=neo4j-0.neo4j.default.svc.cluster.local:5000,neo4j-1.neo4j.default.svc.cluster.local:5000,neo4j-2.neo4j.default.svc.cluster.local:5000\n
                causal_clustering.leader_election_timeout=2s\n
                  \" > /work-dir/neo4j.conf" ],
                "volumeMounts": [
                    {
                        "name": "confdir",
                        "mountPath": "/work-dir"
                    }
                ]
            }
        ]'
      labels:
        app: neo4j
    spec:
      containers:
      - name: neo4j
        image: "neo4j/neo4j-experimental:3.1.0-M13-beta3-enterprise"
        imagePullPolicy: Always
        ports:
        - containerPort: 5000
          name: discovery
        - containerPort: 6000
          name: tx
        - containerPort: 7000
          name: raft
        - containerPort: 7474
          name: browser
        - containerPort: 7687
          name: bolt
        securityContext:
          privileged: true
        volumeMounts:
        - name: datadir
          mountPath: /data
        - name: confdir
          mountPath: /conf
      volumes:
      - name: confdir
  volumeClaimTemplates:
  - metadata:
      name: datadir
      annotations:
        volume.alpha.kubernetes.io/storage-class: anything
    spec:
      accessModes: [ "ReadWriteOnce" ]
      resources:
        requests:
          storage: 1Gi

The main thing I had trouble with was getting the members of the cluster to talk to each other. The default docker config uses hostnames but I found that pods were unable to contact each other unless I specified the FQDN in the config file. We can run the following command to create the PetSet:

$ kubectl create -f neo4j.yaml 
service "neo4j" created
petset "neo4j" created

We can check if the pods are up and running by executing the following command:

$ kubectl get pods
NAME      READY     STATUS    RESTARTS   AGE
neo4j-0   1/1       Running   0          2m
neo4j-1   1/1       Running   0          14s
neo4j-2   1/1       Running   0          10s

And we can tail neo4j’s log files like this:

$ kubectl logs neo4j-0
Starting Neo4j.
2016-11-25 16:39:50.333+0000 INFO  Starting...
2016-11-25 16:39:51.723+0000 INFO  Bolt enabled on 0.0.0.0:7687.
2016-11-25 16:39:51.733+0000 INFO  Initiating metrics...
2016-11-25 16:39:51.911+0000 INFO  Waiting for other members to join cluster before continuing...
2016-11-25 16:40:12.074+0000 INFO  Started.
2016-11-25 16:40:12.428+0000 INFO  Mounted REST API at: /db/manage
2016-11-25 16:40:13.350+0000 INFO  Remote interface available at http://neo4j-0.neo4j.default.svc.cluster.local:7474/
$ kubectl logs neo4j-1
Starting Neo4j.
2016-11-25 16:39:53.846+0000 INFO  Starting...
2016-11-25 16:39:56.212+0000 INFO  Bolt enabled on 0.0.0.0:7687.
2016-11-25 16:39:56.225+0000 INFO  Initiating metrics...
2016-11-25 16:39:56.341+0000 INFO  Waiting for other members to join cluster before continuing...
2016-11-25 16:40:16.623+0000 INFO  Started.
2016-11-25 16:40:16.951+0000 INFO  Mounted REST API at: /db/manage
2016-11-25 16:40:17.607+0000 INFO  Remote interface available at http://neo4j-1.neo4j.default.svc.cluster.local:7474/
$ kubectl logs neo4j-2
Starting Neo4j.
2016-11-25 16:39:57.828+0000 INFO  Starting...
2016-11-25 16:39:59.166+0000 INFO  Bolt enabled on 0.0.0.0:7687.
2016-11-25 16:39:59.176+0000 INFO  Initiating metrics...
2016-11-25 16:39:59.329+0000 INFO  Waiting for other members to join cluster before continuing...
2016-11-25 16:40:19.216+0000 INFO  Started.
2016-11-25 16:40:19.675+0000 INFO  Mounted REST API at: /db/manage
2016-11-25 16:40:21.029+0000 INFO  Remote interface available at http://neo4j-2.neo4j.default.svc.cluster.local:7474/

I wanted to log into the servers from my host machine’s browser so I setup port forwarding for each of the servers:

$ kubectl port-forward neo4j-0 7474:7474 7687:7687

We can then get an overview of the cluster by running the following procedure:

CALL dbms.cluster.overview()
 
╒════════════════════════════════════╤═════════════════════════════════════════════════════╤════════╕
│id                                  │addresses                                            │role    │
╞════════════════════════════════════╪═════════════════════════════════════════════════════╪════════╡
│81d8e5e2-02db-4414-85de-a7025b346e84│[bolt://neo4j-0.neo4j.default.svc.cluster.local:7687,│LEADER  │
│                                    │ http://neo4j-0.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│347b7517-7ca0-4b92-b9f0-9249d46b2ad3│[bolt://neo4j-1.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-1.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│a5ec1335-91ce-4358-910b-8af9086c2969│[bolt://neo4j-2.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-2.neo4j.default.svc.cluster.local:7474]│        │
└────────────────────────────────────┴─────────────────────────────────────────────────────┴────────┘

So far so good. What if we want to have 5 servers in the cluster instead of 3? We can run the following command to increase our replica size:

$ kubectl patch petset neo4j -p '{"spec":{"replicas":5}}'
"neo4j" patched

Let’s run that procedure again:

CALL dbms.cluster.overview()
 
╒════════════════════════════════════╤═════════════════════════════════════════════════════╤════════╕
│id                                  │addresses                                            │role    │
╞════════════════════════════════════╪═════════════════════════════════════════════════════╪════════╡
│81d8e5e2-02db-4414-85de-a7025b346e84│[bolt://neo4j-0.neo4j.default.svc.cluster.local:7687,│LEADER  │
│                                    │ http://neo4j-0.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│347b7517-7ca0-4b92-b9f0-9249d46b2ad3│[bolt://neo4j-1.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-1.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│a5ec1335-91ce-4358-910b-8af9086c2969│[bolt://neo4j-2.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-2.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│28613d06-d4c5-461c-b277-ddb3f05e5647│[bolt://neo4j-3.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-3.neo4j.default.svc.cluster.local:7474]│        │
├────────────────────────────────────┼─────────────────────────────────────────────────────┼────────┤
│2eaa0058-a4f3-4f07-9f22-d310562ad1ec│[bolt://neo4j-4.neo4j.default.svc.cluster.local:7687,│FOLLOWER│
│                                    │ http://neo4j-4.neo4j.default.svc.cluster.local:7474]│        │
└────────────────────────────────────┴─────────────────────────────────────────────────────┴────────┘

Neat! And it’s as easy to go back down to 3 again:

$ kubectl patch petset neo4j -p '{"spec":{"replicas":3}}'
"neo4j" patched
CALL dbms.cluster.overview()
 
╒════════════════════════════════════╤══════════════════════════════════════════════════════╤════════╕
│id                                  │addresses                                             │role    │
╞════════════════════════════════════╪══════════════════════════════════════════════════════╪════════╡
│81d8e5e2-02db-4414-85de-a7025b346e84│[bolt://neo4j-0.neo4j.default.svc.cluster.local:7687, │LEADER  │
│                                    │http://neo4j-0.neo4j.default.svc.cluster.local:7474]  │        │
├────────────────────────────────────┼──────────────────────────────────────────────────────┼────────┤
│347b7517-7ca0-4b92-b9f0-9249d46b2ad3│[bolt://neo4j-1.neo4j.default.svc.cluster.local:7687, │FOLLOWER│
│                                    │http://neo4j-1.neo4j.default.svc.cluster.local:7474]  │        │
├────────────────────────────────────┼──────────────────────────────────────────────────────┼────────┤
│a5ec1335-91ce-4358-910b-8af9086c2969│[bolt://neo4j-2.neo4j.default.svc.cluster.local:7687, │FOLLOWER│
│                                    │http://neo4j-2.neo4j.default.svc.cluster.local:7474]  │        │
└────────────────────────────────────┴──────────────────────────────────────────────────────┴────────┘

Next I need to look at how we can add read replicas into the cluster. These don’t take part in the membership/quorum algorithm so I think I’ll be able to use the more common ReplicationController/Pod architecture for those.

If you want to play around with this the code is available as a gist. I’m using the minikube library for all my experiments but I’ll hopefully get around to trying this on GCE or AWS soon.

Reference: Kubernetes: Spinning up a Neo4j 3.1 Causal Cluster from our JCG partner Mark Needham at the Mark Needham Blog blog.
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Photo of Mark Needham Mark NeedhamNovember 28th, 2016Last Updated: November 28th, 2016
0 16 5 minutes read
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