Be Awesome with Neo4j Graph Database In Kubernetes

Graph DB solution Neo4j is popular with Data Scientists and Data Architects trying to make connections of the nodes and relationships. Neo4j is able to do memory management other in memory operations to allow for efficiency and performance. All of that data needs to eventual persist to a data management platform. This is why I was first asked about Neo4j.

Some cool nodes

There are Community and Enterprise Editions like most software solutions these days and the robust enterprise type functions land in the Enterprise Edition. Things like RBAC and much higher scale.

Neo4j provides a repo of Helm charts and some helpful documentation on running the Graph Database in Kubernetes. Unfortunately, the instructions stop short of many of the K8s flavors supported by the cloud and on premises solutions. Pre-provisioning cloud disks might be great for a point solution of a single app. Most of my interactions with the people running k8s in production are building Platform as a Service (PaaS) or Database as a Service (DBaaS). Nearly all at least want the option of building these solutions to be hybrid or multi cloud capable. Additionally, DR and Backup are requirements to run in any environment that values their data and staying in business.

Portworx in 20 seconds

Portworx is a data platform that allows stateful applications such as Neo4j to run on an Cloud, on Premises Hardware on any K8s Distribution. It was built from the very beginning to run as a container for containers. </end commercial>

In this blog post I want to enhance and clarify the documentation for the Neo4j helm chart so that you can easily run the community or Enterprise Editions in your K8s deployment.

As with any database Neo4j will benefit greatly from running the persistence on Flash. All of my testing was done with a Pure Storage FlashArray.

Step 1

Already have K8s and Portworx installed. I used Portworx 2.9.1.1 and Vanilla K8s 1.22. Also already have Helm installed.
Note: The helm chart was giving me trouble until I updated helm to version 3.8.x

Step 2

Add the Neo4j helm repo

helm repo add neo4j https://helm.neo4j.com/neo4j
helm repo update

Step 3

Create a neo4j storage class

kind: StorageClass
apiVersion: storage.k8s.io/v1
metadata:
  name: neo4j
provisioner: pxd.portworx.com
parameters:
  repl: "2"
  io_profile: db_remote
kubectl apply -f neo4j-storageclass.yaml

Verify the Storage Class is available

kubectl get sc

Step 4

Create your values.yaml for your install.

values-standalone.yaml
neo4j:
  resources:
    cpu: "0.5"
    memory: "2Gi"

  # Uncomment to set the initial password
  #password: "my-initial-password"

  # Uncomment to use enterprise edition
  #edition: "enterprise"
  #acceptLicenseAgreement: "yes"

volumes:
  data:
    mode: "dynamic"
    # Only used if mode is set to "dynamic"
    # Dynamic provisioning using the provided storageClass
    dynamic:
      storageClassName: "neo4j"
      accessModes:
        - ReadWriteOnce
      requests:
        storage: 100Gi

Cluster values.yaml

node[0-x]values-cluster.yaml

Why do I say 0-x? Well neo4j requires a helm release for each core cluster node (read more detail in the neo4j helm docs). Each file for now is the same. Note: neo4j is an in memory database. 2Gi ram is great for the lab, but for really analytics use I would hope to use much more memory.

neo4j:
  name: "my-cluster"
  resources:
    cpu: "0.5"
    memory: "2Gi"
  password: "my-password"
  acceptLicenseAgreement: "yes"

volumes:
  data:
    mode: "dynamic"
    # Only used if mode is set to "dynamic"
    # Dynamic provisioning using the provided storageClass
    dynamic:
      storageClassName: "neo4j"
      accessModes:
        - ReadWriteOnce
      requests:
        storage: 100Gi
Read Replica values

Create another helm yaml file here is rr1-values-cluster.yaml

neo4j:
  name: "my-cluster"
  resources:
    cpu: "0.5"
    memory: "2Gi"
  password: "my-password"
  acceptLicenseAgreement: "yes"

volumes:
  data:
    mode: "dynamic"
    # Only used if mode is set to "dynamic"
    # Dynamic provisioning using the provided storageClass
    dynamic:
      storageClassName: "neo4j"
      accessModes:
        - ReadWriteOnce
      requests:
        storage: 100Gi

Download all the values.yaml from GitHub

Step 5

Install Neo4j (stand alone)

Standalone

The docs say to run this:

helm install my-neo4j-release neo4j/neo4j-standalone -f my-neo4j.values-standalone.yaml

I do the following and I’ll explain why.

helm install -n neo4j-1 neo4j-1 neo4j/neo4j-standalone -f ./values-standalone.yaml --create-namespace

Cluster Install

For each cluster node values.yaml

helm install -n neo4j-cluster neo4j-cluster-3 neo4j/neo4j-cluster-core -f ./node1-values-cluster.yaml --create-namespace

You need a minimum of 3 core nodes to create a cluster. So you must run the helm install command 3 times for the neo4j-cluster-core helm chart.

Successful Cluster Creation
 kubectl -n neo4j-cluster exec neo4j-cluster-0 -- tail /logs/neo4j.log
2022-03-29 19:14:55.139+0000 INFO  Bolt enabled on [0:0:0:0:0:0:0:0%0]:7687.
2022-03-29 19:14:55.141+0000 INFO  Bolt (Routing) enabled on [0:0:0:0:0:0:0:0%0]:7688.
2022-03-29 19:15:09.324+0000 INFO  Remote interface available at http://localhost:7474/
2022-03-29 19:15:09.337+0000 INFO  id: E2E827273BD3E291C8DF4D4162323C77935396BB4FFB14A278EAA08A989EB0D2
2022-03-29 19:15:09.337+0000 INFO  name: system
2022-03-29 19:15:09.337+0000 INFO  creationDate: 2022-03-29T19:13:44.464Z
2022-03-29 19:15:09.337+0000 INFO  Started.
2022-03-29 19:15:35.595+0000 INFO  Connected to neo4j-cluster-3-internals.neo4j-cluster.svc.cluster.local/10.233.125.2:7000 [RAFT version:5.0]
2022-03-29 19:15:35.739+0000 INFO  Connected to neo4j-cluster-2-internals.neo4j-cluster.svc.cluster.local/10.233.127.2:7000 [RAFT version:5.0]
2022-03-29 19:15:35.876+0000 INFO  Connected to neo4j-cluster-3-internals.neo4j-cluster.svc.cluster.local/10.233.125.2:7000 [RAFT version:5.0]
Install Read Replica

The cluster must be up and functioning to install the read replica.

helm install -n neo4j-cluster neo4j-cluster-rr1 neo4j/neo4j-cluster-read-replica -f ./rr1-values-cluster.yaml
Install the Loadbalancer

To access neo4j from an external source you should install the loadbalancer service. Run the following command in our example.

 helm install -n neo4j-cluster lb neo4j/neo4j-cluster-loadbalancer --set neo4j.name=my-cluster
Why the -n tag?

I provide the -n with a namespace and the –create-namespace tag because it allows me to install my helm release in this case neo4j-1 into its own namespace. Which helps with operations for DR, Backup and even lifecycle cleanup down the road. When installing a cluster all the helm releases must be in the same namesapce.

Start Graph Databasing!

As you can see there are plenty of tutorials to see how you may use Neo4j

Some other tips:
https://neo4j.com/docs/operations-manual/current/performance/disks-ram-and-other-tips/

See below for detials of the PX Cluster

Status: PX is operational
Telemetry: Disabled or Unhealthy
License: Trial (expires in 31 days)
Node ID: ade858a2-30d4-41ba-a2ce-7ee1f9b7c4c0
	IP: 10.21.244.207
 	Local Storage Pool: 1 pool
	POOL	IO_PRIORITY	RAID_LEVEL	USABLE	USED	STATUS	ZONE	REGION
	0	HIGH		raid0		297 GiB	12 GiB	Online	default	default
	Local Storage Devices: 2 devices
	Device	Path							Media Type		Size		Last-Scan
	0:1	/dev/mapper/3624a937081f096d1c1642a6900d954aa-part2	STORAGE_MEDIUM_SSD	147 GiB		29 Mar 22 16:21 UTC
	0:2	/dev/mapper/3624a937081f096d1c1642a6900d954ab		STORAGE_MEDIUM_SSD	150 GiB		29 Mar 22 16:21 UTC
	total								-			297 GiB
	Cache Devices:
	 * No cache devices
	Journal Device:
	1	/dev/mapper/3624a937081f096d1c1642a6900d954aa-part1	STORAGE_MEDIUM_SSD
Cluster Summary
	Cluster ID: px-fa-demo1
	Cluster UUID: 76eaa789-384d-4af2-b476-b9b3fd7fdcab
	Scheduler: kubernetes
	Nodes: 8 node(s) with storage (8 online)
	IP		ID					SchedulerNodeName	Auth		StorageNode	Used	Capacity	Status	StorageStatus	Version		Kernel			OS
	10.21.244.203	f917d321-3857-4ee1-bfaf-df6419fdac53	pxfa1-3			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.209	c3bea2dc-10cd-4485-8d02-e65a23bf10aa	pxfa1-9			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.204	b27e351a-fed3-40b9-a6d3-7de2e7e88ac3	pxfa1-4			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.207	ade858a2-30d4-41ba-a2ce-7ee1f9b7c4c0	pxfa1-7			Disabled	Yes		12 GiB	297 GiB		Online	Up (This node)	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.205	a413f877-3199-4664-961a-0296faa3589d	pxfa1-5			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.202	37ae23c7-1205-4a03-bbe1-a16a7e58849a	pxfa1-2			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.206	369bfc54-9f75-45ef-9442-b6494c7f0572	pxfa1-6			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
	10.21.244.208	00683edb-96fc-4861-815d-a0430f8fc84b	pxfa1-8			Disabled	Yes		12 GiB	297 GiB		Online	Up	2.9.1.3-7769924	5.4.0-105-generic	Ubuntu 20.04.4 LTS
Global Storage Pool
	Total Used    	:  96 GiB
	Total Capacity	:  2.3 TiB

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