Home » DevOps » Kubernetes: Copy a dataset to a StatefulSet’s PersistentVolume

About Mark Needham

Kubernetes: Copy a dataset to a StatefulSet’s PersistentVolume

Neo4j Clusters on Kubernetes

This posts assumes that we’re familiar with deploying Neo4j on Kubernetes. I wrote an article on the Neo4j blog explaining this in more detail.

The StatefulSet we create for our core servers require persistent storage, achieved via the PersistentVolumeClaim (PVC) primitive. A Neo4j cluster containing 3 core servers would have the following PVCs:

$ kubectl get pvc
NAME                            STATUS    VOLUME                                     CAPACITY   ACCESS MODES   STORAGECLASS   AGE
datadir-neo-helm-neo4j-core-0   Bound     pvc-043efa91-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            standard       45s
datadir-neo-helm-neo4j-core-1   Bound     pvc-1737755a-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            standard       13s
datadir-neo-helm-neo4j-core-2   Bound     pvc-18696bfd-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            standard       11s

Each of the PVCs has a corresponding PersistentVolume (PV) that satisifies it:

$ kubectl get pv
NAME                                       CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS    CLAIM                                   STORAGECLASS   REASON    AGE
pvc-043efa91-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            Delete           Bound     default/datadir-neo-helm-neo4j-core-0   standard                 41m
pvc-1737755a-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            Delete           Bound     default/datadir-neo-helm-neo4j-core-1   standard                 40m
pvc-18696bfd-cc54-11e7-bfa5-080027ab9eac   10Gi       RWO            Delete           Bound     default/datadir-neo-helm-neo4j-core-2   standard                 40m

The PVCs and PVs are usually created at the same time that we deploy our StatefulSet. We need to intervene in that lifecycle so that our dataset is already in place before the StatefulSet is deployed.

Deploying an existing dataset

We can do this by following these steps:

  • Create PVCs with the above names manually
  • Attach pods to those PVCs
  • Copy our dataset onto those pods
  • Delete the pods
  • Deploy our Neo4j cluster

We can use the following script to create the PVCs and pods:

pvs.sh

#!/usr/bin/env bash
 
set -exuo pipefail
 
for i in $(seq 0 2); do
  cat <<EOF | kubectl apply -f -
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: datadir-neo-helm-neo4j-core-${i}
  labels:
    app: neo4j
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 10Gi
EOF
 
  cat <<EOF | kubectl apply -f -
kind: Pod
apiVersion: v1
metadata:
  name: neo4j-load-data-${i}
  labels:
    app: neo4j-loader
spec:
  volumes:
    - name: datadir-neo4j-core-${i}
      persistentVolumeClaim:
        claimName: datadir-neo-helm-neo4j-core-${i}
  containers:
    - name: neo4j-load-data-${i}
      image: ubuntu
      volumeMounts:
      - name: datadir-neo4j-core-${i}
        mountPath: /data
      command: ["/bin/bash", "-ecx", "while :; do printf '.'; sleep 5 ; done"]
EOF
 
done;

Let’s run that script to create our PVCs and pods:

$ ./pvs.sh 
++ seq 0 2
+ for i in $(seq 0 2)
+ cat
+ kubectl apply -f -
persistentvolumeclaim "datadir-neo-helm-neo4j-core-0" configured
+ cat
+ kubectl apply -f -
pod "neo4j-load-data-0" configured
+ for i in $(seq 0 2)
+ cat
+ kubectl apply -f -
persistentvolumeclaim "datadir-neo-helm-neo4j-core-1" configured
+ cat
+ kubectl apply -f -
pod "neo4j-load-data-1" configured
+ for i in $(seq 0 2)
+ cat
+ kubectl apply -f -
persistentvolumeclaim "datadir-neo-helm-neo4j-core-2" configured
+ cat
+ kubectl apply -f -
pod "neo4j-load-data-2" configured

Now we can copy our database onto the pods:

for i in $(seq 0 2); do
  kubectl cp graph.db.tar.gz neo4j-load-data-${i}:/data/
  kubectl exec neo4j-load-data-${i} -- bash -c "mkdir -p /data/databases && tar -xf  /data/graph.db.tar.gz -C /data/databases"
done

graph.db.tar.gz contains a backup from a local database I created:

$ tar -tvf graph.db.tar.gz 
 
drwxr-xr-x  0 markneedham staff       0 24 Jul 15:23 graph.db/
drwxr-xr-x  0 markneedham staff       0 24 Jul 15:23 graph.db/certificates/
drwxr-xr-x  0 markneedham staff       0 17 Feb  2017 graph.db/index/
drwxr-xr-x  0 markneedham staff       0 24 Jul 15:22 graph.db/logs/
-rw-r--r--  0 markneedham staff    8192 24 Jul 15:23 graph.db/neostore
-rw-r--r--  0 markneedham staff     896 24 Jul 15:23 graph.db/neostore.counts.db.a
-rw-r--r--  0 markneedham staff    1344 24 Jul 15:23 graph.db/neostore.counts.db.b
-rw-r--r--  0 markneedham staff       9 24 Jul 15:23 graph.db/neostore.id
-rw-r--r--  0 markneedham staff   65536 24 Jul 15:23 graph.db/neostore.labelscanstore.db
...
-rw-------  0 markneedham staff     1700 24 Jul 15:23 graph.db/certificates/neo4j.key

We’ll run the following command to check the databases are in place:

$ kubectl exec neo4j-load-data-0 -- ls -lh /data/databases/
total 4.0K
drwxr-xr-x 6 501 staff 4.0K Jul 24 14:23 graph.db
 
$ kubectl exec neo4j-load-data-1 -- ls -lh /data/databases/
total 4.0K
drwxr-xr-x 6 501 staff 4.0K Jul 24 14:23 graph.db
 
$ kubectl exec neo4j-load-data-2 -- ls -lh /data/databases/
total 4.0K
drwxr-xr-x 6 501 staff 4.0K Jul 24 14:23 graph.db

All good so far. The pods have done their job so we’ll tear those down:

$ kubectl delete pods -l app=neo4j-loader
pod "neo4j-load-data-0" deleted
pod "neo4j-load-data-1" deleted
pod "neo4j-load-data-2" deleted

We’re now ready to deploy our Neo4j cluster.

helm install incubator/neo4j --name neo-helm --wait --set authEnabled=false

Finally we’ll run a Cypher query to check that the Neo4j servers used the database that we uploaded:

$ kubectl exec neo-helm-neo4j-core-0 -- bin/cypher-shell "match (n) return count(*)"
count(*)
32314
 
$ kubectl exec neo-helm-neo4j-core-1 -- bin/cypher-shell "match (n) return count(*)"
count(*)
32314
 
$ kubectl exec neo-helm-neo4j-core-2 -- bin/cypher-shell "match (n) return count(*)"
count(*)
32314

Success!

We could achieve similar results by using an init container but I haven’t had a chance to try out that approach yet. If you give it a try let me know in the comments and I’ll add it to the post.

Published on Java Code Geeks with permission by Mark Needham, partner at our JCG program. See the original article here: Kubernetes: Copy a dataset to a StatefulSet’s PersistentVolume

Opinions expressed by Java Code Geeks contributors are their own.

Do you want to know how to develop your skillset to become a Java Rockstar?

Subscribe to our newsletter to start Rocking right now!

To get you started we give you our best selling eBooks for FREE!

 

1. JPA Mini Book

2. JVM Troubleshooting Guide

3. JUnit Tutorial for Unit Testing

4. Java Annotations Tutorial

5. Java Interview Questions

6. Spring Interview Questions

7. Android UI Design

 

and many more ....

 

Receive Java & Developer job alerts in your Area

I have read and agree to the terms & conditions

 

Subscribe
Notify of
guest

This site uses Akismet to reduce spam. Learn how your comment data is processed.

0 Comments
Inline Feedbacks
View all comments