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SUSE Rancher, RKE, MongoDB

MongoDB with SUSE Rancher

Technical Reference Documentation
Getting Started
Samip Parikh, Solution Architect (SUSE)
SUSE Rancher
Rancher Kubernetes Engine
Date: 2021-04-29
This document provides recommendations for deploying and managing a highly available MongoDB NoSQL database on a SUSE Rancher Kubernetes cluster. Disclaimer: Documents published as part of the SUSE Best Practices and the Technical Reference Documentation series have been contributed voluntarily by SUSE employees and third parties. They are meant to serve as examples of how particular actions can be performed. They have been compiled with utmost attention to detail. However, this does not guarantee complete accuracy. SUSE cannot verify that actions described in these documents do what is claimed or whether actions described have unintended consequences. SUSE LLC, its affiliates, the authors, and the translators may not be held liable for possible errors or the consequences thereof.

1 Motivation

Agility is the name of the game in modern application development. This is driving developers toward more agile, cloud native methodologies that focus on microservices architectures and streamlined workflows. Container technologies, like Kubernetes, embody this agile approach and help enable cloud native transformation.

SUSE Rancher simplifies Kubernetes management, empowering you to take control of your IT landscape and create an agile data platform that accelerates achievement of your goals. Rancher enables you to manage dynamic, robust, multi-cluster Kubernetes environments and supports any CNCF-certified Kubernetes distribution. With built-in resilience and scalability, unified security and policy management, and a rich catalog of shared tools and services, Rancher helps you accelerate development-to-production and innovate everywhere.

MongoDB is a cloud native database technology that brings all the power of the traditional, relational database and provides a more natural way to work with modern data. MongoDB offers a variety of compelling features that make it a natural partner for a SUSE Rancher agile data platform. These include:

Flexible Data Model

MongoDB’s dynamic schema is ideal for handling changing requirements and continuous delivery. You can seamlessly roll out new features without having to update existing records — a process that can take weeks for traditional, relational databases. DevOps teams can quickly model data against an ever-changing environment and roll these changes into production. This results in faster time to market and faster time to value.


MongoDB’s replica sets have built-in redundancy, providing greater resilience and enhancing disaster recovery capabilities. Administrators can even isolate operational workloads from analytical reporting in single database cluster to ensure sufficient resources are allocated to handle demand.

Monitoring and Automation

Heterogeneous services increase the level of complexity and can stall productivity. Technology that handles monitoring and automation is critical to keeping DevOps teams productive as their environments evolve. MongoDB Ops Manager features visualization, custom dashboards, and automated alerting. It tracks, reports, processes, and visualizes 100+ key database and systems-health metrics, including operations counters, CPU utilization, replication status, and node status.


MongoDB’s auto-sharding automatically partitions and distributes the database across nodes, serving IT infrastructures that require dynamic, high-performance capabilities. Distribution can even span different geographic regions. MongoDB is ideally suited to scale-out architectures.

With enterprise-grade products, proactive support, and success-focused services and training, SUSE and MongoDB deliver an agile data platform that helps organizations achieve their cloud native goals.

2 Technical overview

SUSE Rancher is a lightweight Kubernetes installer that supports installation on bare-metal and virtualized servers. Rancher solves a common issue in the Kubernetes community: installation complexity. With Rancher, Kubernetes installation is simplified, regardless of what operating systems and platforms you are running.

This document reviews considerations for deploying and managing a highly available, MongoDB NoSQL database on a SUSE Rancher Kubernetes cluster.

In practice, the process is as follows:

  • Install a Kubernetes cluster through Rancher Kubernetes Engine

  • Install a cloud native storage solution on Kubernetes

  • Deploy MongoDB Enterprise Kubernetes Operator

  • Configure a storage class and define storage requirements via Operator

  • Test failover by killing or cordoning nodes in your cluster

3 Value of HA for data

One of the primary benefits of running a Kubernetes environment is flexibility, the ability to easily adapt to varying circumstances. Traditional database deployments exist in fairly static configurations and environments. The beauty of running a data-oriented service on Kubernetes lies in maintaining stability while enabling adaptability to meet real-world situations.

Imagine a scenario where your e-commerce site is consistently taking 100 orders per day. Suddenly, a viral marketing event occurs, and your site is pushed to 5000 orders per day for a day. This increase could easily lead to data overload – or worse, corruption or downtime, which could result to considerable loss of revenue. Having a way to design for such failure scenarios and maintain resilient operations is a tangible market advantage.

MongoDB can run in a single node configuration and in a clustered configuration using replica sets (not to be confused with Kubernetes Stateful Sets). A replica set is a group of MongoDB instances that maintain the same data. A replica set contains several data-bearing nodes and optionally one arbiter node. Of the data-bearing nodes, one and only one member is deemed the primary node, while the other nodes are deemed secondary nodes. Resiliency of the data is achieved, as illustrated below.

rancher mongo 1

In this configuration, the failover process generally completes within a minute. It may take about 30 seconds for the members of a replica set to declare a primary inaccessible. One of the remaining secondaries will then be enabled as the "new primary". The election itself may take another 10 to 30 seconds. During this time, the data will be preserved in a virtually seamless way for dependent services.

4 Setting up a cluster with SUSE Rancher

SUSE Rancher is a tool to install and configure Kubernetes in a choice of environments including bare metal, virtual machines, and IaaS. Rancher is a complete container management platform built on upstream Kubernetes. It consists of three major components:

  • A certified Kubernetes Distribution – Rancher Kubernetes Engine (RKE)

  • A Kubernetes Management platform (Rancher)

  • Application Catalog and management (Third-party)

Rancher has the capabilities to manage any Kubernetes cluster from a central location, via the Rancher server. As illustrated below, Rancher can manage any Kubernetes flavor and is not restricted to RKE.

rancher mongo 2

For reference, see Rancher deployment guides for specific details on installation. By the end of this step, you should have a cluster with one master and three worker nodes.

rancher mongo 3

5 Storage considerations

When deploying an application that needs to retain data, you need to create persistent storage. Persistent storage allows you to store application data external from the pod running your application. This storage practice allows you to maintain application data, even if the application’s pod fails.

A variety of storage options exist and can be used to create an HA data solution with Rancher. Some considerations you may need to follow for your storage solution include:

  • Volumes as persistent storage for the distributed stateful applications

  • Partitioned block storage for Kubernetes volumes with or without a cloud provider

  • Replicated block storage across multiple nodes and data centers to increase availability

  • Secondary data backup storage (for example, NFS or S3)

  • Cross-cluster disaster recovery volumes

  • Recurring volume snapshots

  • Recurring backups to secondary storage

  • Non-disruptive upgrades

Some common storage solutions to consider are as follows:


Distributed block storage system for Kubernetes. Originally developed by Rancher Labs. Currently sandbox project of the Cloud Native Computing Foundation


Open source, CNCF Sandbox storage with flexible storage engine options - requires third-party integration


Powerful, open source, general purpose storage in the CNCF Sandbox – requires third-party integration


Proprietary solution with Rancher certified integration - installation steps can be found here

5.1 Setting up your storage

Before proceeding, be sure that you understand the Kubernetes concepts of persistent volumes, persistent volume claims, and storage classes. For more information, refer to How Persistent Storage Works in the Rancher documentation.

The workflow for setting up existing storage is as follows:

  1. Ensure you have access to set up your persistent storage. This may be storage in an infrastructure provider, or it could be your own storage.

  2. Add a persistent volume (PV) that refers to the persistent storage.

  3. Add a persistent volume claim (PVC) that refers to the PV.

  4. Mount the PVC as a volume in your workload.

For further details and prerequisites, read the Rancher documentation section Setting Up Existing Storage.

The overall workflow for provisioning new storage is as follows:

  1. Add a StorageClass and configure it to use your storage provider. The StorageClass could refer to storage in an infrastructure provider, or it could refer to your own storage.

  2. Add a persistent volume claim (PVC) that refers to the storage class.

  3. Mount the PVC as a volume for your workload.

See section Dynamically Provisioning New Storage in Rancher for details and prerequisites.

5.2 Creating a storage class for MongoDB

When the Kubernetes cluster is running and storage is configured, it is time to deploy a highly available MongoDB database.

MongoDB resources are created in Kubernetes as custom resources. After you create or update a MongoDB Kubernetes resource specification, you direct MongoDB Kubernetes Operator to apply this specification to your Kubernetes environment. Kubernetes Operator creates the defined StatefulSets, services and other Kubernetes resources. After the Operator finishes creating those objects, it updates the Ops Manager deployment configuration to reflect changes.

The following example shows a resource specification for a replica set configuration:

apiVersion: mongodb.com/v1
kind: MongoDB
  name: my-replica-set
  members: 3
  version: "4.2.2-ent"
  service: my-service
  opsManager: # Alias of cloudManager
      name: my-project
  credentials: my-credentials
  persistent: true
  type: ReplicaSet
    cpu: "0.25"
    memory: "512M"
          storage: "10Gi"
          storage: "1Gi"
              app: "my-app"
          storage: "500M"
          storageClass: standard
    podAntiAffinityTopologyKey: nodeId
      - labelSelector:
          - key: security
            operator: In
            - S1
        topologyKey: failure-domain.beta.kubernetes.io/zone
        - matchExpressions:
          - key: kubernetes.io/e2e-az-name
            operator: In
            - e2e-az1
            - e2e-az2
          label1: mycustomlabel
              - podAffinityTerm:
                  topologyKey: "mykey"
                weight: 50
      enabled: true
      enabled: true
      modes: ["X509"]
      internalCluster: "X509"
        mode: preferSSL

Full details can be found here.

6 Creating a persistent volume

You can now create a persistent volume claim (PVC) based on the storage class. Dynamic provisioning will be created without explicitly provisioning a persistent volume (PV). As part of deployment, the Kubernetes operator creates persistent volumes for the Ops Manager StatefulSets. The Kubernetes container uses persistent volumes to maintain the cluster state between restarts.

7 Deploying MongoDB Kubernetes Operator

Kubernetes needs help creating and managing stateful applications like databases. The typical lifecycle events of a MongoDB cluster may include provisioning storage and computing power, configuring network connections, setting up users, and more. This is where the MongoDB Enterprise Kubernetes Operator comes in. It translates the human knowledge of how to create a MongoDB instance into a scalable, repeatable, and standardized methodology. And it does this by using the built-in Kubernetes API and tools. To use the operator, you simply need to provide it with the specifications for your MongoDB cluster. The operator uses this information to direct Kubernetes into performing all the required steps to achieve the end state.

The general commands for deploying the MongoDB Enterprise Operator are:

kubectl describe deployments mongodb-enterprise-operator -n <namespace>

helm install <chart-name> helm_chart \
     --values helm_chart/values.yaml \

The next step after deploying the operator is to create the database using a yaml file, such as:

apiVersion: mongodb.com/v1
kind: MongoDB

  name: <my-standalone>


  version: "4.2.2-ent"


      name: <configMap.metadata.name>

            # Must match metadata.name in ConfigMap file

  credentials: <mycredentials>

  type: Standalone
  persistent: true

Now, you can deploy the database and check the status of the deployment with:

kubectl apply -f <standalone-conf>.yaml

kubectl get mdb <resource-name> -o yaml

At this point, MongoDB has been deployed via the operator. Additional settings can be applied to create replica sets to further enhance data availability. Also, sharded clusters can be created to enable greater throughput across a distributed system.

Additionally, see specific documentation and steps for full installation and configuration options.

8 Deploying MongoDB Ops Manager resource

Kubernetes needs help creating and managing stateful applications like databases. The typical lifecycle events of a MongoDB cluster may include provisioning, storage and compute. Ops Manager can be deployed via the MongoDB Kubernetes Operator to manage MongoDB resources in a cluster. The Operator manages the lifecycle of each of these deployments differently. The Operator manages Ops Manager deployments using the Ops Manager custom resource. The Operator watches the custom resource’s specification for changes. When the specification changes, the Operator validates the changes and makes the appropriate updates to the resources in the cluster. Ops Manager custom resources specification defines the following components: Application Database, Ops Manager application, and Backup Daemon. Summarized instructions to create Ops Manager are below, but full details can be found here.

To begin, run the following command to execute all kubectl commands in the namespace you created:

kubectl config set-context $(kubectl config current-context) --namespace=<namespace>

Create Ops Manager object as below:

apiVersion: mongodb.com/v1
kind: MongoDBOpsManager
  name: <myopsmanager>
  replicas: 1
  version: <opsmanagerversion>
  adminCredentials: <adminusercredentials> # Should match metadata.name
    type: LoadBalancer
    members: 3
    version: <mongodbversion>
    persistent: true

9 Loading and querying the database

When the database has been created, you can populate it with some sample data.

First, find the pod that is running MongoDB:

POD=`kubectl get pods -l app=mongo | grep Running | grep 1/1 | awk '{print $1}'`

Then, access the MongoDB shell on that POD instance:

$ kubectl exec -it $POD mongo
MongoDB shell version v4.0.0
connecting to: mongodb://
MongoDB server version: 4.0.0
Welcome to the MongoDB shell.

Now, using the MongoDB shell, you can populate a collection:

db.ships.insert({name:'USS Enterprise-D',operator:'Starfleet',type:'Explorer',class:'Galaxy',crew:750,codes:[10,11,12]})
db.ships.insert({name:'USS Prometheus',operator:'Starfleet',class:'Prometheus',crew:4,codes:[1,14,17]})
db.ships.insert({name:'USS Defiant',operator:'Starfleet',class:'Defiant',crew:50,codes:[10,17,19]})
db.ships.insert({name:'IKS Buruk',operator:' Klingon Empire',class:'Warship',crew:40,codes:[100,110,120]})
db.ships.insert({name:'IKS Somraw',operator:' Klingon Empire',class:'Raptor',crew:50,codes:[101,111,120]})
db.ships.insert({name:'Scimitar',operator:'Romulan Star Empire',type:'Warbird',class:'Warbird',crew:25,codes:[201,211,220]})
db.ships.insert({name:'Narada',operator:'Romulan Star Empire',type:'Warbird',class:'Warbird',crew:65,codes:[251,251,220]})

And you can run some operations on the MongoDB collection.

For example, find one arbitrary document:

	"_id" : ObjectId("5b5c16221108c314d4c000cd"),
	"name" : "USS Enterprise-D",
	"operator" : "Starfleet",
	"type" : "Explorer",
	"class" : "Galaxy",
	"crew" : 750,
	"codes" : [

You can also find ALL documents and apply some basic formatting:

 	"_id" : ObjectId("5b5c16221108c314d4c000d1"),
 	"name" : "IKS Somraw",
 	"operator" : " Klingon Empire",
 	"class" : "Raptor",
 	"crew" : 50,
 	"codes" : [
 	"_id" : ObjectId("5b5c16221108c314d4c000d2"),
 	"name" : "Scimitar",
 	"operator" : "Romulan Star Empire",
 	"type" : "Warbird",
 	"class" : "Warbird",
 	"crew" : 25,
 	"codes" : [

And you can get a list of the names of the ships:

 db.ships.find({}, {name:true, _id:false})
 { "name" : "USS Enterprise-D" }
 { "name" : "USS Prometheus" }
 { "name" : "USS Defiant" }
 { "name" : "IKS Buruk" }
 { "name" : "IKS Somraw" }
 { "name" : "Scimitar" }
 { "name" : "Narada" }

10 Simulating node failure & restoration

Next, simulate a node failure by cordoning off the node on which MongoDB is running:

$ NODE=`kubectl get pods -l app=mongo -o wide | grep -v NAME | awk '{print $7}'`

$ kubectl cordon ${NODE} node/ip-172-31-29-132.compute.internal cordoned

The above command disables scheduling on one of the nodes. Check this with:

$ kubectl get nodes
NAME                                           STATUS                     ROLES               AGE   VERSION
ip-172-31-24-121.compute.internal   Ready                      worker              47h   v1.13.4
ip-172-31-26-49.compute.internal    Ready                      controlplane,etcd   47h   v1.13.4
ip-172-31-28-65.compute.internal    Ready                      worker              47h   v1.13.4
ip-172-31-29-132.compute.internal   Ready,SchedulingDisabled   worker              47h   v1.13.4

Now, go ahead and delete the MongoDB pod:

$ POD=`kubectl get pods -l app=mongo -o wide | grep -v NAME | awk '{print $1}'`
$ kubectl delete pod ${POD}
pod "mongo-68cc69bc95-7q96h" deleted

When the pod is deleted, it is relocated to the node with the replicated data, even when that node is in a different zone. Each pod is rescheduled on the exact node where the data is stored.

Verify this:

$ kubectl get pods -l app=mongo -o wide
NAME                     READY     STATUS    RESTARTS   AGE       IP               NODE
mongo-68cc69bc95-thqbm   1/1       Running   0          19s   ip-172-31-24-121.compute.internal

Note that a new pod has been created and scheduled in a different node.

Next, uncordon the node to bring it back to action:

$ kubectl uncordon ${NODE}
node/ip-172-31-29-132.compute.internal uncordoned

Finally, verify that the data is still available.

To do so, find the pod name and run the ‘exec’ command, then access the Mongo shell:

POD=`kubectl get pods -l app=mongo | grep Running | grep 1/1 | awk '{print $1}'`
kubectl exec -it $POD mongo
MongoDB shell version v4.0.0
connecting to: mongodb://
MongoDB server version: 4.0.0
Welcome to the MongoDB shell.

After that, query the collection to verify that the data is intact.

Find one arbitrary document:

	"_id" : ObjectId("5b5c16221108c314d4c000cd"),
	"name" : "USS Enterprise-D",
	"operator" : "Starfleet",
	"type" : "Explorer",
	"class" : "Galaxy",
	"crew" : 750,
	"codes" : [

Now, find all documents and apply formatting:

	"_id" : ObjectId("5b5c16221108c314d4c000d1"),
	"name" : "IKS Somraw",
	"operator" : " Klingon Empire",
	"class" : "Raptor",
	"crew" : 50,
	"codes" : [
	"_id" : ObjectId("5b5c16221108c314d4c000d2"),
	"name" : "Scimitar",
	"operator" : "Romulan Star Empire",
	"type" : "Warbird",
	"class" : "Warbird",
	"crew" : 25,
	"codes" : [

For further validation, you can run all the same initial steps to compare that data is still available with originally queried values.

11 Summary

MongoDB with SUSE Rancher makes it possible to easily build, deploy, and manage resilient, scalable data services.

12 Additional resources

For more information, visit:

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You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one.

The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version.


You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.

The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.

In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements".


You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.

You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.


A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation’s users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.

If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document’s Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate.


Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.

If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.


You may not copy, modify, sublicense, or distribute the Document except as expressly provided for under this License. Any other attempt to copy, modify, sublicense or distribute the Document is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.


The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See http://www.gnu.org/copyleft/.

Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version of this License "or any later version" applies to it, you have the option of following the terms and conditions either of that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation.

ADDENDUM: How to use this License for your documents

Copyright (c) YEAR YOUR NAME.
   Permission is granted to copy, distribute and/or modify this document
   under the terms of the GNU Free Documentation License, Version 1.2
   or any later version published by the Free Software Foundation;
   with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
   A copy of the license is included in the section entitled “GNU
   Free Documentation License”.

If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the “ with…​Texts.” line with this:

with the Invariant Sections being LIST THEIR TITLES, with the
   Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.

If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit the situation.

If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your choice of free software license, such as the GNU General Public License, to permit their use in free software.