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Kubernetes Storage on Azure 3 of 3 – Ceph by Rook

Fri, 26 Aug 2022 19:43:00 -0400

In the last two posts, I covered the native storage options on Azure Kubernetes Service, as well as Portworx as an example of a proprietary Software Defined Storage (SDS) solution. There are also a number of open-source alternative SDS solutions. Ceph has nearly a decade of history from prior to containerization, and is the most widely adopted storage platform. In this post, we continue to explore Ceph as an open-source storage solution on Azure Kubernetes.

Ceph by Rook

Ceph is an open-source SDS platform for distributed storage on a cluster and provides object, block and file storage. Installation of Ceph SDS can be complex, especially on Kubernetes platform. Rook is a graduated CNCF project to orchestrate storage platform. Rook by itself is not SDS and it supports:

Ceph: configure a Ceph cluster. Think of this as the equivalent of cephadm on Kubernetes platform.
NFS: configure an NFS server. Think of this as the equivalent of nfsd daemon on Kubernetes platform.
Cassandra: an operator to configure a Cassandra database cluster. It is now deprecated.

We play with Rook Ceph. I also refer to it as Ceph by Rook. The contribution of Rook project is it simplifies the installation as a matter of declaring custom resources using CRDs. Here are some high-level CRDs to know:

CephCluster: creates a Ceph storage cluster
CephBlockPool: represents a block pool
CephFilesystem: represents a file system
CephObjectStore: represents an object store
CephNFS: spins up a NFS Ganesha server to export NFS shares of a CephFilesystem or CephObjectStore.

As with typical Kubernetes resources in controller pattern, Ceph by Rook needs an operator along with custom resources. We can use YAML manifest for both of them, and the manifests are usually very tediously long. We can also use Helm to install both of them, by providing a value file. Now we will install Ceph on AKS.

Install Ceph Operator on AKS

The steps are influenced by two relevant posts (here and here). However, I’ve incorporated the cluster configuration in the Azure directory of the cloudkube project, a modular Terraform template to configure AKS cluster and facilitate storage configuration. The node group and instance sizes are selected to be just enough to run a ceph POC cluster with minimum cost. One of the node groups is tainted with storage-node, as if the following command were run:

kubectl taint nodes my-node-pool-node-name storage-node=true:NoSchedule

You will only need to taint the nodes with the command above if you choose not to use the cloudkube template. The taint ensures that only Pods with corresponding toleration and effect can be scheduled to those nodes.

We use Helm to install Rook Operator. We need a value file (e.g. rook-ceph-operator-values.yaml) with content as below:

# https://github.com/rook/rook/blob/master/Documentation/Helm-Charts/operator-chart.md
crds:
 enabled: true
csi:
 provisionerTolerations:
 - effect: NoSchedule
 key: storage-node
 operator: Exists
 pluginTolerations:
 - effect: NoSchedule
 key: storage-node
 operator: Exists
agent:
 # AKS: https://rook.github.io/docs/rook/v1.7/flexvolume.html#azure-aks
 flexVolumeDirPath: "/etc/kubernetes/volumeplugins"

Then we install the operator with Helm:

helm install rook-ceph-operator rook-ceph --namespace rook-ceph --create-namespace --version v1.9.6 --repo https://charts.rook.io/release/ --values rook-ceph-operator-values.yaml
kubectl -n rook-ceph get po -l app=rook-ceph-operator

After installing the operator, we check the Pod status to make sure it is running. Then we can install the actual Ceph Cluster in one of the two ways. We can declare a CephClusterCRD ourself, or we can use Helm again to declare the CRD. Helm Chart gives us a lot of useful default values and saves us from editing a large body of YAML manifest.

Install Ceph CR on AKS

We use Helm to install CephCluster CRD. We create a value file (e.g. rook-ceph-cluster-values.yaml) with content as below:

# https://github.com/rook/rook/blob/master/Documentation/Helm-Charts/ceph-cluster-chart.md
operatorNamespace: rook-ceph
toolbox:
 enabled: true
cephObjectStores: [] # by default a cephObjectStore will be created. Setting this to null disables it
#cephBlockPools: # by default a cephBlockPool will also be created with default values
#cephFileSystems: # by default a cephFileSystem will also be created with default values

cephClusterSpec:
 mon:
 count: 3
 volumeClaimTemplate:
 spec:
 storageClassName: managed-premium
 resources:
 requests:
 storage: 10Gi
 resources:
 limits:
 cpu: "500m"
 memory: "1Gi"
 requests:
 cpu: "100m"
 memory: "500Mi"
 dashboard:
 enabled: true
 storage:
 storageClassDeviceSets:
 - name: set1
 # The number of OSDs to create from this device set
 count: 3
 # IMPORTANT: If volumes specified by the storageClassName are not portable across nodes
 # this needs to be set to false. For example, if using the local storage provisioner
 # this should be false.
 portable: false
 # Since the OSDs could end up on any node, an effort needs to be made to spread the OSDs
 # across nodes as much as possible. Unfortunately the pod anti-affinity breaks down
 # as soon as you have more than one OSD per node. The topology spread constraints will
 # give us an even spread on K8s 1.18 or newer.
 placement:
 topologySpreadConstraints:
 - maxSkew: 1
 topologyKey: kubernetes.io/hostname
 whenUnsatisfiable: ScheduleAnyway
 labelSelector:
 matchExpressions:
 - key: app
 operator: In
 values:
 - rook-ceph-osd
 tolerations:
 - key: storage-node
 operator: Exists
 preparePlacement:
 tolerations:
 - key: storage-node
 operator: Exists
 nodeAffinity:
 requiredDuringSchedulingIgnoredDuringExecution:
 nodeSelectorTerms:
 - matchExpressions:
 - key: agentpool
 operator: In
 values:
 - storagenp
 topologySpreadConstraints:
 - maxSkew: 1
 # IMPORTANT: If you don't have zone labels, change this to another key such as kubernetes.io/hostname
 topologyKey: topology.kubernetes.io/zone
 whenUnsatisfiable: DoNotSchedule
 labelSelector:
 matchExpressions:
 - key: app
 operator: In
 values:
 - rook-ceph-osd-prepare
 resources:
 limits:
 cpu: "500m"
 memory: "4Gi"
 requests:
 cpu: "500m"
 memory: "2Gi"
 volumeClaimTemplates:
 - metadata:
 name: data
 spec:
 resources:
 requests:
 storage: 100Gi
 storageClassName: managed-premium
 volumeMode: Block
 accessModes:
 - ReadWriteOnce

During the cluster provisioning, there will be a number of preparing Pods. We want those Pods to run on nodes with label agentpool=storagenp. In real life, we need to orchestrate where to run each workload, by restricting the nodes to schedule certain types of workload.

Then we can install the cluster using Helm:

helm install rook-ceph-cluster rook-ceph-cluster --namespace rook-ceph --create-namespace --version v1.9.6 --repo https://charts.rook.io/release/ --values rook-ceph-cluster-values.yaml

After running the Helm install, it may take as long as 15 minutes for all resources to settle. Watch the Pod status in rook-ceph namespace. At the end, make sure that the cluster is created successfully:

kubeadmin@pro-sturgeon-bastion-host:~$ kubectl -n rook-ceph get CephCluster
NAME DATADIRHOSTPATH MONCOUNT AGE PHASE MESSAGE HEALTH EXTERNAL
rook-ceph /var/lib/rook 3 15m Ready Cluster created successfully HEALTH_OK
kubeadmin@pro-sturgeon-bastion-host:~$ kubectl -n rook-ceph get cephBlockPools
NAME PHASE
ceph-blockpool Ready
kubeadmin@pro-sturgeon-bastion-host:~$ kubectl -n rook-ceph get cephFileSystems
NAME ACTIVEMDS AGE PHASE
ceph-filesystem 1 20m Ready

In my case it took 15 minutes before the cluster comes up as created successfully. You should notice that two storage classes were also created as a part of the install. It however did not create a storage class or CRD for object storage, because we explicitly disabled it in the Helm value file by setting cephObjectStores value to null.

Dashboard

We enabled dashboard. To configure the dashboard view properly, we would need an ingress. For a quick view here, we can play port forwarding tricks. First we fetch the admin password for use in the next step. Then expose the dashboard to the bastion host:

$ kubectl -n rook-ceph get secret rook-ceph-dashboard-password -o jsonpath='{.data.password}' | base64 -d
$ kubectl -n rook-ceph port-forward svc/rook-ceph-mgr-dashboard 8443:8443

Since I don’t have UI on the bastion host, I use the port forwarding trick again from my own MacBook. Start a new terminal and SSH to the bastion host with port-forwarding switch:

$ ssh -L 8443:localhost:8443 kubeadmin@20.116.132.8

The command above suppose the public IP of the bastion host is 20.116.132.8. Then from my MacBook I can browse to localhost:8443 (with Safari browser which gives me the option to bypass certificate error). At the web portal, provide username (admin) and password (as retrieved above):

Ceph console for Kubernetes

Apart from the dashboard, we can also use ceph admin tool from a toolbox pod, following this instruction. For monitoring, Ceph by Rook can expose metrics for Prometheus to scrape.

Performance

With default ceph configuration on AKS, I ran quick performance test using kube-str . The result is as follows:

	read_iops	write_iops	read_bw	write_bw
ceph-block	IOPS=464.507294 BW(KiB/s)=1874	IOPS=243.296143 BW(KiB/s)=989	IOPS=509.928162 BW(KiB/s)=65797	IOPS=248.530762 BW(KiB/s)=32338
ceph-filesystem	IOPS=438.701324 BW(KiB/s)=1770	IOPS=226.270660 BW(KiB/s)=920	IOPS=405.936340 BW(KiB/s)=52456	IOPS=208.869293 BW(KiB/s)=27229

The metrics reflects performance under default configuration. It should not be considered as the best performance that Ceph can deliver on Azure Kubernetes.

Summary

I discussed three storage options for Azure Kubernetes but the idea applies to other Kubernetes platform hosted on a CSP. The native storage has significant limitation. NFS has latency. Block storage does not address high availability at the storage layer. Portworx and LINSTOR fill that gap as a commercial solution. Ceph is based on Object storage.

Zookeeper Summary

Wed, 26 Aug 2020 23:10:00 -0400

Distributed systems

Distributed system involves independent computing entities linked together by network. The components communicate and coordinate with each other to achieve a common goal. In early days, designers and developers often had made some assumptions (aka. fallacies) of distributed computing:

The network is reliable
Latency is zero
Bandwidth is infinite
Network is secure
Topology doesn’t change: in reality, components to a network get removed/added over time. the system should tolerate such changes.
There is one administrator: for distributed systems to function, they interact with external system beyond administrative control.
Transport cost is zero: cost is involved everywhere, in the form of CPU cycles spent, to actual dollars paid to service provider.
Network is homogenous

These fallacies make coordinating distributed computing entities a huge challenge and Zookeeper is introduced to address these challenges. Zookeeper implements common tasks for distributed coordination, such as:

Configuration Management (propagate configuration changes to all worker nodes dynamically)
Naming service
Distributed synchronization (locks and barriers)
Cluster membership operations (e.g. detection of node leave/join)

ZooKeeper is a centralized coordination service for the distributed application. ZooKeeper itself is distributed as well. It runs on its own cluster of servers called a ZooKeeper ensemble, separate from application’s cluster. Distributed consensus, group management, presence protocols, and leader election are implemented by the service so that the application developers do not need to reinvent the wheel by implementing them on their own.

Developers will have to use APIs through ZooKeeper’s client library, which has language bindings for almost all popular programming languages. The client library is responsible for the interactions of an application with the ZooKeeper service. For testing with API access one can alternatively use its Java-based command-line shell (zkCli.sh)

$ zkCli.sh -server zknode:2181

How Zookeeper works

Data Model

ZooKeeper allows distributed process to coordinate with each other through a shared hierarchical namespace of data registers (znodes). The hierarchy start with root node which has child znode(s). Each znode can have their children, as well as store its own data (hence the name data register). The data in a znode is stored in byte format for a maximum of 1MB (ZooKeeper by design is just a coordinator service of host application, so its own data set size is fairly small).

Zookeeper data model

Znodes have two types (set at time of creation)

persistent znode: for storing persistent data, such as configuration. The znodes and their data will exist even if the creator client dies.
ephemeral znode: deleted by ZooKeeper service when the creating client’s session ends (due to disconnection or explicit termination). It can also be explicitly deleted by creator client through delete API call. They cannot have children. Their visibility is controlled by ACL policy

ZooKeeper can assign an incremental sequence number as part of znode name during its creation. This makes a sequential node. Both persistent znode and ephemeral znode can be either sequential or not.

In typical client-server architecture, server is passively open and do not initiate communication to client. Client pulls information from server. This is however an anti-pattern for large scale distributed system. ZooKeeper implements a Watch mechanism where clients can get notifications from ZooKeeper service, instead of having to poll for events. Clients can register with the ZooKeeper service (by setting a watch on znode) for any changes associated with a znode. A watch will only trigger notification once, and needs to be re-registered (by client) for trigger the next notification. A watch is triggered upon:

Any changes to the data of a znode;
any changes to the children of a znode;
Creation of deletion of a znode

ZooKeeper guarantees that notifications are delivered in the order of event occurrence. When a client disconnects from ZooKeeper server, it doesn’t receive any watches until the connection is re-established.

API Operations

The ZooKeeper operations are:

Operation	Description
create	Creates a znode in the specified path
delete	Deletes a znodes from the specified path. Not allowed if the znode has children. version number required
exists	Check if a znode at the specified path exists, and get version number; support watch
getChildren	Get a list of children of a znode; support watch
getData	get the data associated with a znode; support watch
setData	writes data into the data field of a znode. Version number required.
getACL	get the ACL of a znode
setACL	set the ACL in a znode
sync	synchronizes a client’s view of a znode

The write operations (setData, create, delete) are atomic, durable and eventually consistent. Every znode has a stat structure including cZxid, mZxid an dpZxid that keeps track of the ID of the transactions that created, last modified this znode, or pertains to adding or removing its children.

Production znode ensemble with more than one node is running in quorum mode. Updates to ZooKeeper tree by clients must be persistently stored in this quorum of nodes for a transaction to be completed successfully. Odd number of node is recommended to avoid split-brain where network partition causes two subsets of servers in the ensemble function independently, and different clients get different results for the same requests, depending upon the server they are connected to.

All ZooKeeper nodes are listed in the configuration for client application to randomly pick from and try to connect and establish a session. The session is associated with every operation the client executes in a ZooKeeper service. The session also has a timeout period specified by the application client during session establishment. If the connection remains idle for more than the timeout period, the server expires the session. Appropriate session timeout should be set based on network condition. Sessions are kept alive by client sending heartbeat to ZooKeeper service. Application developer needs to handle connection-loss scenarios properly.

Leader Election and Atomic Broadcast

ZooKeeper ensemble contains a leader nodes, follower nodes and observer nodes.

The leader node is elected by the cluster. It handles all write requests.
The follower nodes are leader candidates that are not elected. They are backup to the leader nodes. They handle read request, and receive the updates proposed by the leader, and through a majority consensus mechanism, a consistent state is maintained across the ensemble.
The observer nodes are ineligible as leader candidates. They have otherwise the same function as followers.

The service relies on the replication mechanism to ensure that all updates are persistent in all servers that constitute the ensemble. This is the core mechanism in ZooKeeper, implemented as a special atomic messaging protocol called ZooKeeper Atomic Broadcast (ZAB). ZAB (a variant of Paxos algorithm) ensures the election of new leader in the event of old leader crash, and ensures integrity of data. It defines three states (looking, following and leading) of a node, and goes through four phases (election, discovery, sync, broadcast) in its operation.

All read requests (exists, getData, getChildren) are process locally by the ZooKeeper node where the client is connected to. This makes read operation fast. All write requests (create, delete, and setData) are forwarded to the leader in the ensemble, which carries out the client request as a transaction. A transaction is identified by zxid and is idempotent. Transaction also satisfies the property of isolation (no transaction is interfered with by any other transaction). Only after a majority of the followers acknowledge that they have persisted the change does the leader commit the update.

Transaction processing involves two steps in ZooKeeper: leader election and atomic broadcast. This resembles a two-phase commit protocol (which also includes a leader election and an atomic broadcast)

ZooKeeper use local storage to persist transactions. The transactions are logged to transaction logs, in sync’ed write, requiring a dedicated block device separated from boot device of server. The local storage also keep point-in-time copies (snapshots) of the ZooKeeper tree.

ZooKeeper Recipes

The ZooKeeper recipes defines high-level implementation (construct) of some common distributed coordination mechanism:

Barrier: any thread/process must stop at this point and cannot proceed until all other threads/processes reach this barrier.
Queue: allow FIFO in distributed system
Lock: Fully distributed locks that are globally synchronous, meaning at any snapshot in time no two clients think they hold the same lock.
Leader Election: designate a single process as the organizer of some task distributed among several nodes.
Group membership: node may join or leave a group, which needs to be made available to clients. An alternative to ZooKeeper to manage group membership is gossip protocol.
Service discovery: help client to determine IP and port for a service that are hosted by multiple servers.
Two-phase commit: a mechanism for atomic commitment in two steps: first a commit request phase involving a voting by participants; and second, either a commit action, or an abort action, based on the voting result.

Zookeeper Administration

The official documentation includes all we need to know about administration. In addition, we need to configure log4j for proper logging. As best practices, we also should turn off swapping on ZooKeeper. We should clean up the data directory periodically if auto purge is not enabled. For optimal performance, ZooKeeper transaction log should be configured in a dedicated device.

For monitoring, ZooKeeper responds to a small sets of four-letter commands issued through telnet or nc to server’s client port. This allows the admin to check health of server or diagnose any problems. This requires the following property in zoo keeper config:

4lw.commands.whitelist=stat, ruok, conf, isro, wchc

The value can be set to asterick to allow all four-letter keyword. Once enabled, we can check server status

$ echo ruok | nc localhost 2181
imok

More four-letter commands are listed here. Apart from the four-letter commands, ZooKeeper can also be managed through Java Management Extensions (JMX).

Conclusion

Apache ZooKeeper is a coordination service for distributed application. It has become the solution for high availability for many other projects. Some of Apache’s well known open-source distributed services include:

Apache Hadoop (an umbrella of projects including many components for BigData processing such as Hadoop Common, Hadoop Distributed File System (HDFS), Hadoop YARN (yet another resource negotiator) and Hadoop MapReduce)
Apache HBase: non-relational database on top of HDFS
Apache Hive: data warehouse with SQL-like interface
Apache Kafka: stream processing
Apache Nifi: automated data flow processing.

Some of them, such as Nifi, has an embedded implementation of ZooKeeper ensemble if there isn’t a separate ensemble. There is some limitation with embedded Zookeeper ensemble. First, we cannot start ZooKeeper without starting Nifi service on the same server. Second, we need to orchestrate the configuration so that the ZooKeeper ensemble does not grow too large. We need to keep in mind that the ZooKeeper ensemble is a separate cluster of its own, and the it is not recommended to have more than 7 nodes on ZooKeeper.