Containerization of Spark Python Using Kubernetes

Introduction

In this blog, we have detailed the approach of how to use Spark on Kubernetes and also a brief comparison between various cluster managers available for Spark.

Spark

Spark is a general-purpose distributed data processing engine designed for fast computation. The main feature of Spark is its in-memory cluster computing that increases the processing speed of an application. It supports workloads such as batch applications, iterative algorithms, interactive queries and streaming.

During execution, it creates the following components:

Driver
Executor

To manage these components, there is a cluster manager that takes care of resource allocation. Following are the various options available for cluster manager:

Standalone
Apache Mesos
Hadoop YARN
Kubernetes

Standalone Cluster Manager

To use Spark Standalone Cluster manager and execute code, there is no default high availability mode available, so we need additional components like Zookeeper installed and configured.

Hadoop YARN

YARN (Yet Another Resource Negotiator) focuses on distributing MapReduce workloads and is majorly used for Spark workloads.

Apache Mesos

The Mesos kernel runs on every machine and provides applications with APIs for resource management, scheduling across the entire datacenter, and cloud environments. It provides a cluster manager which can execute the Spark code.

Kubernetes

It uses the kube-api server as a cluster manager and handles execution.

Comparison between Hadoop YARN and Kubernetes – as a cluster manager

Brief introduction Kubernetes and its components

Kubernetes is a container orchestration engine which ensures there is always a high availability of resources.
Apart from that it also has below features.

Self healing
Automatic rolling updates and rollback
Resource management
Service discovery
Load balancing
Service discovery

Architecture of Kubernetes

The architecture of Kubernetes has 2 major components, they are:

1. Master components

All the requests from the user using API, kubectl are sent to master component that is the API Server

API Server converts json or yaml requests to http call
ETCD contains the details of the cluster and its components and current state
Controller ensures that the cluster is always in the desired state
Scheduler takes care of object creation based on resource availability

2. Node components

The following are the components that are come under the nodes:

Kubelet is the agent which takes care of the execution of the tasks which have been assigned to it and reports back the status to the api server
Kube Proxy is the networking component that takes care of networking related tasks
Container Runtime it provides an environment on the nodes for container execution

Other components

Kubectl: a utility used to communicate with the Kubernetes cluster

Spark execution on Kubernetes

Below is the pictorial representation of spark-submit to API server.

We can use spark-submit directly to submit a Spark application to a Kubernetes cluster. Once submitted, the following events occur:

Creation of a Spark driver running as a Kubernetes pod.
Creation of executors which are also run within Kubernetes pods, connects to them, and executes the application code
Termination and clean up of executor pods occur when the application completes. But the driver pod persists, logs and remains in “completed” state in the Kubernetes API until it’s eventually garbage collected or manually cleaned up.

There are 2 options available for executing Spark on a EKS cluster:

Option 1: Using Kubernetes Master as Scheduler
Option 2: Using Spark Operator

Option 1: Using Kubernetes master as scheduler

Below are the prerequisites for executing spark-submit using:

A) Docker image with code for execution
B) Service account with access for creation of pods, services, secrets
C) Spark-submit binary in local machine

A. Creating Docker image for Java and PySpark execution

Download Spark binary in the local machine using this link https://archive.apache.org/dist/spark/
In this path spark/kubernetes/dockerfiles/spark there is Dockerfile which can be used to build a docker image for jar execution
Ensure that you are in the Spark directory as it needs jars and other binaries to be copied. So it uses all the directories as context.

docker build -t spark:latest -f kubernetes/dockerfiles/spark/Dockerfile .

Once this image is built, it can be used as a base image for the other code execution.

Docker image creation for PySpark code execution:

In this path: spark/kubernetes/dockerfiles/spark/bindings/python there is a ready Docker file which will be used for PySpark execution.

Ensure that you are in the Spark directory as it needs jars and other binaries to be copied so it will use all the directories as context.

docker build -t sparkpy:latest -f \
kubernetes/dockerfiles/spark/kubernetes/dockerfiles/spark/bindings/python/Dockerfile .

B. Creating Kubernetes service account and cluster-role binding

Components that will be used:

Service account: an account which will be used for authentication of processes running inside the pods
Cluster-Role: defines the access for the service account across the cluster
Cluster-Role Binding: binds and creates the role with the service account

Create a yaml file with below contents

apiVersion: v1
kind: ServiceAccount
metadata:
  name: spark-sa
---
kind: ClusterRole
apiVersion: rbac.authorization.k8s.io/v1
metadata:
  namespace: default
  name: spark-role
rules:
- apiGroups: [""]
  resources: ["pods", "services", "configmaps" ]
  verbs: ["create", "get", "watch", "list", "post", "delete"  ]
---
kind: ClusterRoleBinding
apiVersion: rbac.authorization.k8s.io/v1beta1
metadata:
  name: spark-role-binding
subjects:
- kind: ServiceAccount
  name: spark-sa
roleRef:
  kind: ClusterRole
  name: spark-role
  apiGroup: rbac.authorization.k8s.io
kubectl apply -f rbac.yaml

Getting cluster information:

kubectl cluster-info

This command gives the master url it and it will look as shown below

Kubernetes master is running at

https://ABCDZZZZZZZZZZZZZZZ.sk1.region.eks.amazonaws.com

Make a note of this url

C. Executing Spark-submit:

Now go to the directory which has Spark binary and use the below command:

./spark-submit  
--deploy-mode cluster
--master <master_url> 
--conf spark.kubernetes.authenticate.driver.serviceAccountName=spark-sa
--name spark-pi
--conf spark.executor.instances=5  
--conf spark.kubernetes.driver.container.image=<docker image with code>  
--conf spark.kubernetes.executor.container.image=<docker image with code>  
local:///opt/spark/examples/src/main/python/pi.py

The driver and executor will be created with whatever name is specified as app name. Using the driver pod we can view logs, access url below commands can be used for it.

To view logs

kubectl logs -f spark-pi-1581014997671-driver

To view spark ui

kubectl port-forward (driver-pod-name) 4040:4040

Post execution, the drivers will be available based on the execution state, until it is deleted manually.

Additional useful options that can be used with Spark-submit

Environment Variables:

When the script requires any environment variable that need to be passed, it can be done using Kubernetes secret and referred to it. Details of achieving this are given below.

“spark.kubernetes.executor.secretKeyRef.DB_PASS”: “snowsec:db_pass”,

Create a secret with the name snowsec and in that db_pass is the key and which will be referred to the spark environment using DB_PASS.

Adding labels to the pod:

When we want to add additional labels to pod we can use below options

For driver pod: spark.kubernetes.driver.label.[LabelName]
For executor pod: spark.kubernetes.executor.label.[LabelName]

Using node affinity:

We can control the scheduling of pods on nodes using selector for which options are available in Spark that is

spark.kubernetes.node.selector.[labelKey]

Option 2: Using Spark operator on Kubernetes

Operators

Operator is a method of packaging, deploying and managing a Kubernetes application. Kubernetes application is one that is both deployed on Kubernetes, managed using the Kubernetes APIs and kubectl tooling.

Using Spark operator on Kubernetes

Official link https://operatorhub.io/operator/spark-gcp

Installing Kubernetes operator on EKS:

Prerequisites:

Helm needs to be installed and configured
Verify Helm installation using below command

helm version –short

Adding Helm repo to running EKS
Helm repo add incubator http://storage.googleapis.com/kubernetes-charts-incubator
Installing Helm repo on EKS :

helm install incubator/sparkoperator 
--name sparkv24 
--namespace default 
--set sparkJobNamespace=default  
--set enableWebhook=true

Verifying Installation:

helm ls

Once applied, the following components will be created:

Spark-operator-deployment
Spark-serviceaccount
Spark-rbac
Spark-operator-serviceaccount
Spark-operator-rbac
Webhook-init-job
Webhook-service

Here we need the job in yaml. Once we have yaml file, we can submit the job using the below command:

kubectl apply -f

The Yaml file looks as follows:

apiVersion: "sparkoperator.k8s.io/v1beta2"
kind: SparkApplication
metadata:
  name: spark-pi-jar
  namespace: default
spec:
  type: Scala
  mode: cluster
  image: "gcr.io/spark-operator/spark:v2.4.4"
  imagePullPolicy: Always
  mainClass: org.apache.spark.examples.SparkPi
  mainApplicationFile:     "local:///opt/spark/examples/jars/spark-examples_2.11-2.4.4.jar"
  sparkVersion: "2.4.4"
  restartPolicy:
    type: Never
  volumes:
    - name: "test-volume"
      hostPath:
        path: "/tmp"
        type: Directory
  driver:
    cores: 1
    coreLimit: "1200m"
    memory: "512m"
    labels:
      version: 2.4.4
    serviceAccount: sparkv24-spark
    volumeMounts:
      - name: "test-volume"
        mountPath: "/tmp"
  executor:
    cores: 1
    instances: 1
    memory: "512m"
    labels:
      version: 2.4.4
    volumeMounts:
      - name: "test-volume"
        mountPath: "/tmp"

Once we submit the job, it will create 2 pods:

Executor
Driver

We can verify these using

kubectl get pods

Logs by using below command

kubectl logs -f pod_name

Details of submitted job using below command

kubectl describe sparkapplication

Contains details about Web-UI, service and events that occurred during creation.

Access Web UI:

To access the Web UI for a long running job can be done using port forwarding, using the below mentioned command

kubectl port-forward (driver-pod-name) 4040:4040

Conclusion

Key considerations for Production Spark code on Kubernetes

1. Cost-Effective

No requirement of up and running infrastructure to use Spark on EKS.

2. Build and Deployments

As we deploy the Docker image with the Spark submit, so when we have code changes we need to pass the docker image with Spark submit. These images can be tagged to track the changes.

3. Ideal Use Cases

When workload is less (e.g. 8-10 hr job executions per day) and as batch processing.

4. Availability/Fault Tolerance

Kubernetes has the scheduler which manages the pods created as driver and executor. This enables the usage of pods based on resource availability. Quotas for a namespace can be assigned for better resource management.

5. Resource Tracking

We have used node selectors in Spark submit which allows us to run specific workloads on a specific node. This in turn allows us to track the usage of resources.

6. Monitoring

We have integrated Spark workloads monitoring with Prometheus and Grafana, by using Kube-state-metrics and creating a dashboard. We do a Spark submit by assigning pod labels which allow us to create custom dashboards for specific labels.

7. Logging

We have used the ELK stack for visualizing the logs.

The approach we have detailed is suitable for pipelines which use spark as a containerized service. It also ensures optimal utilization of all the resources as there is no requirement for any component, up and running before doing Spark-submit. Additionally, Spark can utilize features like namespace, quotas along with other features of Kubernetes.

About the Author

Ajaykumar Baljoshi is a Senior Devops Engineer at Sigmoid, who currently works on Containerization, Kubernetes, DevOps and Infrastructure as Code.

Previously published at https://www.sigmoid.com/blogs/containerization-of-pyspark-using-kubernetes/