Step followed - 

Step1: To add init script that will copy the keystore file in the tmp location.

Step2: To add spark config in cluster advance options - 

spark.driver.extraJavaOptions -Djavax.net.ssl.keyStore=/tmp/keystore.jks -Djavax.net.ssl.keyStorePassword=<pass>
spark.executor.extraJavaOptions -Djavax.net.ssl.keyStore=/tmp/keystore.jks -Djavax.net.ssl.keyStorePassword=<pass>

After doing above configuration the cluster doesn't execute any commands. In log4j driver logs their is a constant error message. What is the recommended way to achieve mongo atlas X.509 connectivity?

Error Could not connect to mdb7sywh50xhpr.chkweekm4xjq.us-east-1.rds.amazonaws.com:3306 : readHandshakeRecord