Exadata: how to backup system before upgrade rpm packages?
Answer is the following:
Create LVM Snapshot-Based Backup for your OS.
Refer below link in steps to perform the same. 
https://docs.oracle.com/cd/E50790_01/doc/doc.121/e51951/db_server.htm#DBMMN22020 
2 Maintaining Database Servers of Oracle Exadata Database Machine 
Section: 
Creating a Snapshot-Based Backup of Oracle Linux Database Server