Hi Srihari,
You can have multiple instances of MongoDB on the same server but you have to give each one its own port to listen to, and it own --dbpath directory to put its files. You can also specify separate logpath and pidFilePath.
For example:
mongod --dbpath <path1> --port <port_number1>
mongod --dbpath <path2> --port <port_number2>
You can configure this information in configuration file as well.
Please refer to Run Multiple Database Instances on the Same System for more insights.
The links provided here are for MongoDB v3.2. For other versions of MongoDB, see the appropriate version of the MongoDB Manual.
Point to be noted here is that doing so, all mongod processes would compete for the same resources (RAM, I/O bandwidth etc.).
Regards,
Pooja