I got error like Phusion Passenger is currently not serving any applications.
while trying to restart passenger with passenger-config restart-app
comm
I am betting your passenger is running.
If you look at step 3, it hints at what I am talking about.
https://www.phusionpassenger.com/library/install/nginx/install/oss/trusty/
Nginx will take care of passenger for you if it's set up to do that. Can you try the command in that tutorial and look for passenger processes too ?
sudo /usr/sbin/passenger-memory-stats
Good luck!