I have an AWS instance that I shutdown the following way:
Turned off all services at once with "Shutdown all services" button.
Turned off Ambari server
AWS shutdown all instances at once.
Unfortunately starting them all up again the reverse way, it failed at Zepplin with an error saying it couldn't create /var/run/zepplin due to bad permissions. I manually followed the symlink to /run directory and changed perms to 777 so other services could create directories under it. Then everything started fine. I suspect this is a bug in the Zepplin service start function?