Hi Pankaj,
I user ServerPilot to configure my Ubuntu servers. There is no any caching enabled and its a standard PHP-FPM.
Im running few joomla sites with this server without any issues.
I also try to install JA Intranet template on the same server and it works fine (details added in site credentials). However JA Educatcy seems not working. Can you look at it again as it seems not a server issue.