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Debian 8 php 5.6.33 phpfpm Virtualmin 6 (upgraded from 5.99)
If I change the php execution mode from PHPFPM to FCGId I got a:
Changing PHP execution mode to FCGId (run as virtual server owner) ..
Failed to save website options : No PHP command found!
I suspect that the problem came up after the upgrade from 5.99 to 6. (I've done it updating the ATP repository)