I just installed the FMS 16.0.3 update. When I ran the update it gave me a message, "Unable to install update while server is running. Please stop server" Prior to running the update I had opened the Web/management screen and stopped the server.
I initially tried using fmsadmin with stop server and stop admin server. However these did not resolve the issue.
I was finally able to do the install by using the following set of fmsadmin commands:
fmsadmin Stop -f server
fmsadmin Stop -f adminserver
fmsadmin Stop -f FMSE
fmsadmin Stop -f FMSIB
fmsadmin Stop -f XDBC
fmsadmin Stop -f WPE
Once all of these had completed, the new version did install and everything appears to running correctly.
The server is a Mac Mini ( Late 2012 ) with 16 GBytes ram running OS X 10.11.6