I upgraded an existing ArcGIS 10.1 test server to 10.3.1. The installation
(upgrade) went through without any issues. I can login the local server
manager. But all services (including the system and utility services) appeared
to be “stopping …”. I could stop a service (e.g., system or utility
services), but was unable to start it. It gave this error: "Failed to start the server machine 'xxxx'. Could not start application server within stipulated time". I had rebooted my machine, checked the file/folder permissions and found no issues. The server meets the system requirements as described in http://server.arcgis.com/en/server/10.3/install/windows/arcgis-for-server-system-requirements.htm.
I can not publish a new map service as the System/PublishingTools can not be started.