Each and every desktop or notebook or web server is run by an Operating System - the low-level program which interacts with the hardware, including peripheral devices such as a mouse or a printer, and any apps that are currently installed on the system. Any program input using a command line or a Graphical User Interface (GUI) is processed by sending an Application Program Interface (API) request to the OS. On a server, each app runs within the parameters set by the OS as well - priority, physical memory, processing time, etcetera. This is valid for both standard site scripts and server-side software like a media server. In case a virtual server is set up on a physical one, there can be two independent Operating Systems, called guest OS and host OS, so you will be able to set up a different software environment on a single machine.