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 and a printer, and any applications that are present on your system. Any program input through a command line or a Graphical User Interface (GUI) is processed by sending an Application Program Interface (API) request to the OS. On a web server, each application runs within the parameters set by the OS as well - priority, physical memory, processing time, etcetera. This goes for both standard website scripts and server-side software like a media server. If a virtual server is created on a physical one, there can be two different Operating Systems, called guest OS and host OS, so you will be able to set up a different software environment on the same machine.