Every single desktop or notebook or web server is run by an Operating System - the low-level software that interacts with the computer hardware, including peripherals such as a mouse or a printer, together with any apps 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 Operating System. On a web server, any application runs within the parameters specified by the OS as well - priority, physical memory, processing time, etcetera. This is valid for both standard website scripts and server-side software like a media server. When a virtual server is created on a physical one, there can be two different Operating Systems, named guest OS and host OS, so you'll be able to set up a different software environment on a single machine.