Every single PC or server is run by an Operating System - the low-level software which interacts with the hardware, including peripheral devices such as a mouse and a printer, and any applications that are present on the 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 app runs within the parameters defined by the OS as well - priority, physical memory, processing time, and so on. This goes for both standard site scripts and server-side software like a media server. In case a virtual server is generated on a physical one, there can be two different Operating Systems, called guest OS and host OS, so you'll be able to set up a different software environment on a single machine.