Virtual PCs started as an elaborate game of "let's pretend", in which we simulated a real PC (that is, a physical-hardware PC) in software. A virtual PC doesn't exist -- at least not in any tangible form. It has a processor and memory and disk drives and all the things we normally associate with a PC, but they are all constructed in software. The processor is emulated in software. The memory is emulated in software. The disk drive... you get the idea.
Virtualization offers several advantages. We can create new virtual PCs by simply running another copy of the virtualization software. We can move virtual PCs from one host PC to another host PC. We can make back-up images of virtual PCs by simply copying the files that define the virtual PC. We can take snapshots of the virtual PC at a moment in time, and restore those snapshots at our convenience, which lets us run risky experiments that would "brick" a real PC.
We like to think that virtual PCs are the same as physical PCs, only implemented purely in software. But that is not the case. Virtual PCs are a different breed. I can see three areas that virtual PCs will vary from real PCs.
The first is storage (disk drives) and the file system. Disk drives hold our data; file systems organize that data and let us access it. In real PCs, a disk drive is a fixed size. This makes sense, because a physical disk drive *is* a fixed size. In the virtual world, a disk drive can grow or shrink as needed. I expect that virtual PCs will soon have these flexible disk drives. File systems will have to change; they are built with the assumption of a fixed-size disk. (A reasonable assumption, given that they have been dealing with physical, fixed-size disks.) Linux will probably get a file system called "flexvfs" or something.
The second area that virtual PCs vary from real PCs is virtual memory. The concept of virtual memory is older than virtual PCs or even virtual machines in general (virtual machines date back to the mainframe era). Virtual memory allows a PC to use more memory than it really has, by swapping portions of memory to disk. Virtual PCs currently implement virtual memory because they are faithfully duplicating the behavior of real PCs, but they don't have to. A virtual PC can assume that it has all memory addressable by the processor and let the hypervisor handle the virtualization of memory. Delegating the virtualization of memory to the hypervisor lets the "guest" operating system become simpler, as it does not have to worry about virtual memory.
A final difference between virtual PCs and real PCs is the processor. In a physical PC, the processor is rarely upgraded. An upgrade is an expensive proposition: one must buy a compatible processor, shut down the PC, open the case, remove the old processor, carefully install the new processor, close the case, and start the PC. In a virtual PC, the processor is emulated in software, so an upgrade is nothing more that a new set of definition files. It may be possible to upgrade a processor "on the fly" as the virtual PC is running.
These three differences (flexible file systems, lack of virtual memory, and updateable processors) show that virtual PCs are not the same as the "real" physical-hardware PCs. I expect that the two will diverge over time, and that operating systems for the two will also diverge.
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