Could you run software in conjunction with the OS? although it might not be very practical, I am curious to know if there are any limitations that deem this impossible without regards to performance, ... etc. The way in which I could visualize the system functioning would be in the same manner in which the OS gives the illusion that multiple programs are executed at the same time in order to multitask when in reality only one program operates at a time, but in this case, it is not just the OS and the processes executing on the processor, but a program and a OS at the same time. The processor architecture which I would based this design on would be the x86.
Is it theoretically possible to run software parallel to the OS?
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At its core, a multitasking OS is nothing more than a task switcher. There are two kinds of multitasking which usually exist in parallel - co-operative (like windows 3.1) where the program is responsible for sharing resources (either "I'm waiting for this so do something else in the meantime" or "Give someone else a chance for a while") and preemptive where the OS steps in and says "You've had enough time, now give someone else a chance."
Even the most primitive CPUs have interrupts. Something happens (a key is pressed or a timer goes off) and a function is called to do something before returning to what it was doing. The return from interrupt command restores the registers and returns to the exact instruction that was about to be executed when the interrupt happened.
However, it does not have to return to the same place. When entering the interrupt routine, the return address and registers are on the stack. Take them off and save them somewhere referenced by the current task. Now take those you saved earlier from a different task and put those on the stack (return address last). Now returning from the interrupt will continue executing the task from earlier. You might also want to set a timer before you leave to set a time limit before switching tasks again.
That's the simplest form of task-switching as you describe.