The sentence examples are really too short - they simply do not give enough context in order to show the nuances of "all", "whole" and "entire".
In basic terms All the factory was on fire. - this is not particularly idiomatic - it was a construction that was more common about 200 years ago. You can say "All ofthe factory was on fire." but that does not really differ from on "The factory was on fire."
The whole factory was on fire. / The entire factory was on fire.
Whole sees the factory as a single unit;
Entire sees the factory as the sum the collection of all its smaller units; entire ~ in its entirety; complete. To me, "entire" is more emphatic.