1. A method of diagnosing faults in an emulated computer system that includes--an instruction processor, coupled to a memory, which directly executes a set of native instructions; a plurality of foreign user programs in said memory, each of which is a compilation of foreign instructions and data; a foreign operating system in said memory, which is a compilation of said foreign instructions under which said foreign user programs are run; an emulator program in said memory, which is a compilation of said native instructions that interprets said foreign instructions; a plurality of native user programs in said memory, each of which is a compilation of said native instructions; and, a native operating system in said memory which is a compilation of said native instructions under which said emulator program and said native user programs are run; wherein said method includes the steps of: providing a heterogeneous diagnostic program in said memory which is a compilation of said native instructions that reads all of said foreign user programs and said foreign operating system from said memory and stores them on a magnetic media, but reads and stores none of said native user programs; initiating the execution of said heterogeneous diagnostic program in response to the occurrence of a user selectable event; and, executing said heterogeneous diagnostic program while said native user programs are running and under control of said native operating system.