1. A method for running a virtual machine in a computing system, comprising: (a) launching a virtual machine monitor (VMM) that handles potentially unsafe instructions; (b) launching a virtual machine (VM) running a source guest code; (c) handling interrupts in the VMM when encountering at least some privileged instructions in the source guest code, (d) continuously determining by the VMM, at runtime, if the instruction in the source guest code is safe or potentially unsafe, wherein the potentially unsafe instructions are non-privileged instructions that can execute incorrectly in a context of the VM; (e) natively executing the safe instructions in the source guest code in the VM; and (f) bypassing potentially unsafe instructions using the VMM, including (i) analyzing the source guest code to identify the potentially unsafe instructions, (ii) generating a target guest code with breakpoints to replace the potentially unsafe instructions, and (iii) executing instructions of the target guest code in a context of the VM.