Methods and systems for resolving clock management issues in emulation of a target system on a host system are disclosed. A first set of code instructions of a target program is emulated to generate a first set of emulated instructions that emulate a first component on the host system. A second set of code instructions is emulated to generate a second set of emulated instructions that emulate a second component of the target system on the host system. The first set is executed based on a first clock (which may be a fixed clock) and the second set is executed based on a second clock (which may be a variable clock). The host system adjusts the first or second clock, execution of the first or second sets of instructions or a memory access to maintain a desired synchronization between the first and second sets of instructions.
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