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To obtain measurements that are consistent with an "idealized execution", you map all memory addresses to the same cache set. While this eliminates cache misses, it does not prevent TLB misses.
An example is the 4881c4380800005b5d415c415d415e415f benchmark ("add rsp,0x838; pop rbx; pop rbp; pop r12; pop r13; pop r14; pop r15"). The difference between your measurements/Ithemal (~6 cycles) and IACA (3 cycles) is due to TLB misses.
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