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The binaries are the same on each virtual machine. Are there build optimizations for E3/V5 vs E5/V2 that could make such a difference?
Potentially, yes.
Either way you're not comparing apples to apples using packages from a 3rd party repo built for a different system.
Newer processors have different instruction sets (AVX is a big one). You'd want to make sure you're not only compiling it on each different platform, but also using a new enough compiler to support the instruction sets.
>>march=silvermont
gcc native thinks this e3 is silvermont, a low power SoC.
There was about a 15% performance gain. Nothing that would explain the large difference between E3 and E5.