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Yes you have to set the latency buffer of the native system kind of similar to the TDM system if you want to make an even comparison.
The biggest advantage of TDM is still the 'real-time' behaviour, but native is getting really close now.
Also, there's lots of benchmarking of native systems going on in the nuendo forum, they have also compared a quad woodcrest system (the xeon processors in the Mac Pro) to a quad Opteron system.
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