Run it on linux, compile it for speed, use one of the higher memory configurations for it.
Lots of tips online for optimizing a mysql server. If your on linux, try compiling it yourself with the best optimization flags you can put your mitts on (-funroll-loops -O3 or -O6 if you can get it to work..) I've got a thread in the linux forum with resources for it. If you're on windows, you dont have quite as many options short of looking into the code for ways to optimize the queries..
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