The 3 pieces of hardware are probably going to be processor, memory and hard drive access speed.
After that it comes down to the computer programming. If you want real speed then you need a program that can break the work up to have more than one processor work on it at a time. The other problem with most Operating systems these days is they spend a lot of time doing housekeeping and checking the status of other programs. You don't notice that with the average computer use but when trying to dedicate all the processing power to one thing you should consider a pared down OS.
This board can use 4 dual core processors. Great if you have the program to run on it. A complete waste of resources if you don't.
Quote:TYAN THUNDER K8QSD-PRO S4882UG2NR-D (S4882-D) QUAD CPU DUAL CORE E-ATX SUPPORT DUAL-CORE AMD OPTERON CPU
Since your goal is to max out your processor(s) with calculations you want the best cooling you can get too. The last thing you will want are errors or failure from overheating.