Harpertown: New 45nm Xeons from Intel
Posted on: 09/17/2007 05:00 AM

MyriMatch
MyriMatch is a tool designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins. Whether the program is being run in a single-computer environment or across an entire cluster of processing nodes, it is able to optimally divide work in a much more efficient way than many other database search programs. This is because it only generates candidate sequences from the known database once for the entire set of spectra instead of once for every spectrum. Thus, for each candidate sequence generated, it is compared against every spectrum. The spectra keep a certain (user-defined) number of candidate sequences that had the highest scores.

MyriMatch is designed to take advantage of (symmetric) multiprocessor systems by multithreading the database search. A search process on an SMP system will spawn one worker thread for each processing unit (where a processing unit can be either a core on a multi-core CPU or a separate CPU entirely). The main thread then generates a list of žworker numbersÓ which is equal to the number of worker threads multiplied by this parameter. The worker threads then take a worker number from the list and use that number to iterate through the protein list.
MyriMatch is the last of the new workloads that you will see in this article. It is a pretty complex test that I'm not sure if I even understand.

MyriMatch is designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins.



In a strange turn of events, the Woodcrest Xeons take this test. All I can figure is that the memory bus is getting seriously bogged-down with all those hungry cores looking for data to process. The database being searched is loaded completely into system memory, and it looks like Woodcrests four cores access that memory better under high stress than the quad-core Xeons.

Power Usage



"Performance-per-Watt"



The Woodcrest Xeons squeaked-out a win in MyriMatch performance, and that directly correlates to the overall power usage and the "performance-per-watt" numbers as well.


Printed from 2CPU.com (http://www.2cpu.com/contentteller.php?ct=articles&action=pages&page=harpertown_new_45nm_xeons_from_intel,12.html)