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Life Science Supercomputers Surge in Latest Top500; BlueGene Systems Hit the Top Ten


The latest version of the biannual Top500 list of the world’s most powerful supercomputers includes 14 systems dedicated to life science research applications — twice as many as there were in the previous ranking, released last November [BioInform 11-24-03].

Life science systems also broke into the top ten for the first time, in the form of two prototypes for IBM’s BlueGene/L, which hold the No. 4 and No. 8 spots. Previously, the highest-ranking life science machine was the 2 Tflop/s Dell cluster installed at the Buffalo Center of Excellence in Bioinformatics, which debuted at the No. 22 spot in November 2002. That system has dropped to No. 95 on the current list. The BlueGene/L prototypes — developed in collaboration with Lawrence Livermore National Laboratory — measured 11.7 Tflop/s and 8.7 Tflop/s on the Linpack benchmark.

NEC’s vector-processor-based 35.9 Tflop/s Earth Simulator in Japan topped the list for the third year in a row, but cluster-based systems continued to gain ground over other architectures. More than half of the top 500 computers in the world are now clusters, with 291 such systems on the current version of the list — up from 208 six months ago.

The trend toward commodity chips also continued in the 23rd edition of the ranking, released June 21. The number of systems using Intel processors grew in the last six months from 189 to 287, giving Intel a 57 percent share of all the processors in the top 500, followed by IBM’s Power architecture, HP’s PA-RISC chips, and AMD processors.

IBM is the top manufacturer in the current list, with the highest overall performance as well as the largest number of installed systems. IBM has a total of 224 installed systems and an overall performance of 407 Tflop/s — 50 percent of the total installed performance for all 500 systems on the list. HP follows with 140 installed systems and a total installed performance of 151 Tflop/s. Apple, which made its debut on the Top500 sixth months ago in the form of the “SuperMac” system at Virginia Tech, does not appear in the latest ranking because the university is replacing hardware.

Big Blue also emerged as the leading manufacturer in the life science high-performance computing market, with 10 out of the 14 life science systems in the list.

Almost half the systems on the current list — 242 — exceed the 1 Tflop/s mark on the Linpack benchmark. This is up dramatically from 130 systems over the 1 Tflop/s mark six months ago.

The Top500 list is compiled by Hans Meuer of the University of Mannheim; Erich Strohmaier and Horst Simon of NERSC/Lawrence Berkeley National Laboratory; and Jack Dongarra of the University of Tennessee. The complete list is available at

— BT

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