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Sun Blade System at Tokyo's Human Genome Center Debuts on Top500 Supercomputer List


By Bernadette Toner

A 54-teraflop computer installed earlier this year at the University of Tokyo's Human Genome Center has debuted at the No. 69 spot on the latest Top500 list of the world's fastest supercomputers.

The 5,760-core Sun Microsystems blade system, dubbed "Shirokane," is the second-fastest life science computer on the list. It follows the 97.1-teraflop, 18,176-core "Chinook" HP cluster at Pacific Northwest National Laboratory’s Environmental Molecular Sciences Laboratory, which holds the No. 34 spot in the current list — down from the No. 20 spot in the last version of the twice-yearly ranking, released in November 2008.

Rounding out the list of life science systems on the current Top500 are a 30.1-teraflop Dell system at Arizona State University and the Translational Genomics Research Institute, at the No. 160 spot; IBM’s 18.7 teraflop "Blue Protein" system at the AIST Computational Biology Research Center in Japan, which holds the No. 393 spot; and a 17.2-teraflop IBM cluster at an undisclosed "life science" organization that came in at No. 495 (see Table 1, below, for details of the life science systems on the list).

The 15.6-teraflop Dell “Bio-X2” machine at Stanford University’s Biomedical Computational Facility, which held the No. 362 spot in the November 2008 list [BioInform, Nov. 21, 2008], did not make the 17.1-teraflop minimum performance requirement for the current list.

As for the top contenders on the current Top500, the 1.1-petaflop IBM "Roadrunner" system at Los Alamos National Laboratory and a 1-petaflop Cray XT5 supercomputer at Oak Ridge National Laboratory still hold the No 1 and No. 2 spots, respectively.

HP retains its lead as the manufacturer with the most installed systems in the Top500 list, with 212 systems, an increase of three systems since the November 2008 ranking. IBM, which claimed 186 systems on the list six months ago, has 188 installed systems this time around.

Despite the overall dominance of HP and IBM, the Top500 list organizers note that Cray’s XT system series "is very popular for big customers," with 10 systems, or 20 percent of the top 50 computers in the list. Cray and Sun both claim 20 systems in the total list, while Dell follows with 14 (see Table 2, below, for details on manufacturer rankings).

Clusters remain the most common architecture in the Top500, with the rankings nearly unchanged from the November 2008 list: there are 410 cluster-based systems in the current list compared to 409 six months ago (see Table 3, below, for details).

Quad-core processor-based systems have "taken over" the Top500, according to the list organizers, and are now found in 383 systems, compared to 336 six months ago, while 102 systems in the current list are based on dual-core processors, down from 153 in the last version of the list. Only four systems still use single-core processors.

The HPC community is clearly moving to adopt systems beyond four cores. Four of the current Top500 systems use IBM's 9-core Sony PlayStation 3 processor, and two of the Cray systems are using six-core Shanghai AMD Opteron processors (see Table 4, below, for details).

The Linpack benchmark, which is used to determine the Top500 ranking, "can utilize multi-core processors very well, which led to performance levels increasing above average across the whole list," the Top500 organizers said.

A total of 399 systems now use Intel processors, an increase from 379 systems in November 2008. IBM Power processors are the second most commonly used processor family with 55 systems, down from 60 six months ago. The AMD Opteron claims 43 systems in the current list, down from 59 in November 2008.

On the operating system front, the share of Linux machines increased to 443 systems from 439 in the November ranking. “Mixed” operating systems were the next-most popular, with 29 systems on the Top500, followed by Unix machines, which made up 22 systems on the current list.

There are five Windows systems on the current list, including a Dawning 5000A at the Shanghai Supercomputer Center, which the Top500 organizers deemed "notable" because it is "the largest system which can be operated with the Windows HPC 2008 operating system." The 30.7-teraflop machine holds the No. 15 spot on the list.

The complete Top500 ranking is available here.