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Two Life Science Systems Dropped from Latest Top500 Supercomputer Ranking

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By Bernadette Toner

The latest roundup of the world's fastest supercomputers has two fewer life science machines than it did six months ago, when the Top500 list included seven systems dedicated to life science computing (BI 11/19/2010).

Two life science computers — a 35.8-teraflop Dell system at the Howard Hughes Medical Institute's Janelia Farm Campus and a 34.7-teraflop Fujitsu system at the Laboratory for Systems Biology and Medicine at the University of Tokyo — did not meet the 40.1-teraflop benchmark for inclusion in the 37th edition of the twice-yearly ranking.

The fastest life science machine remains a 97.1-teraflop, 18,176-core HP cluster at Pacific Northwest National Laboratory’s Environmental Molecular Sciences Laboratory. The system, dubbed "Chinook," debuted at the No. 20 spot in the Top500 in November 2008 and has held the title of the fastest life science machine since that time. The PNNL computer is currently ranked No. 91 on the Top500 list, down from No. 75 in the October 2010 version of the ranking.

Four other life science systems remain from the October list: a 54-teraflop, 5,760-core Sun Microsystems blade system at the University of Tokyo's Human Genome Center that is now No. 230, down from No. 138 in October; a 53.1-teraflop, 8,640-core system at the Georgia Institute of Technology's Center for the Study of Systems Biology that slipped to the No. 251 spot from No. 140 six months ago; a 48.1 teraflop, 8,064-core HP Cluster Platform at MD Anderson Cancer Center, which debuted at No. 169 on the list in October but is now ranked No. 339; and a 47.3-teraflop, 5,040-core IBM iDataPlex at the BC Genome Science Center machine, which came in at No. 350, compared to No. 178 six months ago (see Table 1, below, for details of the life science systems on the list).

HPC Trends

The Top500 list underscores how the rapidly the field of high-performance computing is advancing. For example, the June 2008 Top500 list marked the first time a system broke the one-petaflop barrier, but the top 10 systems on the current list all boast performance of a petaflop or more.

Meantime, the fastest system on the list, the K Computer at the RIKEN Advanced Institute for Computational Science, achieved 8.16 petaflops on the Linpack benchmark — more powerful than the next five computers on the list combined. Its developers aim to eventually achieve performance of 10 petaflops (the computer’s name derives from the Japanese word "Kei" for 10 quadrillion).

The K Computer, built by Fujitsu, is built with 68,544 SPARC64 VIIIfx CPUs, each with eight cores, for a total of 548,352 cores — nearly twice as many as any other system in the Top500list.

While there has been a recent trend in the Top500 to use graphics processing units in combination with standard CPUs to gain additional speed — 19 systems on the current list rely on GPUs for a performance boost — the Riken system does not use GPUs or other accelerators.

The K Computer displaced the Tianhe-1A supercomputer at the National Supercomputing Center in Tianjin, China, which secured the No. 1 spot on the October 2010 list with a performance at 2.56 petaflops.

IBM has maintained its position as the top supercomputing vendor, with 212 systems on the current list — an increase of 12 placements over the November ranking. HP and Cray took second and third place in the manufacturer ranking, with 155 and 29 placements in the current list, respectively (see Table 2, below, for details on manufacturer rankings).

Clusters remain the most common architecture for systems in the Top500 list, though the latest list marks the second consecutive drop in the total number of clusters. The current ranking includes 411 clusters, which represents a drop of four from the October list. There were 424 cluster-based systems one year ago.

Massively parallel processing systems, meantime, are gaining ground with 87 systems in the current list, compared to 83 in October and 74 a year ago (see Table 3, below, for details).

Intel continues to provide processors for the most systems on the list — 386 computers on the current ranking run Intel chips, though this is down from 398 six months ago. The company's Westmere processors comprise 169 systems on the list now, compared with 56 in October.

AMD's Opteron family follows Intel with 66 systems, up from 57 six months ago, while IBM Power processors increased to 45 systems from 40 in October (see Table 4, below, for details).

Quad-core processors are used in 231 systems on the Top500 list, a decrease from 365 quad-core systems six months ago. The current ranking includes 212 machines that use processors with six or more cores — a dramatic increase from 95 such systems in the October ranking.

In terms of operating systems, Linux continues to be the dominant choice, with 455 computers in the current list, though this is a slight dip from 459 in the October ranking. Unix systems were the next most popular, with 23 systems on the current list, followed by "mixed" operating systems with 15 (see Table 5, below, for details).

The complete Top500 ranking is available here.


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