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One New Life Science Machine Joins Top500 Supercomputer List as Two are Dropped

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By Bernadette Toner

A 63.9-teraflop computer at the Polish Academy of Science's Institute of Bioorganic Chemistry has debuted in the No. 298 spot in the latest version of the Top500 list of the world's fastest supercomputers, released this week at the SC11 supercomputing conference.

The system, housed at the Poznan Supercomputing and Networking Center, was manufactured by Rackable and includes 5,540 cores.

Two life science computers — a 48.1 teraflop, 8,064-core HP Cluster Platform at MD Anderson Cancer Center and 47.3-teraflop, 5,040-core IBM iDataPlex at the BC Genome Science Center — did not meet the 50.9-teraflop benchmark for inclusion in the latest edition of the twice-yearly ranking.

A total of four life science systems reside on the current list, but none of them broke into the top 100.

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, which 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 system is currently ranked No. 127 on the Top500 list, down from No. 91 in the June 2011 version of the ranking (BI 6/24/20110).

Two other life science systems remain from the June ranking: a 54-teraflop, 5,760-core Sun Microsystems blade system at the University of Tokyo's Human Genome Center that is now No. 414, down from No. 230 in June; and a 53.1-teraflop, 8,640-core system at the Georgia Institute of Technology's Center for the Study of Systems Biology that fell to the No. 444 spot from No. 251 six months ago (see Table 1, below, for details of the life science systems on the list).

Breaking the 10-Petaflop Barrier

The Top500 list reached a new milestone with the debut of the first system to break the 10-petaflop barrier — Japan’s K Computer, which underwent an upgrade since June that secured it the No. spot with a speed around four times as powerful as its nearest competitor.

Installed at the Riken Advanced Institute for Computational Science, the 705,024-core K Computer reached 10.51 petaflops on the Linpack benchmark. The same system achieved 8.16 petaflops in June.

K Computer broke the 10-petaflop barrier just three and a half years after the Top500 list reached the one-petaflop milestone in June 2008.

"Contrary to many other recent very large systems, [K Computer] does not utilize graphics processors or other accelerators," the Top500 organizers noted in a statement.

China's 2.57-petaflop Tianhe-1A system retains the No. 2 position that it held six months ago, and the remaining systems in the top 10 were also unchanged from the June list.

“This is the first time since we began publishing the list back in 1993 that the top 10 systems showed no turnover,” said Top500 editor Erich Strohmaier.

Other high-performance computing trends underscored by the current list include a sharp rise in the use of GPUs as accelerators — to 39 from 17 six months ago. Of these, 35 use Nvidia chips, two use Cell processors, and two use ATI Radeon.

Multicore systems also continue to advance, with 310, or 62 percent, of the systems in the current list boasting processors with six or more cores. The June list included 212 systems with six or more cores.

Intel remains the leading provider of processors for systems on the Top500 list, though its share has remained stable, with 384 of the total systems as opposed to 386 in the June list.

Intel is followed by the AMD Opteron family, with 63 systems, down from 66 in June; while IBM Power processors run 49 systems in the current list, a slight increase from 45 six months ago.

IBM has held onto its lead as the leading vendor for high-performance computing systems with 223 systems on the current list, an increase of 11 over the June list.

HP is still the second most common vendor on the list, though its share of Top500 systems slipped to 141 from 155 six months ago (see Table 2, below, for details of manufacturer rankings).

Clusters retain their lead as the most popular architecture for systems in the Top500 list, though massively parallel processing systems are gaining ground. The current ranking includes 89 MPP systems, an increase from 87 in the June list and 83 in the November 2010 list (see Table 3, below, for details).

Linux continues to be the dominant choice for HPC operating system, with 457 computers in the current list, a slight increase over 455 in the June ranking. Unix systems were the next most popular, with 30 systems on the current list, followed by "mixed" operating systems with 11 (see Table 4, below, for details).

The complete Top500 ranking is available here.


Have topics you'd like to see covered in BioInform? Contact the editor at btoner [at] genomeweb [.] com.

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