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Japan Contributes Two New Life Science Systems to Latest Version of Top500 Supercomputer List

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Two supercomputers dedicated to life science research — both from Japan — have joined the ranks of the world's fastest supercomputers, according to the twice-yearly Top500 list released earlier this month.

The Shirokane2 system at the University of Tokyo's Human Genome Center debuted on the list at the No. 183 spot, making it the fastest life science computing system. The 100.6-teraflop Hitachi system, which includes 16,128 cores, adds to the center's 54.2-teraflop Shirokane1 system, which debuted on the Top500 list at the No. 69 spot in June 2009 but did not make the 60.8 teraflop cutoff for the current ranking. Six months ago, the entry level for inclusion in the Top500 list was 50.9 teraflops.

The second new life science system on the twice-yearly list — an 82.9-teraflop, 5,616-core Hewlett-Packard cluster — is installed at Japan's National Institute of Genetics.

The total number of life science machines on the list holds steady at four as two systems — Shirokane1 and a 53.1-teraflop Penguin Computing system at the University of Georgia — did not make the minimum performance requirement for the current ranking.

The remaining life science systems include 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 held the title of the fastest life science machine until the current ranking. It now holds the No. 193 spot, down from No. 127 in the November 2011 version of the list (BI 11/18/2011).

Another life science holdover from the last version of the Top500 has moved up due to a system upgrade. A Rackable cluster at the Polish Academy of Science's Institute of Bioorganic Chemistry has been expanded to include 9,498 cores compared to 5,540 cores in the November lineup. The resulting performance boost — to 89.8 teraflops from 63.9 teraflops — bumped the system up in the rankings to the No. 233 spot from the No. 298 spot six months ago (see Table 1, below, for details of the life science systems on the list).

Supercomputing Trends

The fastest computer on the Top500 list is an IBM BlueGene/Q system installed at the Department of Energy’s Lawrence Livermore National Laboratory. The system, called Sequoia, comprises 1,572,864 cores and clocked in at 16.32 petaflops on the Linpack performance benchmark.

Continuing a trend that has emerged in recent years, multicore systems make up the bulk of the hardware on the list — 374 machines in the current list use processors with six or more cores, up from 310 six months ago.

Likewise, the supercomputing community is rapidly adopting accelerators or co-processors, with 57 systems in the current list using such chips, up from 39 in November. Of such systems in the current ranking, 52 use Nvidia chips, two use Cell processors, two use ATI Radeon, and one uses Intel MIC technology.

Intel continues to provide processors for the bulk of Top500 systems, with 372 machines in the current list using Intel chips. This is down from six months ago, when 384 systems ran Intel chips. The AMD Opteron family is the second most popular processor, with 63 systems in the current list, unchanged from the November ranking.

In another high-performance computing trend of note, InfiniBand technology has for the first time displaced Gigabit Ethernet as the most-used interconnect technology. In the current list, 207 systems use Gigabit Ethernet, down from 224 systems six months ago. InfiniBand-based clusters account for 208 systems on the current list.

IBM has retained its lead as the leading vendor for high-performance computing systems, though its total placements have declined to 213 from 223 systems in the November list.

HP is still the second most common vendor on the list, though its share of Top500 systems also fell slightly — to 138 from 141 six months ago (see Table 2, below, for details of manufacturer rankings).

Clusters are still the most popular architecture for supercomputers in the Top500 list, though massively parallel processing systems continue to advance. The current list includes 93 MPP systems, an increase from 89 in the June list (see Table 3, below, for details).

In terms of operating systems, Linux continues to be the top choice for Top500 machines, with 462 computers in the current list, a slight increase over 457 in the November version. Unix systems remained the next most popular, but slid slightly to 24 systems on the current list from 30 six months ago (see Table 4, below, for details).

The complete Top500 ranking is available here.

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