The Inquirer says that the first petaflop computing system will be Japanese, and published two articles on the subject in two days, "RIKEN races to be the first PetaFLOP supercomputer site" and "Details of Japanese PetaFLOP system revealed."
This will be a specialized system, named Protein Explorer, and designed exclusively for molecular dynamics calculations and simulations at the RIKEN Genomic Sciences Center, based in in Yokohama, Japan.
The Inquirer gives details on this proprietary system and its MDGRAPE-3 chips. You can find additional details in this paper, "Protein Explorer: A Petaflops Special-Purpose Computer for Molecular Dynamics Simulations" (PDF format: 109 KB).
The proprietary system design features dedicated pipelines (for more efficient scheduling) and broadcast memory parallelization (for highly-parallel calculations with low bandwidth, sharing a common memory unit and use the same data for all pipelines). The MDGRAPE-3 custom pipeline LSI for the Protein Explorer, with 20 pipelines, each calculating a pairwise interaction per cycle -- a total of 200 gigaflops peak per each MDGRAPE-3 chip. The modules also include local memory for storing of particle coordinates, as well as interchip communication circuits.
The Protein Explorer system actually uses a simple PC cluster with 128 nodes as the host computer. The dedicated special-purpose engines are just inserted in each PC node PCI-X bus slot. Each node reaches 8 teraflops performance (with 40 MDGRAPE-3 chips sitting on the ultra-dense PCI-X cards inside -- imagine the density). The entire Protein Explorer is going to have 5,120 chips in total to achieve the peak performance of 1 petaflops.
Here is a block diagram of the Protein Explorer system (Credit: RIKEN Genomic Sciences Center).
At this stage, no other details are provided about the availability or the cost of such a system. But I'm sure that some additional information will emerge during the SC2003 Conference, which will be held in Phoenix, Arizona, on November 15 to 21.
Source: Nebojsa Novakovic, The Inquirer, September 30 and October 1, 2003
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