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RIKEN's New Supercomputer Up and Running

- Cluster of 1,024 PRIMERGY RX200 S5 computing nodes achieving highest performance in Japan -

Fujitsu Limited

Tokyo, August 07, 2009

Fujitsu today announced that it has recently completed the deployment of a new supercomputer for Japan's Institute of Physical and Chemical Research, known as RIKEN. The system began operations in August.

The new supercomputer system achieved a LINPACK(1) benchmark performance of 97.94 teraflops(2). In comparison to the PC cluster systems included in the June 2009 world TOP500 list(3), the system's performance ranks first in Japan.

About the new supercomputer

The new system, called the RIKEN Integrated Cluster of Clusters (RICC), is a complex system comprised of three separate computing sub-systems, each with a specific purpose: a massively parallel PC cluster, a large capacity memory server, and multipurpose parallel PC cluster. In addition, each computing sub-system is connected to a common front-end system, and disk and tape systems.

Massively Parallel PC Cluster

The massively parallel PC cluster is comprised of 1,024 of Fujitsu's PRIMERGY RX200 S5 PC servers, with 2,048 CPUs (8,192 cores).

The supercomputer's operating environment includes Parallelnavi, Fujitsu's HPC middleware which integrates the system management functions, high-speed file system, and program-development environment. The system is also equipped with an HPC job-management tool, the "Meta-Job Scheduler," which enables integrated management of massively parallel jobs on multiple clusters as a whole.

Benchmark testing

LINPACK benchmark measurements produced the following result, based primarily on the 1,024-node massively parallel cluster of PRIMERGY RX200 S5 servers. This result places it first in performance among PC cluster systems currently in operation in Japan.

  Result Rank on TOP500 list
(June 2009)
Rank among PC clusters
on TOP500 list (June 2009)
Performance 97.94 teraflops 34th worldwide 1st in Japan

How this performance was achieved

The benchmark test result can be attributed to a combination of factors: the high performance of hardware and HPC middleware Parallelnavi, as well as advanced system integration technologies such as program tuning.

Because Parallelnavi's math library dictates LINPACK's processing performance to a large extent, it played a significant role in contributing to the latest result. The math library, realizing world-class performance, leverages R&D achievements of Fujitsu Laboratories.

In addition to high-performance hardware, Fujitsu's strength also lies in its ability to offer middleware which incorporates its leading-edge R&D achievements, and provide comprehensive system integration support that flexibly responds to customers needs.

About "Meta-Job Scheduler", the HPC job-management tool

The "Meta-Job Scheduler" is a high-performance scheduler developed through collaboration between RIKEN, Fujitsu, and Fujitsu Laboratories in the course of developing and operating the previous RIKEN Super Combined Cluster (RSCC) system.

The following functions make it possible to eliminate the waste from scheduling of computation center users' multiple jobs as well as minimize job latency in order to maximize the system's utilization.

  • Multi-layer scheduling: Scheduling operates at a highly elaborated level, managing computing resources at the core, CPU, server, and cluster layers.
  • Fair share: The system refers to each user's assigned rank and past execution log to ensure that all jobs are scheduled in an equitable manner.
  • Back file: This function reorders the sequence of standby jobs to make effective use of empty resources.

Comment from Ryutaro Himeno, Director of RIKEN's Advanced Center for Computing and Communication

"We have deployed and brought online the new RICC as the next step beyond the previous RSCC, which itself was praised for its innovation. The new system delivers the following to researchers at RIKEN:

  1. The ability to perform, on a regular basis, massively parallel jobs, which are required of program-development platforms that leverage the capabilities of next-generation supercomputers.
  2. The ability to process high-volume experimental data using advanced DNA sequencers, accelerators, and X-FEL (X-ray Free Electron Laser).
  3. The ability to use the system for advance computational software development using MDGRAPE-3(4), GPGPU(5), and other accelerators.

The new system also marks the first instance of the Intel® Xeon® processor 5500 series being deployed and used in a large-scale cluster in Japan. We are amazed at the system's performance, and we are grateful to Fujitsu for how smoothly the new system was deployed."

  • [1] LINPACK

    A program for measuring computer performance. The LINPACK benchmark is the standard used by the TOP500 project, which compares the performance of supercomputers.

  • [2] Teraflop

    One trillion floating point operations per second.

  • [3] TOP 500 list

    A ranking of the world's fastest supercomputers.

  • [4] MDGRAPE-3

    A specialized computer for molecular dynamics simulations developed by RIKEN. It is used as part of the supercomputer's multipurpose PC cluster.

  • [5] GPGPU

    Acronym for General Purpose computing on Graphic Processing Unit. It is a technology that enables the use of graphic processing units for purposes other than graphic processing.

About Fujitsu

Fujitsu is a leading provider of IT-based business solutions for the global marketplace. With approximately 175,000 employees supporting customers in 70 countries, Fujitsu combines a worldwide corps of systems and services experts with highly reliable computing and communications products and advanced microelectronics to deliver added value to customers. Headquartered in Tokyo, Fujitsu Limited (TSE:6702) reported consolidated revenues of 4.6 trillion yen (US$47 billion) for the fiscal year ended March 31, 2009. For more information, please see:

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Date: 07 August, 2009
City: Tokyo
Company: Fujitsu Limited, , , , ,