MDGRAPE-3 is an ultra-high performance

petascale Petascale computing refers to computing systems capable of performing at least 1 quadrillion (10^15) floating-point operations per second (FLOPS). These systems are often called petaflops systems and represent a significant leap from traditional ...

supercomputer A supercomputer is a type of computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instruc ...

system developed by the

Riken is a national scientific research institute in Japan. Founded in 1917, it now has about 3,000 scientists on seven campuses across Japan, including the main site at Wakō, Saitama, Wakō, Saitama Prefecture, on the outskirts of Tokyo. Riken is a ...

research institute in

Japan Japan is an island country in East Asia. Located in the Pacific Ocean off the northeast coast of the Asia, Asian mainland, it is bordered on the west by the Sea of Japan and extends from the Sea of Okhotsk in the north to the East China Sea ...

. It is a special purpose system built for

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...

simulations, especially

protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ...

. MDGRAPE-3 consists of 201 units of 24 custom MDGRAPE-3 chips (4,824 total), plus additional dual-core Intel

Xeon Xeon (; ) is a brand of x86 microprocessors designed, manufactured, and marketed by Intel, targeted at the non-consumer workstation, server, and embedded markets. It was introduced in June 1998. Xeon processors are based on the same archite ...

processors (codename "Dempsey") which serve as host machines. In June 2006 Riken announced its completion,Riken press release,
Completion of a one-petaflops computer system for simulation of molecular dynamics
' achieving the

petaFLOPS Floating point operations per second (FLOPS, flops or flop/s) is a measure of computer performance in computing, useful in fields of scientific computations that require floating-point calculations. For such cases, it is a more accurate measu ...

level of

floating point In computing, floating-point arithmetic (FP) is arithmetic on subsets of real numbers formed by a ''significand'' (a signed sequence of a fixed number of digits in some base) multiplied by an integer power of that base. Numbers of this form ...

arithmetic performance. This was more than three times faster than the 2006 version of the IBM Blue Gene/L system, which then led the

TOP500 The TOP500 project ranks and details the 500 most powerful non-distributed computing, distributed computer systems in the world. The project was started in 1993 and publishes an updated list of the supercomputers twice a year. The first of these ...

list of supercomputers at 0.28 petaFLOPS. Because it's not a general-purpose machine capable of running the

LINPACK benchmarks The LINPACK benchmarks are a measure of a system's floating-point computing power. Introduced by Jack Dongarra, they measure how fast a computer solves a dense ''n'' × ''n'' system of linear equations ''Ax'' = ''b'', which i ...

, MDGRAPE-3 does not qualify for the TOP500 list.

References

* Makoto Taiji, "MDGRAPE-3 chip: A 165-Gflops application-specific LSI for Molecular Dynamics Simulations", 16th IEEE Hot Chips Symposium, August 2004

External links

MD-GRAPE Project@IBM

High-Performance Molecular Simulation Team@Riken

Tetsu Narumi's MDGRAPE page

Molecular Dynamics Machine
using MDGRAPE-2 {{DEFAULTSORT:Riken Mdgrape-3 Computer-related introductions in 2006 Petascale computers Riken Molecular dynamics Supercomputers Supercomputing in Japan

See also

References

External links