MDGRAPE-3 is an ultra-high performance petascale supercomputer system developed by the Riken research institute in Japan. It is a special purpose system built for

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the 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 dynamic "evolution" of t ...

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 secondary and tertiary structure from primary structure. Structure prediction is different ...

. 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 system markets. It was introduced in June 1998. Xeon processors are based on the same a ...

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

level of

floating point In computing, floating-point arithmetic (FP) is arithmetic that represents real numbers approximately, using an integer with a fixed precision, called the significand, scaled by an integer exponent of a fixed base. For example, 12.345 can b ...

arithmetic performance. This was more than three times faster than the 2006 version of the IBM

Blue Gene/L Blue Gene is an IBM project aimed at designing supercomputers that can reach operating speeds in the petaFLOPS (PFLOPS) range, with low power consumption. The project created three generations of supercomputers, Blue Gene/L, Blue Gene/P, ...

system, which then led the

TOP500 The TOP500 project ranks and details the 500 most powerful non- 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 updates always coinci ...

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'' by ''n'' system of linear equations ''Ax'' = ''b'', which is a commo ...

, 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