MDGRAPE-3 is an ultra-high performance
petascale
Petascale computing refers to computing systems capable of calculating at least 1015 floating point operations per second (1 petaFLOPS). Petascale computing allowed faster processing of traditional supercomputer applications. The first system ...
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.
See also
* Supercomputing in Japan
* MDGRAPE-4 MDGRAPE-4 is a supercomputer under development at the RIKEN Quantitative Biology Center (QBiC) in Suita
is a city located in northern Osaka Prefecture, Japan. As of October 1, 2016, the city has an estimated population of 378,322 and a populat ...
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