RIKEN MDGRAPE-3
Encyclopedia
Petascale
In computing, petascale refers to a computer system capable of reaching performance in excess of one petaflop, i.e. one quadrillion floating point operations per second. The standard benchmark tool is LINPACK and Top500.org is the organisation which tracks the fastest supercomputers...
supercomputer
Supercomputer
A supercomputer is a computer at the frontline of current processing capacity, particularly speed of calculation.Supercomputers are used for highly calculation-intensive tasks such as problems including quantum physics, weather forecasting, climate research, molecular modeling A supercomputer is a...
system developed by the RIKEN
RIKEN
is a large natural sciences research institute in Japan. Founded in 1917, it now has approximately 3000 scientists on seven campuses across Japan, the main one in Wako, just outside Tokyo...
research institute in Japan
Japan
Japan is an island nation in East Asia. Located in the Pacific Ocean, it lies to the east of the Sea of Japan, China, North Korea, South Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea and Taiwan in the south...
. It is a special purpose system built for molecular dynamics
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
simulations, especially protein structure prediction
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
.
MDGRAPE-3 consists of 201 units of 24 custom MDGRAPE-3 chips (4808 total), plus additional dual-core Intel Xeon
Xeon
The Xeon is a brand of multiprocessing- or multi-socket-capable x86 microprocessors from Intel Corporation targeted at the non-consumer server, workstation and embedded system markets.-Overview:...
processors (codename "Dempsey") which serve as host machines.
In June 2006 RIKEN announced its completion, achieving the PetaFLOPS level of floating point
Floating point
In computing, floating point describes a method of representing real numbers in a way that can support a wide range of values. Numbers are, in general, represented approximately to a fixed number of significant digits and scaled using an exponent. The base for the scaling is normally 2, 10 or 16...
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
TOP500
The TOP500 project ranks and details the 500 most powerful known computer systems in the world. The project was started in 1993 and publishes an updated list of the supercomputers twice a year...
list of supercomputers at 0.28 PetaFLOPS. Because it's not a general-purpose machine capable of running the LINPACK
LINPACK
LINPACK is a software library for performing numerical linear algebra on digital computers. It was written in Fortran by Jack Dongarra, Jim Bunch, Cleve Moler, and Gilbert Stewart, and was intended for use on supercomputers in the 1970s and early 1980s...
benchmark, MDGRAPE-3 does not qualify for the TOP500
TOP500
The TOP500 project ranks and details the 500 most powerful known computer systems in the world. The project was started in 1993 and publishes an updated list of the supercomputers twice a year...
list.