What is MD-GRAPE?

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Upon hearing the word "MD-GRAPE", most of the general public would respond, "MD-what?". The IBM Research Division and the Institute of Chemical Research (RIKEN) in Tokyo have been collaborating during the last few years to produce an accelerator chip (pictured left) that can rapidly calculate all of the interatomic forces in a molecular dynamics simulation with millions of particles -- a task that would take a room full of conventional computers. These chips will be combined with other special chips at RIKEN later this year to make a Molecular Dynamics Machine, which will run at a whopping 100 Teraflops speed, the fastest for any computer in the world. For comparison, the fastest PC runs at about one one-hundred-thousandth of this speed. The MD-GRAPE chip is the next in a series of GRAPE chips, which have won the Gordon Bell Award for Fastest Computer (given by the IEEE Computer Society) in 1995 and 1996, and for Best Price/Performance Ratio in 1999. MD-GRAPE's speed results from the combination of many things.




Why use MD-GRAPE?

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Many physical problems can be simplified by approximating the real world with an array of particles, each representing a small piece of the total space. In the case of chemical reactions or the intricate workings of proteins and enzymes, these representative particles are the individual atoms of the molecules involved. For fluid dynamics problems, such as weather forecasting, numerical wind tunnel experiments on cars, ships and aircraft, turbulence, and so on, the model particles can be imaginary pieces of the fluid, written either as points that carry along with them the pressure, temperature, and other fluid properties, or as vectors (arrows), that mark the local vorticity (spin). Even galaxies in space, which may contain thousands of millions of stars, can be represented fairly accurately by only several million "star" particles in a simulation. For these types problems, a computer has to do the same time-consuming operation over and over again: calculate the distances between all pairs of particles, and from these distances, calculate the mutual forces between all pairs, and then sum up these forces for each particle. This calculation involves a number of operations that is equal to the square of the number of particles, and this square rapidly grows so large with large simulations that a conventional computer will just grind to a virtual halt. MD-GRAPE solves this problem by specializing in just this mutual force calculation and summation, and it does this part at extreme speed.

How does MD-GRAPE work?

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MD-GRAPE boards attach to a normal computer by fitting into the PCI slots. The host computer and the MD-GRAPE board work together to solve the physical problem. The host, which can be anything from a small PC to a giant array of parallel workstations, such as IBM's RS 6000 SP supercomputer, does all of the work involving single particles, such as moving them along in time, but after each time step, the host sends the most recent particle information to the MD-GRAPE boards. These boards automatically calculate and return to the host all of the forces on each particle. If desired, the boards can also return the energy of each particle. These forces are then used by the host to move the particles along, until the next time step begins.

A standard PCI board made by Advanet, Inc. (Japan) with four of the MD-GRAPE chips runs at about 64 Gflops on any PC or RISC workstation. One source of MD-GRAPE's attractiveness is that it runs independently at the command of a host computer, prompted by FORTRAN or C subroutine calls that are easily embedded into standard software.

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