Ryutaro Susukita

Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations

Abstract We are now developing Molecular Dynamics Machine (MDM), a special-purpose computer for classical molecular dynamics simulations. It accelerates the calculation of non-bonding force, Coulomb and van der Waals forces, because the calculation cost for Coulomb force dominates the total calculation time when we treat a large system of charged particles without truncating Coulomb force. When we use Ewald method, the Coulomb force can be calculated by dividing it into real-space and wavenumber-space parts. MDM is composed of MDGRAPE-2, WINE-2, and a host computer. MDGRAPE-2 calculates van der Waals force and real-space part of Coulomb force. WINE-2 calculates wavenumber-space part of Coulomb force. The host computer calculates bonding-force and updates positions and velocities of atoms. The target performance of MDM is 100 Tflops and will sustain about 30 Tflops in realistic applications. It can calculate 3.2 × 106 time-steps of MD simulation with a million atoms in a week. Total system will be complete...

Hardware accelerator for molecular dynamics: MDGRAPE-2

Abstract We developed MDGRAPE-2, a hardware accelerator that calculates forces at high speed in molecular dynamics (MD) simulations. MDGRAPE-2 is connected to a PC or a workstation as an extension board. The sustained performance of one MDGRAPE-2 board is 15 Gflops, roughly equivalent to the peak performance of the fastest supercomputer processing element. One board is able to calculate all forces between 10xa0000 particles in 0.28xa0s (i.e. 310000 time steps per day). If 16 boards are connected to one computer and operated in parallel, this calculation speed becomes ∼10 times faster. In addition to MD, MDGRAPE-2 can be applied to gravitational N -body simulations, the vortex method and smoothed particle hydrodynamics in computational fluid dynamics.

An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM

We performed molecular dynamics (MD) simulation of 33 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 8.61 Tflop/s. In this calculation we used a special-purpose computer, MDM, which we have developed for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large scale MD simulations without truncating the Coulomb force. It is composed of MDGRAPE-2, WINE-2 and a host computer. MDGRAPE-2 accelerates the calculation for real-space part of the Coulomb and van der Waals forces. WINE-2 accelerates the calculation for wavenumber-space part of the Coulomb force. The host computer performs other calculations. With the completed MDM system we performed an MD simulation similar to what was the basis of our SC2000 submission for a Gordon Bell prize. With this large scale MD simulation, we can dramatically decrease the fluctuation of the temperature less than 0.1 Kelvin.

46 TFLOPS special-purpose computer for molecular dynamics simulations: WINE-2

We developed WINE-2, a 46 TFLOPS computer, to accelerate molecular dynamics (MD) simulations. We need a huge computational power to understand the dynamics of large and complex molecules such as those of proteins and nucleic acids. WINE-2 is a specialized computer to accelerate the wavenumber-space part of the Ewald (1921) summation for calculating the Coulomb forces among atoms. It has a highly parallel architecture and is composed of 2,304 WINE-2 chips. We measured 29 TFLOPS of performance in the case of 24 million atoms and a half million wavenumber vectors. This sustained speed is more than seven times faster than the peak speed of the fastest supercomputer in the world.

Molecular dynamics study of the solidification process in alkali halide cluster

Abstract Molecular dynamics (MD) simulations of the solidification process of an NaCl cluster are carried out. Voronoi analysis is employed to distinguish a crystal nucleus from molten NaCl. In the early stage of simulation, some small solid clusters of size smaller than the critical nucleus size are repeatedly formed and broken. Under the low-temperature condition ( T =700 K), in the later stage of the simulation, a polycrystal NaCl solid, in which two or three large solid grains survive, appears. Under the high-temperature condition ( T =740 K), one large single crystal cluster is formed. All simulations of this work are performed in a special-purpose computer for MD simulation, called MDGRAPE-2.

Simulations of magnetic materials with MDGRAPE-2

The use of accelerator hardware for micromagnetics simulations is described, along with some initial results. The accelerator calculates the dipole interactions at 400 gigaflops, allowing large simulations to be performed with arbitrary geometries. Two research programs are highlighted, the simulation of a curved MRAM cell and the simulation of the write head in a computer disk drive.