Simulations of diocotron instability using a special-purpose computer, MDGRAPE-2

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bond...

Parallelized Simulation of Molecular Dynamics with a Special-Purpose Computer: MDGRAPE-2

1 High Performance Biocomputing Research Team, Bioinformatics Group, Genomic Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan 2 Computational Science Division, Advanced Computing Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 3 Saitama Institute of Technology, 1690 Husaiji, Okabemachi, Osatogun, Saitama 3690293, Japan 4 Department of Mechanical Engine...

Implementation of Fast Multipole Algorithm on Special-Purpose Computer MDGRAPE-2

N -body simulation is a time consuming task in which force calculation part is most dominant part. The simplest and most accurate algorithm for force calculation is direct summation which has time complexity O(N). It is not practically suitable for large-scale simulations on most general-purpose computers. To cut down cost of force calculation one applies fast algorithms or performs force calcu...

A special purpose computer for ab initio molecular dynamics simulations

Simulations of magnetic materials with MDGRAPE-2

of magnetic materials with MDGRAPE-2 B. G. Elmegreen R. H. Koch M. E. Schabes T. Crawford T. Ebisuzaki H. Furusawa T. Narumi R. Susukita K. Yasuoka 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. ...