Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers
- 1 April 2006
- conference paper
- Published by Institute of Electrical and Electronics Engineers (IEEE)
Abstract
With advances in re configurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications, such as those in scientific computing. There has been a resulting development of reconfigurable computers - computers which have both general purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we study the acceleration of molecular dynamics simulations using reconfigurable computers. We describe how we partition the application between software and hardware and then model the performance of several alternatives for the task mapped to hardware. We describe an implementation of one of these alternatives on a reconfigurable computer and demonstrate that for two real-world simulations, it achieves a 2 times speed-up over the software baseline. We then compare our design and results to those of prior efforts and explain the advantages of the hardware/software approach, including flexibilityKeywords
This publication has 7 references indexed in Scilit:
- Accelerating molecular dynamics simulations with configurable circuitsIEE Proceedings - Computers and Digital Techniques, 2006
- Scalable hybrid designs for linear algebra on reconfigurable computing systemsPublished by Institute of Electrical and Electronics Engineers (IEEE) ,2006
- GROMACS: Fast, flexible, and freeJournal of Computational Chemistry, 2005
- Reconfigurable Molecular Dynamics SimulatorPublished by Institute of Electrical and Electronics Engineers (IEEE) ,2004
- Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic InteractionsBiophysical Journal, 2003
- NAMD2: Greater Scalability for Parallel Molecular DynamicsJournal of Computational Physics, 1999
- The interaction of shocks and defects in Lennard-Jones crystalsJournal of Physics: Condensed Matter, 1993