Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers

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 flexibility

[1]  C. Brooks.  Computer simulation of liquids , 1989 .

[2]  Paul Chow,et al.  Reconfigurable molecular dynamics simulator , 2004, 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines.

[3]  Pavle Belanovic,et al.  A Library of Parameterized Floating-Point Modules and Their Use , 2002, FPL.

[4]  M. Patra,et al.  Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. , 2003, Biophysical journal.

[5]  Viktor K. Prasanna,et al.  Scalable hybrid designs for linear algebra on reconfigurable computing systems , 2006, 12th International Conference on Parallel and Distributed Systems - (ICPADS'06).

[6]  Viktor K. Prasanna,et al.  Computing Lennard-Jones Potentials and Forces with Reconfigurable Hardware , 2004, ERSA.

[7]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[8]  Elaine S. Oran,et al.  The interaction of shocks and defects in Lennard-Jones crystals , 1993 .

[9]  Martin C. Herbordt,et al.  Accelerating molecular dynamics simulations with configurable circuits , 2005, International Conference on Field Programmable Logic and Applications, 2005..

[10]  Jeffrey S. Vetter,et al.  Accelerating scientific applications with the SRC-6 reconfigurable computer: methodologies and analysis , 2005, 19th IEEE International Parallel and Distributed Processing Symposium.

[11]  Viktor K. Prasanna,et al.  A Library of Parameterizable Floating-Point Cores for FPGAs and Their Application to Scientific Computing , 2005, ERSA.

[12]  Laxmikant V. Kale,et al.  NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .

[13]  Maya Gokhale,et al.  A Preliminary Study of Molecular Dynamics on Reconfigurable Computers , 2003, Engineering of Reconfigurable Systems and Algorithms.