Implementation methodology for emerging reconfigurable systems
Phillip Murray Martin, Melissa C. Smith, Sadaf R. Alam, Pratul K. Agarwal · 2008
The widespread adoption of reconfigurable (FPGA) accelerator devices for scientific computing faces two critical challenges: first, sustaining performance in the presence of data transfer overheads and second, the availability of a portable interface in a high-level language to target multiple devices. The XtremeData XD1000 is one available system that addresses the first challenge by coupling the reconfigurable hardware with the host muP on a dual-core Opteron motherboard. The ImpulseC development environment, addresses the challenge of portability and programmability by enabling development of applications in C that are capable of targeting multiple reconfigurable hardware platforms. We present a workflow methodology for accelerating a production-level biomolecular simulation framework called LAMMPS in ImpulseC. Using LAMMPS as an example scientific application, we explore the design space and characterize the performance of our implementation on the XD1000 platform.