A case study in porting a production scientific supercomputing application to a reconfigurable computer

TLDR

NAMD is a molecular dynamics code widely used in computational biophysics, optimized for von Neumann processors, which makes porting it to FPGA architecture challenging. The study aims to outline the rationale and framework for porting NAMD to the SRC‑6 reconfigurable platform. The authors describe the SRC‑6 architecture and detail the challenges, solutions, and porting process applied to NAMD. The porting results and methods are applicable to a broad class of scientific computing problems.

Abstract

This case study presents the results of porting a production scientific code, called NAMD, to the SRC-6 high-performance reconfigurable computing platform based on field programmable gate array (FPGA) technology. NAMD is a molecular dynamics code designed to run on large supercomputing systems and used extensively by the computational biophysics community. NAMD's computational kernel is highly optimized to run on conventional von Neumann processors; this presents numerous challenges to its reimplementation on FPGA architecture. This paper presents an overview of the SRC-6 architecture and the NAMD application and then discusses the challenges, solutions, and results of the porting effort. The rationale in choosing the development path taken and the general framework for porting an existing scientific code, such as NAMD, to the SRC-6 platform are presented and discussed in detail. The results and methods presented in this paper are applicable to the large class of problems in scientific computing