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

Volodymyr Kindratenko, David Pointer

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationProceedings - 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006
Pages13-22
Number of pages10
DOIs
StatePublished - Dec 1 2006
Event14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006 - Napa, CA, United States
Duration: Apr 24 2006Apr 26 2006

Publication series

NameProceedings - 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006

Other

Other14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006
Country/TerritoryUnited States
CityNapa, CA
Period4/24/064/26/06

ASJC Scopus subject areas

  • Hardware and Architecture
  • Software

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