TY - GEN
T1 - A case study in porting a production scientific supercomputing application to a reconfigurable computer
AU - Kindratenko, Volodymyr
AU - Pointer, David
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33846844133&partnerID=8YFLogxK
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U2 - 10.1109/FCCM.2006.5
DO - 10.1109/FCCM.2006.5
M3 - Conference contribution
AN - SCOPUS:33846844133
SN - 0769526616
SN - 9780769526614
T3 - Proceedings - 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006
SP - 13
EP - 22
BT - Proceedings - 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006
T2 - 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, FCCM 2006
Y2 - 24 April 2006 through 26 April 2006
ER -