Compiled hardware acceleration of molecular dynamics code

Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL

Volumn , Issue , 2008, Pages 667-670

  Villarreal, Jason ^a   Najjar, Walid A ^a  

^a University of California Riverside   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR; HARDWARE ACCELERATIONS; MD SIMULATIONS; MOLECULAR DYNAMICS CODES; PIPELINED CIRCUITS; SOFTWARE BASED; TOOLSET;

ATOMIC PHYSICS; ATOMS; CODES (SYMBOLS); FIELD PROGRAMMABLE GATE ARRAYS (FPGA); MOLECULAR DYNAMICS; QUANTUM CHEMISTRY;

DYNAMICS;

EID: 54849430268     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FPL.2008.4630035     Document Type: Conference Paper

References (11)

1. B. Buyukkurt, Z. Guo, and W. Najjar. Impact of Loop Unrolling on Area, Throughput and Clock Frequency in ROCCC: C to VHDL Compiler for FPGAs. International Workshop On Applied Reconfigurable Computing, Delft, The Netherlands, March 2006.
2. Z. Guo, B. Buyukkurt, W. Najjar and K. Vissers. Optimized Generation of Data-Path from C Codes. In ACM/IEEE Design Automation and Test Europe (DATE), Munich, Germany, March 2005.
3. Z. Guo, A. B. Buyukkurt and W. Najjar. Input Data Reuse In Compiling Window Operations Onto Reconfigurable Hardware, Proc. ACM Symp. On Languages, Compilers and Tools for Embedded Systems (LCTES 2004), Washington DC, June 2004.
4. The MDGRAPE-3 computer. http://mdgrape.gsc.riken.jp
5. J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. Skeel, L. Kale, and K. Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26:1781-1802, 2005.
6. V. Kindratenko and D. Pointer. A case study in porting a production scientific supercomputing application to a reconfigurable computer. IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM), 2006.
7. Reconfigurable Application-Specific Computing User's Guide. SGI, 2006.
8. R. Scrofano and V. Prasanna. Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers. International Conference for High Performance Computing, Networking, Storage and Analysis, 2006.
9. R. Scrofano and V. Prasanna. Computing Lennard-Jones Potentials and Forces with Reconfigurable Hardware. Engineering of Reconfigurable Systems and Algorithms, 2004.
10. D. E. Shaw et al. Anton, a special-purpose machine for molecular dynamics simulation. International Symposium on Computer Architecture (ISCA), 2007
11. J. Villarreal, J. Cortes, and W. Najjar. Compiled Code Acceleration of NAMD on FPGAs. Reconfigurable Systems Summer Institute (RSSI), 2007.