Paper Citing NAMD - Abstract
Herbordt, Martin C.
Architecture/Algorithm Codesign of Molecular Dynamics Processors
2013 ASILOMAR CONFERENCE ON SIGNALS, SYSTEMS AND COMPUTERS, 1442-1446, 2013
Molecular Dynamics is notable in High Performance Computing in that it is both sufficiently critical, and not well-enough served by off-the-shelf processors, that it has been continually targeted with domain-specific architectures. These range from the common, i.e., use of accelerators, to FPGA-centric servers describe here, to full-scale ASIC-based systems (e.g., the Anton processor). The strict constraints on achieving strong scaling leads to novel designs, which in turn suggest restructurings of the underlying algorithms. These in turn suggest some changes to the hardware. We discuss the technological issues involved, the implications of various approaches on architecture/algorithm codesign, and how these are likely to affect future high-end processors, both domain-specific and off-the-shelf.
