FPGA-Accelerated Range-Limited Molecular Dynamics
Long timescale Molecular Dynamics (MD) simulation of small molecules is crucial in drug design and basic science. To accelerate a small data set that is executed for a large number of iterations, high-efficiency is required. Recent work in this domain has demonstrated that among COTS devices only FPGA-centric clusters can scale beyond a few processors. The problem addressed here is that, as the number of on-chip processors has increased from fewer than 10 into the hundreds, previous intra-chip routing solutions are no longer viable. We find, however, that through various design innovations, high efficiency can be maintained. These include replacing the previous broadcast networks with ring-routing and then augmenting the rings with out-of-order and caching mechanisms. Others are adding a level of hierarchical filtering and memory recycling. Two novel optimized architectures emerge, together with a number of variations. These are validated, analyzed, and evaluated. We find that in the domain of interest speed-ups over GPUs are achieved. Finally, the potential impact is that this system promises to be the basis for scalable long timescale MD with commodity clusters.
- Research Organization:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
- Grant/Contract Number:
- AC05-76RL01830
- OSTI ID:
- 2425935
- Report Number(s):
- PNNL-SA--185033
- Journal Information:
- IEEE Transactions on Computers, Journal Name: IEEE Transactions on Computers Journal Issue: 6 Vol. 73; ISSN 0018-9340
- Publisher:
- IEEECopyright Statement
- Country of Publication:
- United States
- Language:
- English
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