The Art of Molecular Dynamics Simulation
The Art of Molecular Dynamics Simulation
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
ACM Transactions on Mathematical Software (TOMS)
Reconfigurable Molecular Dynamics Simulator
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Massively Parallel Processors Generator for Reconfigurable System
FCCM '05 Proceedings of the 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Parallel multigrid summation for the N-body problem
Journal of Parallel and Distributed Computing
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
General purpose molecular dynamics simulations fully implemented on graphics processing units
Journal of Computational Physics
GPU acceleration of cutoff pair potentials for molecular modeling applications
Proceedings of the 5th conference on Computing frontiers
Fpga acceleration of molecular dynamics simulations
Fpga acceleration of molecular dynamics simulations
Reconfigurable Computing: The Theory and Practice of FPGA-Based Computation
Reconfigurable Computing: The Theory and Practice of FPGA-Based Computation
Self-Alignment Schemes for the Implementation of Addition-Related Floating-Point Operators
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
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The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA’s resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.