A fast algorithm for particle simulations
Journal of Computational Physics
Computer simulation using particles
Computer simulation using particles
Algorithmic challenges in computational molecular biophysics
Journal of Computational Physics - Special issue on computational molecular biophysics
Understanding Molecular Simulation: From Algorithms to Applications
Understanding Molecular Simulation: From Algorithms to Applications
An overview of the BlueGene/L Supercomputer
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
Computational Physics
Scalable algorithms for molecular dynamics simulations on commodity clusters
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
Anton, a special-purpose machine for molecular dynamics simulation
Communications of the ACM - Web science
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
The Journal of Supercomputing
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Particle simulations in fields ranging from biochemistry to astrophysics require the evaluation of interactions between all pairs of particles separated by less than some fixed interaction radius. The applicability of such simulations is often limited by the time required for calculation, but the use of massive parallelism to accelerate these computations is typically limited by inter-processor communication requirements. Recently, Snir [M. Snir, A note on N-body computations with cutoffs, Theor. Comput. Syst. 37 (2004) 295-318] and Shaw [D.E. Shaw, A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions, J. Comput. Chem. 26 (2005) 1318-1328] independently introduced two distinct methods that offer asymptotic reductions in the amount of data transferred between processors. In the present paper, we show that these schemes represent special cases of a more general class of methods, and introduce several new algorithms in this class that offer practical advantages over all previously described methods for a wide range of problem parameters. We also show that several of these algorithms approach an approximate lower bound on inter-processor data transfer.