Computer simulation using particles
Computer simulation using particles
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Parallel many-body simulations without all-to-all communication
Journal of Parallel and Distributed Computing
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Understanding Molecular Simulation: From Algorithms to Applications
Understanding Molecular Simulation: From Algorithms to Applications
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
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
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
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
Blue Gene/L advanced diagnostics environment
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Progress in scaling biomolecular simulations to petaflop scale platforms
Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
Parallel implementation of the replica exchange molecular dynamics algorithm on blue gene/L
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Performance measurements of the 3D FFT on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Blue matter: strong scaling of molecular dynamics on blue gene/l
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Anton, a special-purpose machine for molecular dynamics simulation
Communications of the ACM - Web science
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Beyond homogeneous decomposition: scaling long-range forces on Massively Parallel Systems
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Communication analysis of parallel 3D FFT for flat cartesian meshes on large Blue Gene systems
HiPC'08 Proceedings of the 15th international conference on High performance computing
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N-body simulations present some of the most interesting challenges in the area of massively parallel computing, especially when the object is to improve the time to solution for a fixed-size problem. The Blue Matter molecular simulation framework was developed specifically to address these challenges, to explore programming models for massively parallel machine architectures in a concrete context, and to support the scientific goals of the IBM Blue Gene® Project. This paper reviews the key issues involved in achieving ultrastrong scaling of methodologically correct biomolecular simulations, particularly the treatment of the long-range electrostatic forces present in simulations of proteins in water and membranes. Blue Matter computes these forces using the particle-particle particle-mesh Ewald (P3ME) method, which breaks the problem up into two pieces, one that requires the use of three-dimensional fast Fourier transforms with global data dependencies and another that involves computing interactions between pairs of particles within a cutoff distance. We summarize our exploration of the parallel decompositions used to compute these finite-ranged interactions, describe some of the implementation details involved in these decompositions, and present the evolution of strong-scaling performance achieved over the course of this exploration, along with evidence for the quality of simulation achieved.