NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
A Framework for Collective Personalized Communication
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
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
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
Blue Gene/L torus interconnection network
IBM Journal of Research and Development
Blue Gene/L advanced diagnostics environment
IBM Journal of Research and Development
Design and implementation of message-passing services for the Blue Gene/L supercomputer
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Achieving strong scaling with NAMD 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: approaching the limits of concurrency for classical molecular dynamics
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
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Fine-Grained Data Distribution Operations for Particle Codes
Proceedings of the 16th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface
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
Using HPX and LibGeoDecomp for scaling HPC applications on heterogeneous supercomputers
ScalA '13 Proceedings of the Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems
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This paper presents strong scaling performance data for the Blue Matter molecular dynamics framework using a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per time-step of under 2.3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of over 76 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as continued speed-up to fewer than three atoms per node. On a smaller, solvated lipid system with 13,758 atoms, we have achieved continued speedups through fewer than one atom per node and less than 2 milliseconds/time-step. On a 92,224 atom system, we have achieved floating point performance of over 1.8 TeraFlops/second on 16,384 nodes. Strong scaling of fixed-size classical molecular dynamics of biological systems to large numbers of nodes is necessary to extend the simulation time to the scale required to make contact with experimental data and derive biologically relevant insights.