A fast algorithm for particle simulations
Journal of Computational Physics
Computer simulation using particles
Computer simulation using particles
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Generic programming and the STL: using and extending the C++ Standard Template Library
Generic programming and the STL: using and extending the C++ Standard Template Library
Tiling optimizations for 3D scientific computations
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
An overview of the BlueGene/L Supercomputer
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
NAMD: biomolecular simulation on thousands of processors
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
IBM Journal of Research and Development
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
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
Systems research challenges: a scale-out perspective
IBM Journal of Research and Development
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
A study of the effects of machine geometry and mapping on distributed transpose performance
Proceedings of the 5th conference on Computing frontiers
Massively parallel molecular dynamics simulations of lysozyme unfolding
IBM Journal of Research and Development
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Iterative induced dipoles computation for molecular mechanics on GPUs
Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units
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
Early experience with scientific applications on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel 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
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In this paper we describe the context, architecture, and challenges of Blue Matter, the application framework being developed in conjunction with the science effort within IBM's Blue Gene project. The study of the mechanisms behind protein folding and related topics can require long time simulations on systems with a wide range of sizes and the application supporting these studies must map efficiently onto a large range of parallel partition sizes to optimize scientific throughput for a particular study. The design goals for the Blue Matter architecture include separating the complexities of the parallel implementation on a particular machine from those of the scientific simulation as well as minimizing system environmental dependencies so that running an application within a low overhead kernel with minimal services is possible. We describe some of the parallel decompositions currently being explored that target the first member of the Blue Gene family, BG/L, and present simple performance models for these decompositions that we are using to prioritize our development work. Preliminary results indicate that the high-performance networks on BG/L will allow us to use FFT-based techniques for periodic electrostatics with reasonable speedups on 512-1024 node count partitions even for systems with as few as 5000 atoms.