Backward Error Analysis for Numerical Integrators
SIAM Journal on Numerical Analysis
Understanding Molecular Simulation
Understanding Molecular Simulation
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
Monitoring energy drift with shadow Hamiltonians
Journal of Computational Physics
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
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
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
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
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Beyond homogeneous decomposition: scaling long-range forces on Massively Parallel Systems
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
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This paper describes some of the issues involved with scaling biomolecular simulations onto massively parallel machines drawing on the Blue Matter application team's experiences with Blue Gene/L. Our experiences in scaling biomolecular simulation to one atom/node on BG/L should be relevant to scaling biomolecular simulations onto larger peta-scale platforms because the path to increased performance is through the exploitation of increased concurrency so that even larger systems will have to operate in the extreme strong scaling regime. Petascale platforms also present challenges with regard to the correctness of biomolecular simulations since longer time-scale simulations are more likely to encounter significant energy drift. Total energy drift data for a microsecond-scale simulation is presented along with the measured scalability of various components of a molecular dynamics time-step.