Scaling of Multimillion-Atom MD Simulation on Petascale Supercomputers
 The performance of multimillion-atom MD simulations on petascale supercomputers is limited by the most commonly used electrostatic method: PME. Particle mesh ewald (PME) requires two 3D fast fourier transforms (FFT) and these in turn require global communication. These global communications are very time consuming on massively parallel supercomputers, such as Jaguar at ORNL. Our recent paper shows that for the chosen test system (lignocellulosic biomass) the reaction field (RF) method produces very accurate results when compared to results obtained using PME. As seen in the graph, a simulation using RF shows significant better scaling than one of the same system using PME. |
 Scaling of 3.3M atom Lignocellulose system with RF (using GROMACS) and PME (using NAMD). Scaling of 100M peptide-water test-system up to 150k cores on Jaguar. |
See also:
Schulz R, Lindner B, Petridis L, and Smith JC (in press).
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.
J. Chem. Theory Comput., 2009, 5 (10), pp 2798–2808
Schulz R, Lindner B, Petridis L, and Smith JC (poster)
Scaling of Multimillion-Atom MD Simulation on a Petascale Supercomputer
Presented at: Fall Creek 2009
Scaling of Multimillion-Atom MD Simulation on a Petascale Supercomputer
Presented at: Molecular Kinetics 2009,
