Fault Tolerant and Energy Efficient Algorithms in Molecular Simulations

September 5, 2011 to September 7, 2011
Location : CECAM-HQ-EPFL, Lausanne, Switzerland
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Perspectives for efficient simulations of long range interactions with multi-billion particles.

Ivo Kabadshow
Research Center Julich, Germany


The simulation of pairwise interactions in huge particle ensembles is a vital issue in scientific research. Especially the calculation of long-range interactions poses limitations to the system size, since these interactions scale quadratically with the number of particles. This talk is divided into two parts. First I will present the open source ScaFaCoS library. The purpose of the framework is to provide a unified parallel library for various methods including the fast multipole method, the Barnes-Hut tree method, particle-mesh Ewald methods or multigrid methods to solve electrostatic and gravitational problems in large particle simulations. In the second part I will highlight one specific method of the library, namely the FMM. We improved the fast summation algorithm by adding a tight error control scheme and on-the-fly runtime minimization. The current code also benefits from a reduced memory footprint and is therefore capable of computing all pairwise interactions for systems with open, 1D, 2D and 3D periodic boundaries on 300k BG/P cores with up to three trillion particles. To achieve strong parallel scaling, the code employs a one-sided, non-blocking parallelization scheme with small communication overhead.