GPU-accelerated molecular mechanics computations
| Autor: | Athanasios Anthopoulos, Andrea Brancale, Ian John Grimstead |
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| Rok vydání: | 2013 |
| Předmět: |
Cell lists
Computer science Static Electricity General Chemistry Parallel computing Load balancing (computing) Intrinsics Molecular Dynamics Simulation Computational science Computer graphics Computational Mathematics CUDA Computer Graphics Graphics General-purpose computing on graphics processing units Scaling Algorithms Software |
| Zdroj: | Journal of computational chemistry. 34(26) |
| ISSN: | 1096-987X |
| Popis: | In this article, we describe an improved cell-list approach designed to match the Kepler architecture of General-purpose graphics processing units (GPGPU). We explain how our approach improves load balancing for the above algorithm and how warp intrinsics are used to implement Newton's third law for the nonbonded force calculations. We also talk through our approach to exclusions handling together with a method to calculate bonded forces and 1-4 electrostatic scaling using a single Cuda kernel. Performance benchmarks are included in the last sections to show the linear scaling of our implementation using a step minimization method. In addition, multiple performance benchmarks demonstrate the contribution of various optimizations we used for our implementations. © 2013 Wiley Periodicals, Inc. |
| Databáze: | OpenAIRE |
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