By Ari Harju, Topi Siro, Filippo Federici Canova, Samuli Hakala, Teemu Rantalaiho (auth.), Pekka Manninen, Per Öster (eds.)

This quantity constitutes the refereed court cases of the eleventh overseas convention on utilized Parallel and clinical Computing, PARA 2012, held in Helsinki, Finland, in June 2012. The 35 revised complete papers provided have been chosen from quite a few submissions and are geared up in 5 technical classes masking the themes of advances in HPC purposes, parallel algorithms, functionality analyses and optimization, software of parallel computing in and engineering, and HPC period equipment. furthermore, 3 of the topical minisymposia are defined via a corresponding evaluate article at the minisymposia subject. for you to disguise the state of the art of the sector, on the finish of the e-book a suite of abstracts describe many of the convention talks now not elaborated into complete articles.

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These cards in particular will be used on several new Cray installations. (II) Multi-grid solvers for efficient PME electrostatics : The vast majority of biomolecular simulations rely on particle-mesh Ewald (PME) lattice summation to handle long-range electrostatic interactions. Since this in turn relies on 3D FFTs, the associated all-to-all communication pattern is a major bottleneck for scaling. A. ˚ Astr¨ om et al. communicating grids over all processors. This can currently be achieved either through multipole-based [11], or multigrid-based [12] methods, and we intend to investigate both.

305–314. ACM, New York (2010) 22. : Large-scale FFT on GPU clusters. In: Proceedings of the 24th ACM International Conference on Supercomputing, ICS 2010, pp. 315–324. ACM, New York (2010) 23. : A comparative benchmarking of the FFT on Fermi and Evergreen GPUs. In: 2011 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), pp. 127–128 (2011) 24. : Multiple grid methods for classical molecular dynamics. Journal of Computational Chemistry 23(6), 673–684 (2002) 25.

Within the EC-funded project CRESTA (Collaborative Research into Exascale Sytemware, Tools and Applications) [1], a set of six applications codes are being investigated and optimized with the objective of preparing them for exascale. The codes are ELMFIRE, GROMACS, IFS, HemeLB, NEK5000 and OpenFOAM. ELMFIRE [2] is a gyro-kinetic particle-in-cell code that simulates movement and interaction between high-speed particles on a three dimensional grid in torusshaped atomic fusion reactors. The particles are held together by an external magnetic field.

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