MATEC Web Conf.
Volume 125, 201721st International Conference on Circuits, Systems, Communications and Computers (CSCC 2017)
|Number of page(s)||6|
|Published online||04 October 2017|
Molecular Dynamics on FPGA Based Accelerated Processing Units
1 Computer Science Dept., Anselm College, Manchester, NH
2 Faculty of Electronics, Tc. & IT, Politehnica University of Bucharest, Bucharest, Romania
3 Faculty of Electronics, Tc. & IT, Politehnica University of Bucharest, Bucharest, Romania
One of the main problems in providing the amount of computation requested by the Molecular Dynamic domain is to offer an appropriate architectural environment for solving all the aspects of the intense parts of the involved computation. Current solutions accelerate only partially the intense computation – forces com putation & position and speed updates, which represents around 75% from the total computational effort – thus limiting the help provided by the parallel computing resources involved. The aim of this paper is to introduce a parallel accelerator featured with functions able to add to the accelerated functions the neighbourhood list building, which represent around 25% from the total computation. Thus, accelerations higher than the current ~ 4× are expected. Our proposal, the MapReduce Accelerator, is evaluated using the Gromacs system. The Martini water example, running on a cycle accurate simulator, is used to evaluate the speed-up and the energy.
© The Authors, published by EDP Sciences, 2017
This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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