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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
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Number of Authors: 5
2015 (English)In: Solving Software Challenges for Exascale / [ed] Markidis, S.; Laure, E., 2015, 3-27 p.Conference paper (Refereed)
Abstract [en]

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.

Place, publisher, year, edition, pages
2015. 3-27 p.
, Lecture Notes in Computer Science, ISSN 0302-9743 ; 8759
National Category
Computer and Information Science
URN: urn:nbn:se:su:diva-119036DOI: 10.1007/978-3-319-15976-8_1ISI: 000355749700001ISBN: 978-3-319-15975-1ISBN: 978-3-319-15976-8OAI: diva2:843017
2nd International Conference on Exascale Applications and Software (EASC), APR 02-03, 2014, Stockholm, Sweden
Available from: 2015-07-24 Created: 2015-07-24 Last updated: 2015-07-24Bibliographically approved

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Lindahl, Erik
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Department of Biochemistry and Biophysics
Computer and Information Science

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