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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-0603-5514
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-6363-2521
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2015 (English)In: Solving software challenges for exascale, Springer Publishing Company, 2015, 3-27 p.Conference paper, Published 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
Springer Publishing Company, 2015. 3-27 p.
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 8759
National Category
Computer Science
Identifiers
URN: urn:nbn:se:kth:diva-170715DOI: 10.1007/978-3-319-15976-8_1ISI: 000355749700001Scopus ID: 2-s2.0-84928911118ISBN: 978-3-319-15975-1 (print)ISBN: 978-3-319-15976-8 (print)OAI: oai:DiVA.org:kth-170715DiVA: diva2:839933
Conference
2nd International Conference on Exascale Applications and Software (EASC), APR 02-03, 2014, Stockholm, SWEDEN
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20150706

Available from: 2015-07-06 Created: 2015-07-03 Last updated: 2016-05-20Bibliographically approved

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Páll, SzilardAbraham, Mark JamesLindahl, Erik

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