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Accelerating Sparse Arithmetic in the Context of Newton's Method for Small Molecules with Bond Constraints
Umeå University, Faculty of Science and Technology, High Performance Computing Center North (HPC2N). Umeå University, Faculty of Science and Technology, Department of Computing Science.
2016 (English)In: Parallel Processing and Applied Mathematics, PPAM 2015, Part I / [ed] Wyrzykowski, R Deelman, E Dongarra, J Karczewski, K Kitowski, J Wiatr, K, Cham: Springer International Publishing Switzerland , 2016, 160-171 p.Conference paper, Published paper (Refereed)
Abstract [en]

Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrain bond lengths in order to increase the time step of the simulation. Here we accelerate Newton's method for solving the constraint equations for a system consisting of many identical small molecules. Starting with a modular and generic base code using a sequential data layout, we apply three different optimization techniques. The compiled code approach is used to generate subroutines equivalent to a single step of Newton's method for a user specified molecule. Differing from the generic subroutines, these specific routines contain no loops and no indirect addressing. Interleaving the data describing different molecules generates vectorizable loops. Finally, we apply task fusion. The simultaneous application of all three techniques increases the speed of the base code by a factor of 15 for single precision calculations.

Place, publisher, year, edition, pages
Cham: Springer International Publishing Switzerland , 2016. 160-171 p.
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 9573
Keyword [en]
Newton's method, Non-linear equations, Molecular dynamics, Constraints, SHAKE, RATTLE, LINCS, mpiled code approach, Vector level parallelism, Vectorizing compiler, SIMD
National Category
Computer Engineering
Identifiers
URN: urn:nbn:se:umu:diva-135304DOI: 10.1007/978-3-319-32149-3_16ISI: 000400134500016ISBN: 978-3-319-32149-3 (electronic)ISBN: 978-3-319-32148-6 (print)OAI: oai:DiVA.org:umu-135304DiVA: diva2:1098380
Conference
11th International Conference on Parallel Processing and Applied Mathematics (PPAM), SEP 06-09, 2015, Krakow, POLAND
Available from: 2017-05-24 Created: 2017-05-24 Last updated: 2017-05-24Bibliographically approved

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Kjelgaard Mikkelsen, Carl Christian
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High Performance Computing Center North (HPC2N)Department of Computing Science
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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
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  • Other style
More styles
Language
  • de-DE
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Output format
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