61447 20250612142454.0 doi 10.1007/978-3-319-32149-3_16 sideral 95003 ART-2016-95003 eng Mikkelsen, C.C.K. Accelerating sparse arithmetic in the context of newton’s method for small molecules with bond constraints 2016 Access copy available to the general public Unrestricted 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. info:eu-repo/semantics/openAccess All rights reserved http://www.europeana.eu/rights/rr-f/ 0.339 2016 Computer Science (miscellaneous) 2016 Q2 Theoretical Computer Science 2016 Q3 info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion Alastruey-Benedé, J. Universidad de Zaragoza (orcid)0000-0003-4164-5078 Ibáñez-Marín, P. Universidad de Zaragoza (orcid)0000-0002-5916-7898 Risueño, P.G. 5007 035 Universidad de Zaragoza Dpto. Informát.Ingenie.Sistms. Área Arquit.Tecnología Comput. 9573 (2016), 160-171 Lect. notes comput. sci. Lecture Notes in Computer Science 0302-9743 292848 http://zaguan.unizar.es/record/61447/files/texto_completo.pdf Postprint 56898 http://zaguan.unizar.es/record/61447/files/texto_completo.jpg?subformat=icon icon Postprint oai:zaguan.unizar.es:61447 articulos driver 2025-06-12-14:23:36 ARTICLE