000061447 001__ 61447
000061447 005__ 20200221144249.0
000061447 0247_ $$2doi$$a10.1007/978-3-319-32149-3_16
000061447 0248_ $$2sideral$$a95003
000061447 037__ $$aART-2016-95003
000061447 041__ $$aeng
000061447 100__ $$aMikkelsen, C.C.K.
000061447 245__ $$aAccelerating sparse arithmetic in the context of newton’s method for small molecules with bond constraints
000061447 260__ $$c2016
000061447 5060_ $$aAccess copy available to the general public$$fUnrestricted
000061447 5203_ $$aMolecular 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.
000061447 540__ $$9info:eu-repo/semantics/openAccess$$aAll rights reserved$$uhttp://www.europeana.eu/rights/rr-f/
000061447 592__ $$a0.339$$b2016
000061447 593__ $$aComputer Science (miscellaneous)$$c2016$$dQ2
000061447 593__ $$aTheoretical Computer Science$$c2016$$dQ3
000061447 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/acceptedVersion
000061447 700__ $$0(orcid)0000-0003-4164-5078$$aAlastruey-Benedé, J.$$uUniversidad de Zaragoza
000061447 700__ $$0(orcid)0000-0002-5916-7898$$aIbáñez-Marín, P.$$uUniversidad de Zaragoza
000061447 700__ $$aRisueño, P.G.
000061447 7102_ $$15007$$2035$$aUniversidad de Zaragoza$$bDpto. Informát.Ingenie.Sistms.$$cÁrea Arquit.Tecnología Comput.
000061447 773__ $$g9573 (2016), 160-171$$pLect. notes comput. sci.$$tLecture Notes in Computer Science$$x0302-9743
000061447 8564_ $$s292848$$uhttps://zaguan.unizar.es/record/61447/files/texto_completo.pdf$$yPostprint
000061447 8564_ $$s56898$$uhttps://zaguan.unizar.es/record/61447/files/texto_completo.jpg?subformat=icon$$xicon$$yPostprint
000061447 909CO $$ooai:zaguan.unizar.es:61447$$particulos$$pdriver
000061447 951__ $$a2020-02-21-13:26:48
000061447 980__ $$aARTICLE