u 2013

Parallel methods for calculation of long-range electrostatic interactions

PAZÚRIKOVÁ, Jana and Luděk MATYSKA

Basic information

Original name

Parallel methods for calculation of long-range electrostatic interactions

Name in Czech

Paralelné metódy pre výpočet ďaleko-dosahových elektrostatických interakcií

Authors

PAZÚRIKOVÁ, Jana (703 Slovakia, guarantor, belonging to the institution) and Luděk MATYSKA (203 Czech Republic)

Edition

18 pp. 2013

Publisher

arXiv

Other information

Language

English

Type of outcome

Účelové publikace

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

RIV identification code

RIV/00216224:14330/13:00070602

Organization unit

Faculty of Informatics

Keywords in English

molecular dynamics; long-range interaction; parallel in time
Změněno: 17/4/2014 10:53, RNDr. Pavel Šmerk, Ph.D.

Abstract

V originále

Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space simulations, we suggest to calculate the bottleneck---the long-range interactions---parallel in time. This technical report aims to present the combination of parareal method and multilevel summation method. We thoroughly describe both methods and reasons for their particular combination. We also propose several optimizations that should provide the acceleration by an order of magnitude.

Links

MUNI/A/0760/2012, interní kód MU
Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace II. (Acronym: FI MAV II.)
Investor: Masaryk University, Category A