Parallel methods for calculation of long-range electrostatic interactions

PAZÚRIKOVÁ, Jana and Luděk MATYSKA. Parallel methods for calculation of long-range electrostatic interactions. arXiv, 2013, 18 pp.

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

• Original language: English
• Type of outcome: Special-purpose publication
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• RIV identification code: RIV/00216224:14330/13:00070602
• Organization unit: Faculty of Informatics
• Keywords in English: molecular dynamics; long-range interaction; parallel in time

Abstract

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