Large scale simulation of parallel molecular dynamics

Author

Bernard, Pierre-Eric ; Gautier, Thierry ; Trystram, Denis

Author_Institution

INRIA Lorraine, Villers les Nancy, France

fYear

1999

fDate

12-16 Apr 1999

Firstpage

638

Lastpage

644

Abstract

This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the simulation of molecular dynamics designed to handle large proteins in biology. The implementation is based on the multi-threading parallel programming environment, called ATHAPASCAN which allows to implement and evaluate easily several load-balancing strategies. Some experiments run on one of the largest molecule ever simulated (a hydrated β-galactosidase with 413039 atoms) show the interest of such a parallel programming environment

Keywords

biology computing; digital simulation; multi-threading; programming environments; proteins; resource allocation; ATHAPASCAN; TAKAKAW; biology; hydrated β-galactosidase; large proteins; large scale simulation; load balancing strategies; multi-threading parallel programming environment; parallel molecular dynamics; Biological system modeling; Biology computing; Computational modeling; Equations; High performance computing; Large-scale systems; Load management; Microwave integrated circuits; Proteins; Solid modeling;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel Processing, 1999. 13th International and 10th Symposium on Parallel and Distributed Processing, 1999. 1999 IPPS/SPDP. Proceedings

Conference_Location

San Juan

Print_ISBN

0-7695-0143-5

Type

conf

DOI

10.1109/IPPS.1999.760544

Filename

760544