Analysis of Gromacs MPI Using the Opportunistic Cloud Infrastructure UnaCloud

Author

Garcés, Nathalia ; Castro, Harold ; Delgado, Paula ; Gonz´lez, A. ; Jaramillo, Carlos A. ; Peñaranda, Natalia ; Delgado, María Del Pilar

Author_Institution

Syst. & Comput. Eng. Dept., Univ. de Los Andes, Bogota, Colombia

fYear

2012

fDate

4-6 July 2012

Firstpage

1001

Lastpage

1006

Abstract

This paper shows and analyzes the execution of a molecular dynamic application that uses Message Passing Interface (MPI) mechanism-Gromacs MPI-over a cloud infrastructure (UnaCloud) supported by desktop computers. The main objective is to find a solution to support Gromacs-MPI on UnaCloud. This coupling was carried out in order to predict and to redefine the Helicobacter pylori Cag A protein 3D structure. Although the structure of eight indigenous sequences was obtained, the handle of resource discovery and failure recovery on the opportunistic infrastructure was achieved manually, restricting the application scope of the solution. To eliminate these restrictions, a mechanism to automate the process execution on UnaCloud was identified and proposed.

Keywords

biology computing; cloud computing; message passing; desktop computers; failure recovery; gromacs MPI; helicobacter pylori cag A protein 3D structure; indigenous sequences; message passing interface mechanism; molecular dynamic application; opportunistic cloud infrastructure unacloud; resource discovery; Central Processing Unit; Computational modeling; Computers; Fault tolerance; Libraries; Proteins; Software; Cloud Computing; Gromacs-MPI; Molecular Dynamics; Opportunistic Infrastructure;

fLanguage

English

Publisher

ieee

Conference_Titel

Complex, Intelligent and Software Intensive Systems (CISIS), 2012 Sixth International Conference on

Conference_Location

Palermo

Print_ISBN

978-1-4673-1233-2

Type

conf

DOI

10.1109/CISIS.2012.142

Filename

6245724