Title :
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
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;
Conference_Titel :
Complex, Intelligent and Software Intensive Systems (CISIS), 2012 Sixth International Conference on
Conference_Location :
Palermo
Print_ISBN :
978-1-4673-1233-2
DOI :
10.1109/CISIS.2012.142