2010 International Conference on Complex, Intelligent and Software Intensive Systems (2012)
July 4, 2012 to July 6, 2012
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.
Computers, Proteins, Central Processing Unit, Computational modeling, Software, Libraries, Fault tolerance, Gromacs-MPI, Opportunistic Infrastructure, Cloud Computing, Molecular Dynamics
Carlos A. Jaramillo, Andres Gonz'lez, Paula Delgado, Harold Castro, Nathalia Garces, Natalia Penaranda, Maria del Pilar Delgado, "Analysis of Gromacs MPI Using the Opportunistic Cloud Infrastructure UnaCloud", 2010 International Conference on Complex, Intelligent and Software Intensive Systems, vol. 00, no. , pp. 1001-1006, 2012, doi:10.1109/CISIS.2012.142