The Impact of Virtualization on Grid Parallel Molecular Dynamics Simulations
Lino García-Tarrés (Fundación Centro Tecnolóxico de Supercomputación de Galicia (CESGA))Elvira Guàrdia (Dep. de Física i Enginyeria Nuclear. Univ. Politècnica de Catalunya)
Joaquim Casulleras (Dep. de Física i Enginyeria Nuclear. Univ. Politècnica de Catalunya)
Abstract:
The influence of the Xen virtualization technology on a parallel Molecular Dynamics simulation algorithm has been studied by the use of the Interactive European Grid infrastructure. Two parallelization strategies have been implemented; the first one is based on the Message Passing Interface (MPI) standard while the second one uses the low level shared memory (SHM) UNIX system V communication capabilities between processors. In order to compare the benefits of these methodologies and technologies, four sets of pure water physical systems have been simulated.
Keywords:
Parallel and Distributed Computing, Grid Computing (middleware, algorithms, performance evaluation, ...), Computing in Healthcare and Biosciences, Virtualization
