Implementation of parallelization and nano simulation using multi-scale modeling on various HPC setups

We have implemented multifarious aspects of nano simulation using multi scale modeling on various HPC (High Performance Computing) setups. Distribution of jobs from macro to nano scale has been shown which holds the essence of simulation at nano scale. This distribution is substantiated on MPI (Message Passing Interface) and PVM (Parallel Virtual Machine) on MATLAB, Linux and WCCS (Windows Compute Cluster Server) environments. In this paper we have shown the connections and a novel way of implementing multi scale computations on an HPC setup. We have also compared the implementation of MPI and PVM based HPC setup for MATLAB, Linux and WCCS environments. The selection criteria for identification and proposition of the tool, protocol and environment for an HPC setup plays an important role in deciding the tool to be used. Comparison of the advantages and disadvantages of each of the methodologies being put forward. MPI.NET was used under WCCS where C# was used. The latest versions were used for PVM Linux based setup where Open SUSE Linux was used as the operating system. The main two criteria user friendly and performance were compared and the recommendations are made for making the right balance between them.