Parallel molecular dynamics visualization using MPI with MPE graphics

Presents an MPI (Message Passing Interface) implementation of a molecular dynamics (MD) simulation using force decomposition as a parallelization strategy. In contrast to atom decomposition and spatial decomposition techniques, this method affords ease of load balancing and performs well for an intermediate number of atoms, even for irregular geometries. The interactions between the atoms are calculated in a separate module. Periodic boundary conditions are used to simulate an infinitely replicated confined region in space. The main thrust of our research efforts is currently directed towards in situ visualization of the MD simulations. This is accomplished using simple X-Windows calls available through the MPE (MPI Extensions) extension to the MPI routines. Our implementation using MPI with MPE graphics makes the algorithm portable. The code has been tested on a range of platforms, including clusters of workstations as well as the the IBM SP2 at the Maul High-Performance Supercomputing Center (MHPCC) and the IBM SP1 at the Albuquerque Resource Center of the University of New Mexico. We have also adapted our code to interact with a high-end graphics computer (SGI Onyx) using the OpenGL graphics library, which allows for real-time manipulation of 3D objects. The communication between the MD simulation and the graphics renderer was achieved with the use of sockets. The use of sockets allows the parallel MD simulation to run independently of the application used for graphics rendering.