A Novel Force Matrix Transformation with Optimal Load-Balance for 3-Body Potential Based Parallel Molecular Dynamics Using Atom-Decomposition in a Heterogeneous Cluster Environment [chapter]

J. V. Sumanth, David Swanson, Hong Jiang
High Performance Computing – HiPC 2007  
Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve
more » ... e running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present two force matrix transformations that are capable of exploiting the symmetries in a 3-body force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The first transformation distributes the number of interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. The second transformation distributes interactions to be computed uniformly over the entire volume of the force matrix allowing us to perform a block decomposition of the force matrix. The transformed force matrix can be scheduled by any block level scheduling algorithm. We also derive theoretical bounds for efficiency and load balance for prior work in the literature. We then prove some interesting and useful properties of our transformations and evaluate their advantages and disadvantages. A loop reordering optimization for our transformations is also described. The performance of an MPI implementation of the transformations is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.
doi:10.1007/978-3-540-77220-0_50 dblp:conf/hipc/SumanthSJ07 fatcat:6u35sauvpncxtnoldjtm6gb4r4