We present an easy to use and flexible grid library for developing highly scalable parallel simulations. The distributed cartesian cell-refinable grid (dccrg) supports adaptive mesh refinement and allows an arbitrary C++ class to be used as cell data. The amount of data in grid cells can vary both in space and time allowing dccrg to be used in very different types of simulations, for example in fluid and particle codes. Dccrg transfers the data between neighboring cells on different processes transparently and asynchronously allowing one to overlap computation and communication. This enables excellent scalability at least up to 32 k cores in magnetohydrodynamic tests depending on the problem and hardware. In the version of dccrg presented here part of the mesh metadata is replicated between MPI processes reducing the scalability of adaptive mesh refinement (AMR) to between 200 and 600 processes. Dccrg is free software that anyone can use, study and modify and is available at https://gitorious.org/dccrg. Users are also kindly requested to cite this work when publishing results obtained with dccrg.
Adaptive scientific computations require that periodic repartitioning (load balancing) occur dynamically to maintain load balance. Hypergraph partitioning is a successful model for minimizing communication volume in scientific computations, and partitioning software for the static case is widely available. In this paper, we present a new hypergraph model for the dynamic case, where we minimize the sum of communication in the application plus the migration cost to move data, thereby reducing total execution time. The new model can be solved using hypergraph partitioning with fixed vertices. We describe an implementation of a parallel multilevel repartitioning algorithm within the Zoltan load-balancing toolkit, which to our knowledge is the first code for dynamic load balancing based on hypergraph partitioning. Finally, we present experimental results that demonstrate the effectiveness of our approach on a Linux cluster with up to 64 processors. Our new algorithm compares favorably to the widely used ParMETIS partitioning software in terms of quality, and would have reduced total execution time in most of our test cases. * Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin
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