ExaStamp: A Parallel Framework for Molecular Dynamics on Heterogeneous Clusters
E Cieren and L Colombet and S Pitoiset and R Namyst, EURO-PAR 2014: PARALLEL PROCESSING WORKSHOPS, PT II, 8806, 121-132 (2014).
Recent evolution of supercomputer architectures toward massively multi- cores nodes equipped with many-core accelerators is leading to make MPI- only applications less effective. To fully tap into the potential of these architectures, hybrid approaches - mixing MPI, threads and CUDA or OpenCL - usually meet performance expectations, but at the price of huge development and optimization efforts. In this paper, we present a programming framework specialized for molecular dynamics simulations. This framework allows end-users to develop their computation kernels in the form of sequential-looking functions and generates multi-level parallelism combining vectorized and SIMD kernels, multi-threading and communications. We report on preliminary performance results obtained on different architectures with widely used force computation kernels.
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