Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

General fuzzy min-max neural network for clustering and classification

This paper describes a general fuzzy min-max (GFMM) neural network which is a generalization and extension of the fuzzy min-max clustering and classification algorithms of Simpson (1992, 1993). The GFMM method combines supervised and unsupervised learning in a single training algorithm. The fusion of clustering and classification resulted in an algorithm that can be used as pure clustering, pure classification, or hybrid clustering classification. It exhibits a property of finding decision boundaries between classes while clustering patterns that cannot be said to belong to any of existing classes. Similarly to the original algorithms, the hyperbox fuzzy sets are used as a representation of clusters and classes. Learning is usually completed in a few passes and consists of placing and adjusting the hyperboxes in the pattern space; this is an expansion-contraction process. The classification results can be crisp or fuzzy. New data can be included without the need for retraining. While retaining all the interesting features of the original algorithms, a number of modifications to their definition have been made in order to accommodate fuzzy input patterns in the form of lower and upper bounds, combine the supervised and unsupervised learning, and improve the effectiveness of operations. A detailed account of the GFMM neural network, its comparison with the Simpson's fuzzy min-max neural networks, a set of examples, and an application to the leakage detection and identification in water distribution systems are given

Hybrid-parallel sparse matrix-vector multiplication with explicit communication overlap on current multicore-based systems

We evaluate optimized parallel sparse matrix-vector operations for several representative application areas on widespread multicore-based cluster configurations. First the single-socket baseline performance is analyzed and modeled with respect to basic architectural properties of standard multicore chips. Beyond the single node, the performance of parallel sparse matrix-vector operations is often limited by communication overhead. Starting from the observation that nonblocking MPI is not able to hide communication cost using standard MPI implementations, we demonstrate that explicit overlap of communication and computation can be achieved by using a dedicated communication thread, which may run on a virtual core. Moreover we identify performance benefits of hybrid MPI/OpenMP programming due to improved load balancing even without explicit communication overlap. We compare performance results for pure MPI, the widely used "vector-like" hybrid programming strategies, and explicit overlap on a modern multicore-based cluster and a Cray XE6 system.Comment: 16 pages, 10 figure

Achieving Efficient Strong Scaling with PETSc using Hybrid MPI/OpenMP Optimisation

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on massively parallel systems scientific software must evolve across the entire stack to exploit the multiple levels of parallelism exposed in modern architectures. In this paper we demonstrate the use of hybrid MPI/OpenMP parallelisation to optimise parallel sparse matrix-vector multiplication in PETSc, a widely used scientific library for the scalable solution of partial differential equations. Using large matrices generated by Fluidity, an open source CFD application code which uses PETSc as its linear solver engine, we evaluate the effect of explicit communication overlap using task-based parallelism and show how to further improve performance by explicitly load balancing threads within MPI processes. We demonstrate a significant speedup over the pure-MPI mode and efficient strong scaling of sparse matrix-vector multiplication on Fujitsu PRIMEHPC FX10 and Cray XE6 systems