3,594 research outputs found

    Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

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    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

    Evolutionary algorithm-based analysis of gravitational microlensing lightcurves

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    A new algorithm developed to perform autonomous fitting of gravitational microlensing lightcurves is presented. The new algorithm is conceptually simple, versatile and robust, and parallelises trivially; it combines features of extant evolutionary algorithms with some novel ones, and fares well on the problem of fitting binary-lens microlensing lightcurves, as well as on a number of other difficult optimisation problems. Success rates in excess of 90% are achieved when fitting synthetic though noisy binary-lens lightcurves, allowing no more than 20 minutes per fit on a desktop computer; this success rate is shown to compare very favourably with that of both a conventional (iterated simplex) algorithm, and a more state-of-the-art, artificial neural network-based approach. As such, this work provides proof of concept for the use of an evolutionary algorithm as the basis for real-time, autonomous modelling of microlensing events. Further work is required to investigate how the algorithm will fare when faced with more complex and realistic microlensing modelling problems; it is, however, argued here that the use of parallel computing platforms, such as inexpensive graphics processing units, should allow fitting times to be constrained to under an hour, even when dealing with complicated microlensing models. In any event, it is hoped that this work might stimulate some interest in evolutionary algorithms, and that the algorithm described here might prove useful for solving microlensing and/or more general model-fitting problems.Comment: 14 pages, 3 figures; accepted for publication in MNRA

    Formal Derivation of Concurrent Garbage Collectors

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    Concurrent garbage collectors are notoriously difficult to implement correctly. Previous approaches to the issue of producing correct collectors have mainly been based on posit-and-prove verification or on the application of domain-specific templates and transformations. We show how to derive the upper reaches of a family of concurrent garbage collectors by refinement from a formal specification, emphasizing the application of domain-independent design theories and transformations. A key contribution is an extension to the classical lattice-theoretic fixpoint theorems to account for the dynamics of concurrent mutation and collection.Comment: 38 pages, 21 figures. The short version of this paper appeared in the Proceedings of MPC 201

    Mapping Framework for Heterogeneous Reconfigurable Architectures:Combining Temporal Partitioning and Multiprocessor Scheduling

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    Efficient Sampling of Random Permutations

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    International audienceWe show how to uniformly distribute data at random (not to be confounded with permutation routing) in two settings that are able to deal with massive data: coarse grained parallelism and external memory. In contrast to previously known work for parallel setups, our method is able to fulfill the three criteria of uniformity, work-optimality and balance among the processors simultaneously. To guarantee the uniformity we investigate the matrix of communication requests between the processors. We show that its distribution is a generalization of the multivariate hypergeometric distribution and we give algorithms to sample it efficiently in the two settings

    Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

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    [Abstract] Background The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times. Here we present a novel parallel method, self-adaptive cooperative enhanced scatter search (saCeSS), to accelerate the solution of this class of problems. The method is based on the scatter search optimization metaheuristic and incorporates several key new mechanisms: (i) asynchronous cooperation between parallel processes, (ii) coarse and fine-grained parallelism, and (iii) self-tuning strategies. Results The performance and robustness of saCeSS is illustrated by solving a set of challenging parameter estimation problems, including medium and large-scale kinetic models of the bacterium E. coli, bakerés yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The results consistently show that saCeSS is a robust and efficient method, allowing very significant reduction of computation times with respect to several previous state of the art methods (from days to minutes, in several cases) even when only a small number of processors is used. Conclusions The new parallel cooperative method presented here allows the solution of medium and large scale parameter estimation problems in reasonable computation times and with small hardware requirements. Further, the method includes self-tuning mechanisms which facilitate its use by non-experts. We believe that this new method can play a key role in the development of large-scale and even whole-cell dynamic models.Ministerio de Economía y Competitividad; DPI2011-28112-C04-03Ministerio de Economía y Competitividad; DPI2011-28112-C04-04Ministerio de Economía y Competitividad; DPI2014-55276-C5-2-RMinisterio de Economía y Competitividad; TIN2013-42148-PMinisterio de Economía y Competitividad; TIN2016-75845-PGalicia. Consellería de Cultura, Educación e Ordenación Universitaria; R2014/041Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; R2016/045Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; GRC2013/05

    Higher-Order Process Modeling: Product-Lining, Variability Modeling and Beyond

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    We present a graphical and dynamic framework for binding and execution of business) process models. It is tailored to integrate 1) ad hoc processes modeled graphically, 2) third party services discovered in the (Inter)net, and 3) (dynamically) synthesized process chains that solve situation-specific tasks, with the synthesis taking place not only at design time, but also at runtime. Key to our approach is the introduction of type-safe stacked second-order execution contexts that allow for higher-order process modeling. Tamed by our underlying strict service-oriented notion of abstraction, this approach is tailored also to be used by application experts with little technical knowledge: users can select, modify, construct and then pass (component) processes during process execution as if they were data. We illustrate the impact and essence of our framework along a concrete, realistic (business) process modeling scenario: the development of Springer's browser-based Online Conference Service (OCS). The most advanced feature of our new framework allows one to combine online synthesis with the integration of the synthesized process into the running application. This ability leads to a particularly flexible way of implementing self-adaption, and to a particularly concise and powerful way of achieving variability not only at design time, but also at runtime.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455
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