22,960 research outputs found

    Accelerating scientific codes by performance and accuracy modeling

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    Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used suboptimally. In a typical scenario, accuracy requirements are imposed, and attained through suboptimal performance. In this paper, we present a methodology for the automatic selection of parameters for simulation codes, and a corresponding prototype tool. To be amenable to our methodology, the target code must expose the parameters affecting accuracy and performance, and there must be formulas available for error bounds and computational complexity of the underlying methods. As a case study, we consider the particle-particle particle-mesh method (PPPM) from the LAMMPS suite for molecular dynamics, and use our tool to identify configurations of the input parameters that achieve a given accuracy in the shortest execution time. When compared with the configurations suggested by expert users, the parameters selected by our tool yield reductions in the time-to-solution ranging between 10% and 60%. In other words, for the typical scenario where a fixed number of core-hours are granted and simulations of a fixed number of timesteps are to be run, usage of our tool may allow up to twice as many simulations. While we develop our ideas using LAMMPS as computational framework and use the PPPM method for dispersion as case study, the methodology is general and valid for a range of software tools and methods

    Using Variable Dwell Time to Accelerate Gaze-Based Web Browsing with Two-Step Selection

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    In order to avoid the "Midas Touch" problem, gaze-based interfaces for selection often introduce a dwell time: a fixed amount of time the user must fixate upon an object before it is selected. Past interfaces have used a uniform dwell time across all objects. Here, we propose a gaze-based browser using a two-step selection policy with variable dwell time. In the first step, a command, e.g. "back" or "select", is chosen from a menu using a dwell time that is constant across the different commands. In the second step, if the "select" command is chosen, the user selects a hyperlink using a dwell time that varies between different hyperlinks. We assign shorter dwell times to more likely hyperlinks and longer dwell times to less likely hyperlinks. In order to infer the likelihood each hyperlink will be selected, we have developed a probabilistic model of natural gaze behavior while surfing the web. We have evaluated a number of heuristic and probabilistic methods for varying the dwell times using both simulation and experiment. Our results demonstrate that varying dwell time improves the user experience in comparison with fixed dwell time, resulting in fewer errors and increased speed. While all of the methods for varying dwell time resulted in improved performance, the probabilistic models yielded much greater gains than the simple heuristics. The best performing model reduces error rate by 50% compared to 100ms uniform dwell time while maintaining a similar response time. It reduces response time by 60% compared to 300ms uniform dwell time while maintaining a similar error rate.Comment: This is an Accepted Manuscript of an article published by Taylor & Francis in the International Journal of Human-Computer Interaction on 30 March, 2018, available online: http://www.tandfonline.com/10.1080/10447318.2018.1452351 . For an eprint of the final published article, please access: https://www.tandfonline.com/eprint/T9d4cNwwRUqXPPiZYm8Z/ful

    Enhancing speed and scalability of the ParFlow simulation code

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    Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

    Grid simulation services for the medical community

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    The first part of this paper presents a selection of medical simulation applications, including image reconstruction, near real-time registration for neuro-surgery, enhanced dose distribution calculation for radio-therapy, inhaled drug delivery prediction, plastic surgery planning and cardio-vascular system simulation. The latter two topics are discussed in some detail. In the second part, we show how such services can be made available to the clinical practitioner using Grid technology. We discuss the developments and experience made during the EU project GEMSS, which provides reliable, efficient, secure and lawful medical Grid services

    Panel on future challenges in modeling methodology

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    This panel paper presents the views of six researchers and practitioners of simulation modeling. Collectively we attempt to address a range of key future challenges to modeling methodology. It is hoped that the views of this paper, and the presentations made by the panelists at the 2004 Winter Simulation Conference will raise awareness and stimulate further discussion on the future of modeling methodology in areas such as modeling problems in business applications, human factors and geographically dispersed networks; rapid model development and maintenance; legacy modeling approaches; markup languages; virtual interactive process design and simulation; standards; and Grid computing

    Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

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    Shelf and coastal sea processes extend from the atmosphere through the water column and into the sea bed. These processes are driven by physical, chemical, and biological interactions at local scales, and they are influenced by transport and cross strong spatial gradients. The linkages between domains and many different processes are not adequately described in current model systems. Their limited integration level in part reflects lacking modularity and flexibility; this shortcoming hinders the exchange of data and model components and has historically imposed supremacy of specific physical driver models. We here present the Modular System for Shelves and Coasts (MOSSCO, http://www.mossco.de), a novel domain and process coupling system tailored---but not limited--- to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the existing coupling technology Earth System Modeling Framework and on the Framework for Aquatic Biogeochemical Models, thereby creating a unique level of modularity in both domain and process coupling; the new framework adds rich metadata, flexible scheduling, configurations that allow several tens of models to be coupled, and tested setups for coastal coupled applications. That way, MOSSCO addresses the technology needs of a growing marine coastal Earth System community that encompasses very different disciplines, numerical tools, and research questions.Comment: 30 pages, 6 figures, submitted to Geoscientific Model Development Discussion
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