In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation.

Q2 Computer Science

Supercomputing Frontiers and Innovations Pub Date : 2017-07-01 DOI:10.14529/jsfi170304

Nuttiiya Seekhao, Joseph JaJa, Luc Mongeau, Nicole Y K Li-Jessen

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引用次数: 6

Abstract

A fast and insightful visualization is essential in modeling biological system behaviors and understanding underlying inter-cellular mechanisms. High fidelity models produce billions of data points per time step, making in situ visualization techniques extremely desirable as they mitigate I/O bottlenecks and provide computational steering capability. In this work, we present a novel high-performance scheme to couple in situ visualization with the simulation of the vocal fold inflammation and repair using little to no extra cost in execution time or computing resources. The visualization component is first optimized with an adaptive sampling scheme to accelerate the rendering process while maintaining the precision of the displayed visual results. Our software employs VirtualGL to perform visualization in situ. The scheme overlaps visualization and simulation, resulting in the optimal utilization of computing resources. This results in an in situ system biology simulation suite capable of remote simulation of 17 million biological cells and 1.2 billion chemical data points, remote visualization of the results, and delivery of visualized frames with aggregated statistics to remote clients in real-time.

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基于agent的三维声带炎症和修复模拟的原位可视化。

一个快速和深刻的可视化是必不可少的建模生物系统的行为和理解潜在的细胞间机制。高保真模型每个时间步产生数十亿个数据点，使得原位可视化技术非常可取，因为它们可以缓解I/O瓶颈并提供计算转向能力。在这项工作中，我们提出了一种新的高性能方案，将原位可视化与声带炎症和修复的模拟结合起来，在执行时间或计算资源方面几乎没有额外的成本。首先使用自适应采样方案对可视化组件进行优化，以加速渲染过程，同时保持显示可视化结果的精度。我们的软件使用VirtualGL来执行现场可视化。该方案将可视化和仿真相结合，实现了计算资源的优化利用。这就产生了一个原位系统生物学模拟套件，能够远程模拟1700万个生物细胞和12亿个化学数据点，远程可视化结果，并实时向远程客户端提供汇总统计数据的可视化框架。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Supercomputing Frontiers and Innovations Computer Science-Computational Theory and Mathematics

CiteScore

1.60

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： The Journal of Supercomputing Frontiers and Innovations (JSFI) is a new peer reviewed publication that addresses the urgent need for greater dissemination of research and development findings and results at the leading edge of high performance computing systems, highly parallel methods, and extreme scaled applications. Key topic areas germane include, but not limited to: Enabling technologies for high performance computing Future generation supercomputer architectures Extreme-scale concepts beyond conventional practices including exascale Parallel programming models, interfaces, languages, libraries, and tools Supercomputer applications and algorithms Distributed operating systems, kernels, supervisors, and virtualization for highly scalable computing Scalable runtime systems software Methods and means of supercomputer system management, administration, and monitoring Mass storage systems, protocols, and allocation Energy and power minimization for very large deployed computers Resilience, reliability, and fault tolerance for future generation highly parallel computing systems Parallel performance and correctness debugging Scientific visualization for massive data and computing both external and in situ Education in high performance computing and computational science.