Abstract
The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment ...and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.
A terminology for in situ visualization and analysis systems Childs, Hank; Ahern, Sean D.; Ahrens, James ...
International journal of high performance computing applications/The international journal of high performance computing applications,
11/2020, Volume:
34, Issue:
6
Journal Article
Peer reviewed
Open access
The term “in situ processing” has evolved over the last decade to mean both a specific strategy for visualizing and analyzing data and an umbrella term for a processing paradigm. The resulting ...confusion makes it difficult for visualization and analysis scientists to communicate with each other and with their stakeholders. To address this problem, a group of over 50 experts convened with the goal of standardizing terminology. This paper summarizes their findings and proposes a new terminology for describing in situ systems. An important finding from this group was that in situ systems are best described via multiple, distinct axes: integration type, proximity, access, division of execution, operation controls, and output type. This paper discusses these axes, evaluates existing systems within the axes, and explores how currently used terms relate to the axes.
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We present the Exascale Framework for High Fidelity coupled Simulations (EFFIS), a workflow and code coupling framework developed as part of the Whole Device Modeling Application (WDMApp) in the ...Exascale Computing Project. EFFIS consists of a library, command line utilities, and a collection of run-time daemons. Together, these software products enable users to easily compose and execute workflows that include: strong or weak coupling, in situ (or offline) analysis/visualization/monitoring, command-and-control actions, remote dashboard integration, and more. We describe WDMApp physics coupling cases and computer science requirements that motivate the design of the EFFIS framework. Furthermore, we explain the essential enabling technology that EFFIS leverages: ADIOS for performant data movement, PerfStubs/TAU for performance monitoring, and an advanced COUPLER for transforming coupling data from its native format to the representation needed by another application. Finally, we demonstrate EFFIS using coupled multi-simulation WDMApp workflows and exemplify how the framework supports the project’s needs. We show that EFFIS and its associated services for data movement, visualization, and performance collection does not introduce appreciable overhead to the WDMApp workflow and that the resource-dominant application’s idle time while waiting for data is minimal.
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The VTK-m software library enables scientific visualization on exascale-class supercomputers. Exascale machines are particularly challenging for software development in part because they use GPU ...accelerators to provide the vast majority of their computational throughput. Algorithmic designs for GPUs and GPU-centric computing often deviate from those that worked well on previous generations of high-performance computers that relied on traditional CPUs. Fortunately, VTK-m provides scientific visualization algorithms for GPUs and other accelerators. VTK-m also provides a framework that simplifies the implementation of new algorithms and adds a porting layer to work across multiple processor types. This paper describes the main challenges encountered when making scientific visualization available at exascale. We document the surprises and obstacles faced when moving from pre-exascale platforms to the final exascale designs and the performance on those systems including scaling studies on Frontier, an exascale machine with over 37,000 AMD GPUs. We also report on the integration of VTK-m with other exascale software technologies. Finally, we show how VTK-m helps scientific discovery for applications such as fusion and particle acceleration that leverage an exascale supercomputer.
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The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and ...reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high quality tomogram is available within 30 minutes. Real time tomography is integrated into tomviz, an open source and cross platform 3D analysis tool that contains intuitive graphical user interfaces (GUI) to enable any scientist to characterize biological and material structure in 3D.
As the visualization research community reorients its software to address up-coming challenges, it must successfully deal with diverse processor architectures, distributed systems, various data ...sources, massive parallelism, multiple input and output devices, and interactivity.
Nonlinear resonance of rectangular plates Geveci, Berk; Walker, J.D.A.
Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences,
05/2001, Volume:
457, Issue:
2009
Journal Article
Peer reviewed
Nonlinear flow-induced oscillations of a thin rectangular plate are studied using a spectral method to calculate the vertical and tangential displacements. When the plate is subjected to forcing near ...the first linear resonance frequency, a complex motion with amplitude comparable to the plate thickness occurs in the form of a modulated high-frequency vibration. Numerical solutions for two- and three-dimensional plates are obtained to establish the nature of these oscillations. The numerical results are supported by an asymptotic analysis describing nonlinear resonance for rectangular plates.
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