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DAiSES: Dynamic Adaptivity in Support of Extreme Scale Department of Energy Project No. ER25622 Prime Contract No. DE-FG02-04ER25622 Final Report for September 15, 2004-September 14, 2008

Description: The DAiSES project [Te04] was focused on enabling conventional operating systems, in particular, those running on extreme scale systems, to dynamically customize system resource management in order to offer applications the best possible environment in which to execute. Such dynamic adaptation allows operating systems to modify the execution environment in response to changes in workload behavior and system state. The main challenges of this project included determination of what operating system (OS) algorithms, policies, and parameters should be adapted, when to adapt them, and how to adapt them. We addressed these challenges by using a combination of static analysis and runtime monitoring and adaptation to identify a priori profitable targets of adaptation and effective heuristics that can be used to dynamically trigger adaptation. Dynamic monitoring and adaptation of the OS was provided by either kernel modifications or the use of KernInst and Kperfmon [Wm04]. Since Linux, an open source OS, was our target OS, patches submitted by kernel developers and researchers often facilitated kernel modifications. KernInst operates on unmodified commodity operating systems, i.e., Solaris and Linux; it is fine-grained, thus, there were few constraints on how the underlying OS can be modified. Dynamically adaptive functionality of operating systems, both in terms of policies and parameters, is intended to deliver the maximum attainable performance of a computational environment and meet, as best as possible, the needs of high-performance applications running on extreme scale systems, while meeting system constraints. DAiSES research endeavored to reach this goal by developing methodologies for dynamic adaptation of OS parameters and policies to manage stateful and stateless resources [Te06] and pursuing the following two objectives: (1) Development of mechanisms to dynamically sense, analyze, and adjust common performance metrics, fluctuating workload situations, and overall system environment conditions. (2) Demonstration, via Linux prototypes and experiments, of dynamic self-tuning and ...
Date: May 5, 2009
Creator: PI: Patricia J. Teller, Ph.D. University of Texas-El Paso Department of Computer Science
Partner: UNT Libraries Government Documents Department

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

Description: The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii) evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.
Date: May 12, 2008
Creator: Data Analysis and Visualization (IDAV) and the Department of Computer Science, University of California, Davis, One Shields Avenue, Davis CA 95616, USA,; nternational Research Training Group ``Visualization of Large and Unstructured Data Sets,'' University of Kaiserslautern, Germany; Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA; Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA,; Computer Science Division,University of California, Berkeley, CA, USA, et al.
Partner: UNT Libraries Government Documents Department