Multiprocessor sparse L/U decomposition with controlled fill-in

Generation of the maximal compatibles of pivot elements for a class of small sparse matrices is studied. The algorithm involves a binary tree search and has a complexity exponential in the order of the matrix. Different strategies for selection of a set of compatible pivots based on the Markowitz criterion are investigated. The competing issues of parallelism and fill-in generation are studied and results are provided. A technque for obtaining an ordered compatible set directly from the ordered incompatible table is given. This technique generates a set of compatible pivots with the property of generating few fills. A new hueristic algorithm is then proposed that combines the idea of an ordered compatible set with a limited binary tree search to generate several sets of compatible pivots in linear time. Finally, an elimination set to reduce the matrix is selected. Parameters are suggested to obtain a balance between parallelism and fill-ins. Results of applying the proposed algorithms on several large application matrices are presented and analyzed

Performance of the estimators of stable law parameters

In this paper, we discuss the issue of estimation of the parameters of stable laws. We present an overview of the known methods and compare them on samples of different sizes and for different values of the parameters. Performance tables are provided.Stable distribution, Simulation, Random variable

Automatic Generation of Models of Microarchitectures

Detailed microarchitectural models are necessary to predict, explain, or optimize the performance of software running on modern microprocessors. Building such models often requires a significant manual effort, as the documentation provided by hardware manufacturers is typically not precise enough. The goal of this thesis is to develop techniques for generating microarchitectural models automatically. In the first part, we focus on recent x86 microarchitectures. We implement a tool to accurately evaluate small microbenchmarks using hardware performance counters. We then describe techniques to automatically generate microbenchmarks for measuring the performance of individual instructions and for characterizing cache architectures. We apply our implementations to more than a dozen different microarchitectures. In the second part of the thesis, we study more general techniques to obtain models of hardware components. In particular, we propose the concept of gray-box learning, and we develop a learning algorithm for Mealy machines that exploits prior knowledge about the system to be learned. Finally, we show how this algorithm can be adapted to minimize incompletely specified Mealy machines—a well-known NP-complete problem. Our implementation outperforms existing exact minimization techniques by several orders of magnitude on a number of hard benchmarks; it is even competitive with state-of-the-art heuristic approaches.Zur Vorhersage, Erklärung oder Optimierung der Leistung von Software auf modernen Mikroprozessoren werden detaillierte Modelle der verwendeten Mikroarchitekturen benötigt. Das Erstellen derartiger Modelle ist oft mit einem hohen Aufwand verbunden, da die erforderlichen Informationen von den Prozessorherstellern typischerweise nicht zur Verfügung gestellt werden. Das Ziel der vorliegenden Arbeit ist es, Techniken zu entwickeln, um derartige Modelle automatisch zu erzeugen. Im ersten Teil beschäftigen wir uns mit aktuellen x86-Mikroarchitekturen. Wir entwickeln zuerst ein Tool, das kleine Microbenchmarks mithilfe von Performance Countern auswerten kann. Danach beschreiben wir Techniken, um automatisch Microbenchmarks zu erzeugen, mit denen die Leistung einzelner Instruktionen gemessen sowie die Cache-Architektur charakterisiert werden kann. Im zweiten Teil der Arbeit betrachten wir allgemeinere Techniken, um Hardwaremodelle zu erzeugen. Wir schlagen das Konzept des “Gray-Box Learning” vor, und wir entwickeln einen Lernalgorithmus für Mealy-Maschinen, der bekannte Informationen über das zu lernende System berücksichtigt. Zum Abschluss zeigen wir, wie dieser Algorithmus auf das Problem der Minimierung unvollständig spezifizierter Mealy-Maschinen übertragen werden kann. Hierbei handelt es sich um ein bekanntes NP-vollständiges Problem. Unsere Implementierung ist in mehreren Benchmarks um Größenordnungen schneller als vorherige Ansätze

Short Software Descriptions

This paper presents briefly the software for interactive decision support and software tools for developing decision support systems, developed in years 1985-1988 within the contracted study agreement between the System and Decision Sciences Program at IIASA and several Polish scientific institutions, including the following: Institute of Automatic Control, Warsaw University of Technology; Institute of Systems Research, Polish Academy of Sciences; Institute of Informatics, Warsaw University; Institute of Automatics, Academy of Mining and Metallurgy, Krakow. The theoretical part of the results developed within the project is presented in the IIASA Working Paper WP-88-071 entitled "Theory, Software and Testing Examples in Decision Support Systems". This volume contains also the theoretical and methodological backgrounds of the software systems developed within the project. These are presented shortly in this paper. Detailed software descriptions and user manuals have been published as separate IIASA Working Papers. Each Working Paper describes one software product and the title of such a paper corresponds to the title of the section in this paper. All software products in executable form are available to educational and scientific institutions, assuming that these products will not be used for commercial applications. Inquires for software should be directed to the System and Decision Sciences Program at IIASA, Methodology of Decision Analysis Project

Ab initio RNA folding

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure

Users manual for the Automated Performance Test System (APTS)

The characteristics of and the user information for the Essex Automated Performance Test System (APTS) computer-based portable performance assessment battery are given. The battery was developed to provide a menu of performance test tapping the widest possible variety of human cognitive and motor functions, implemented on a portable computer system suitable for use in both laboratory and field settings for studying the effects of toxic agents and other stressors. The manual gives guidance in selecting, administering and scoring tests from the battery, and reviews the data and studies underlying the development of the battery. Its main emphasis is on the users of the battery - the scientists, researchers and technicians who wish to examine changes in human performance across time or as a function of changes in the conditions under which test data are obtained. First the how to information needed to make decisions about where and how to use the battery is given, followed by the research background supporting the battery development. Further, the development history of the battery focuses largely on the logical framework within which tests were evaluated

SEAPAK user's guide, version 2.0. Volume 1: System description

The SEAPAK is a user interactive satellite data analysis package that was developed for the processing and interpretation of Nimbus-7/Coastal Zone Color Scanner (CZCS) and the NOAA Advanced Very High Resolution Radiometer (AVHRR) data. Significant revisions were made to version 1.0 of the guide, and the ancillary environmental data analysis module was expanded. The package continues to emphasize user friendliness and user interactive data analyses. Additionally, because the scientific goals of the ocean color research being conducted have shifted to large space and time scales, batch processing capabilities for both satellite and ancillary environmental data analyses were enhanced, thus allowing large quantities of data to be ingested and analyzed in background