Parallel symbolic state-space exploration is difficult, but what is the alternative?

State-space exploration is an essential step in many modeling and analysis problems. Its goal is to find the states reachable from the initial state of a discrete-state model described. The state space can used to answer important questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a starting point for sophisticated investigations expressed in temporal logic. Unfortunately, the state space is often so large that ordinary explicit data structures and sequential algorithms cannot cope, prompting the exploration of (1) parallel approaches using multiple processors, from simple workstation networks to shared-memory supercomputers, to satisfy large memory and runtime requirements and (2) symbolic approaches using decision diagrams to encode the large structured sets and relations manipulated during state-space generation. Both approaches have merits and limitations. Parallel explicit state-space generation is challenging, but almost linear speedup can be achieved; however, the analysis is ultimately limited by the memory and processors available. Symbolic methods are a heuristic that can efficiently encode many, but not all, functions over a structured and exponentially large domain; here the pitfalls are subtler: their performance varies widely depending on the class of decision diagram chosen, the state variable order, and obscure algorithmic parameters. As symbolic approaches are often much more efficient than explicit ones for many practical models, we argue for the need to parallelize symbolic state-space generation algorithms, so that we can realize the advantage of both approaches. This is a challenging endeavor, as the most efficient symbolic algorithm, Saturation, is inherently sequential. We conclude by discussing challenges, efforts, and promising directions toward this goal

A compiler extension for parallelizing arrays automatically on the cell heterogeneous processor

This paper describes the approaches taken to extend an array programming language compiler using a Virtual SIMD Machine (VSM) model for parallelizing array operations on Cell Broadband Engine heterogeneous machine. This development is part of ongoing work at the University of Glasgow for developing array compilers that are beneficial for applications in many areas such as graphics, multimedia, image processing and scientific computation. Our extended compiler, which is built upon the VSM interface, eases the parallelization processes by allowing automatic parallelisation without the need for any annotations or process directives. The preliminary results demonstrate significant improvement especially on data-intensive applications

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Freeform User Interfaces for Graphical Computing

報告番号: 甲15222 ; 学位授与年月日: 2000-03-29 ; 学位の種別: 課程博士 ; 学位の種類: 博士(工学) ; 学位記番号: 博工第4717号 ; 研究科・専攻: 工学系研究科情報工学専

Three Dimensional Software Modelling

Traditionally, diagrams used in software systems modelling have been two dimensional (2D). This is probably because graphical notations, such as those used in object-oriented and structured systems modelling, draw upon the topological graph metaphor, which, at its basic form, receives little benefit from three dimensional (3D) rendering. This paper presents a series of 3D graphical notations demonstrating effective use of the third dimension in modelling. This is done by e.g., connecting several graphs together, or in using the Z co-ordinate to show special kinds of edges. Each notation combines several familiar 2D diagrams, which can be reproduced from 2D projections of the 3D model. 3D models are useful even in the absence of a powerful graphical workstation: even 2D stereoscopic projections can expose more information than a plain planar diagram

Design of testbed and emulation tools

The research summarized was concerned with the design of testbed and emulation tools suitable to assist in projecting, with reasonable accuracy, the expected performance of highly concurrent computing systems on large, complete applications. Such testbed and emulation tools are intended for the eventual use of those exploring new concurrent system architectures and organizations, either as users or as designers of such systems. While a range of alternatives was considered, a software based set of hierarchical tools was chosen to provide maximum flexibility, to ease in moving to new computers as technology improves and to take advantage of the inherent reliability and availability of commercially available computing systems

How Do Gestures Influence Thinking and Speaking? The Gesture-for-Conceptualization Hypothesis.

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