Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications

Recovering Grammar Relationships for the Java Language Specification

Grammar convergence is a method that helps discovering relationships between different grammars of the same language or different language versions. The key element of the method is the operational, transformation-based representation of those relationships. Given input grammars for convergence, they are transformed until they are structurally equal. The transformations are composed from primitive operators; properties of these operators and the composed chains provide quantitative and qualitative insight into the relationships between the grammars at hand. We describe a refined method for grammar convergence, and we use it in a major study, where we recover the relationships between all the grammars that occur in the different versions of the Java Language Specification (JLS). The relationships are represented as grammar transformation chains that capture all accidental or intended differences between the JLS grammars. This method is mechanized and driven by nominal and structural differences between pairs of grammars that are subject to asymmetric, binary convergence steps. We present the underlying operator suite for grammar transformation in detail, and we illustrate the suite with many examples of transformations on the JLS grammars. We also describe the extraction effort, which was needed to make the JLS grammars amenable to automated processing. We include substantial metadata about the convergence process for the JLS so that the effort becomes reproducible and transparent

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

Learning to Extract Keyphrases from Text

Many academic journals ask their authors to provide a list of about five to fifteen key words, to appear on the first page of each article. Since these key words are often phrases of two or more words, we prefer to call them keyphrases. There is a surprisingly wide variety of tasks for which keyphrases are useful, as we discuss in this paper. Recent commercial software, such as Microsoft?s Word 97 and Verity?s Search 97, includes algorithms that automatically extract keyphrases from documents. In this paper, we approach the problem of automatically extracting keyphrases from text as a supervised learning task. We treat a document as a set of phrases, which the learning algorithm must learn to classify as positive or negative examples of keyphrases. Our first set of experiments applies the C4.5 decision tree induction algorithm to this learning task. The second set of experiments applies the GenEx algorithm to the task. We developed the GenEx algorithm specifically for this task. The third set of experiments examines the performance of GenEx on the task of metadata generation, relative to the performance of Microsoft?s Word 97. The fourth and final set of experiments investigates the performance of GenEx on the task of highlighting, relative to Verity?s Search 97. The experimental results support the claim that a specialized learning algorithm (GenEx) can generate better keyphrases than a general-purpose learning algorithm (C4.5) and the non-learning algorithms that are used in commercial software (Word 97 and Search 97)

Structured Review of the Evidence for Effects of Code Duplication on Software Quality

This report presents the detailed steps and results of a structured review of code clone literature. The aim of the review is to investigate the evidence for the claim that code duplication has a negative effect on code changeability. This report contains only the details of the review for which there is not enough place to include them in the companion paper published at a conference (Hordijk, Ponisio et al. 2009 - Harmfulness of Code Duplication - A Structured Review of the Evidence)

A model-based framework to bridge architecting, engineering, and testing

The purpose of this project is to construct a model-based framework to bridge architecting, engineering, and testing. The framework supports software development teams in analyzing the architecture of software (Architecture Analysis) and the impacts of changes (Impact Analysis) during software’s development and maintenance.The software, which the project focused on, is one of the controllers composing the printing products. The controller is complex due to its development history, context, and techniques. Its current characteristics have the possibility of causing costly errors and delays in the controller’s evolution. One solution to prevent such risks is formulating an overview of the controller’s architecture.The framework realizes the solution by modeling the controller’s structure and interface definitions. Therefore, the controller development team is able to interpret the controller’s architecture comprehensively, discover the controller’s deficiencies promptly, investigate influences of changes efficiently, and document design decisions regularly