A Sparse Program Dependence Graph For Object Oriented Programming Languages

The Program Dependence Graph (PDG) has achieved widespread acceptance as a useful tool for software engineering, program analysis, and automated compiler optimizations. This thesis presents the Sparse Object Oriented Program Dependence Graph (SOOPDG), a formalism that contains elements of traditional PDG\u27s adapted to compactly represent programs written in object-oriented languages such as Java. This formalism is called sparse because, in contrast to other OO and Java-specific adaptations of PDG\u27s, it introduces few node types and no new edge types beyond those used in traditional dependence-based representations. This results in correct program representations using smaller graph structures and simpler semantics when compared to other OO formalisms. We introduce the Single Flow to Use (SFU) property which requires that exactly one definition of each variable be available for each use. We demonstrate that the SOOPDG, with its support for the SFU property coupled with a higher order rewriting semantics, is sufficient to represent static Java-like programs and dynamic program behavior. We present algorithms for creating SOOPDG representations from program text, and describe graph rewriting semantics. We also present algorithms for common static analysis techniques such as program slicing, inheritance analysis, and call chain analysis. We contrast the SOOPDG with two previously published OO graph structures, the Java System Dependence Graph and the Java Software Dependence Graph. The SOOPDG results in comparatively smaller static representations of programs, cleaner graph semantics, and potentially more accurate program analysis. Finally, we introduce the Simulation Dependence Graph (SDG). The SDG is a related representation that is developed specifically to represent simulation systems, but is extensible to more general component-based software design paradigms. The SDG allows formal reasoning about issues such as component composition, a property critical to the creation and analysis of complex simulation systems and component-based design systems

Modern Programming Language Julia

Tato práce popisuje dynamický programovací jazyk Julia. Nejprve uživatele seznámí s jeho syntaxí a implementací. Dále popisuje základní pravidla pro efektivní psaní kódu a optimalizaci. Tento dokument také uvádí některé příklady použití ve vědeckých pracích. Nakonec je v experimentální části provedeno porovnání Julie s jazykem Python a C, kteří byli vybráni jako zástupci nejpoužívanějšího statického a dynamického jazyka.This work describes dynamic programming language Julia. Firstly, user is introduced to syntax and implementation of this language. Next there are advices for writing effective code and his optimalization. Also some examples of using Julia in scientific projects are described. Comparison between Julia, C and Python is in experimental part. Python and C were chosen as examples of statically and dynamically typed languages.

Higher-Order, Data-Parallel Structured Deduction

State-of-the-art Datalog engines include expressive features such as ADTs (structured heap values), stratified aggregation and negation, various primitive operations, and the opportunity for further extension using FFIs. Current parallelization approaches for state-of-art Datalogs target shared-memory locking data-structures using conventional multi-threading, or use the map-reduce model for distributed computing. Furthermore, current state-of-art approaches cannot scale to formal systems which pervasively manipulate structured data due to their lack of indexing for structured data stored in the heap. In this paper, we describe a new approach to data-parallel structured deduction that involves a key semantic extension of Datalog to permit first-class facts and higher-order relations via defunctionalization, an implementation approach that enables parallelism uniformly both across sets of disjoint facts and over individual facts with nested structure. We detail a core language, $DL_s$, whose key invariant (subfact closure) ensures that each subfact is materialized as a top-class fact. We extend $DL_s$ to Slog, a fully-featured language whose forms facilitate leveraging subfact closure to rapidly implement expressive, high-performance formal systems. We demonstrate Slog by building a family of control-flow analyses from abstract machines, systematically, along with several implementations of classical type systems (such as STLC and LF). We performed experiments on EC2, Azure, and ALCF's Theta at up to 1000 threads, showing orders-of-magnitude scalability improvements versus competing state-of-art systems

Ernst Denert Award for Software Engineering 2020

This open access book provides an overview of the dissertations of the eleven nominees for the Ernst Denert Award for Software Engineering in 2020. The prize, kindly sponsored by the Gerlind & Ernst Denert Stiftung, is awarded for excellent work within the discipline of Software Engineering, which includes methods, tools and procedures for better and efficient development of high quality software. An essential requirement for the nominated work is its applicability and usability in industrial practice. The book contains eleven papers that describe the works by Jonathan Brachthäuser (EPFL Lausanne) entitled What You See Is What You Get: Practical Effect Handlers in Capability-Passing Style, Mojdeh Golagha’s (Fortiss, Munich) thesis How to Effectively Reduce Failure Analysis Time?, Nikolay Harutyunyan’s (FAU Erlangen-Nürnberg) work on Open Source Software Governance, Dominic Henze’s (TU Munich) research about Dynamically Scalable Fog Architectures, Anne Hess’s (Fraunhofer IESE, Kaiserslautern) work on Crossing Disciplinary Borders to Improve Requirements Communication, Istvan Koren’s (RWTH Aachen U) thesis DevOpsUse: A Community-Oriented Methodology for Societal Software Engineering, Yannic Noller’s (NU Singapore) work on Hybrid Differential Software Testing, Dominic Steinhofel’s (TU Darmstadt) thesis entitled Ever Change a Running System: Structured Software Reengineering Using Automatically Proven-Correct Transformation Rules, Peter Wägemann’s (FAU Erlangen-Nürnberg) work Static Worst-Case Analyses and Their Validation Techniques for Safety-Critical Systems, Michael von Wenckstern’s (RWTH Aachen U) research on Improving the Model-Based Systems Engineering Process, and Franz Zieris’s (FU Berlin) thesis on Understanding How Pair Programming Actually Works in Industry: Mechanisms, Patterns, and Dynamics – which actually won the award. The chapters describe key findings of the respective works, show their relevance and applicability to practice and industrial software engineering projects, and provide additional information and findings that have only been discovered afterwards, e.g. when applying the results in industry. This way, the book is not only interesting to other researchers, but also to industrial software professionals who would like to learn about the application of state-of-the-art methods in their daily work

Ernst Denert Award for Software Engineering 2020

This open access book provides an overview of the dissertations of the eleven nominees for the Ernst Denert Award for Software Engineering in 2020. The prize, kindly sponsored by the Gerlind & Ernst Denert Stiftung, is awarded for excellent work within the discipline of Software Engineering, which includes methods, tools and procedures for better and efficient development of high quality software. An essential requirement for the nominated work is its applicability and usability in industrial practice. The book contains eleven papers that describe the works by Jonathan Brachthäuser (EPFL Lausanne) entitled What You See Is What You Get: Practical Effect Handlers in Capability-Passing Style, Mojdeh Golagha’s (Fortiss, Munich) thesis How to Effectively Reduce Failure Analysis Time?, Nikolay Harutyunyan’s (FAU Erlangen-Nürnberg) work on Open Source Software Governance, Dominic Henze’s (TU Munich) research about Dynamically Scalable Fog Architectures, Anne Hess’s (Fraunhofer IESE, Kaiserslautern) work on Crossing Disciplinary Borders to Improve Requirements Communication, Istvan Koren’s (RWTH Aachen U) thesis DevOpsUse: A Community-Oriented Methodology for Societal Software Engineering, Yannic Noller’s (NU Singapore) work on Hybrid Differential Software Testing, Dominic Steinhofel’s (TU Darmstadt) thesis entitled Ever Change a Running System: Structured Software Reengineering Using Automatically Proven-Correct Transformation Rules, Peter Wägemann’s (FAU Erlangen-Nürnberg) work Static Worst-Case Analyses and Their Validation Techniques for Safety-Critical Systems, Michael von Wenckstern’s (RWTH Aachen U) research on Improving the Model-Based Systems Engineering Process, and Franz Zieris’s (FU Berlin) thesis on Understanding How Pair Programming Actually Works in Industry: Mechanisms, Patterns, and Dynamics – which actually won the award. The chapters describe key findings of the respective works, show their relevance and applicability to practice and industrial software engineering projects, and provide additional information and findings that have only been discovered afterwards, e.g. when applying the results in industry. This way, the book is not only interesting to other researchers, but also to industrial software professionals who would like to learn about the application of state-of-the-art methods in their daily work

CAD Tools for DNA Micro-Array Design, Manufacture and Application

Motivation: As the human genome project progresses and some microbial and eukaryotic genomes are recognized, numerous biotechnological processes have attracted increasing number of biologists, bioengineers and computer scientists recently. Biotechnological processes profoundly involve production and analysis of highthroughput experimental data. Numerous sequence libraries of DNA and protein structures of a large number of micro-organisms and a variety of other databases related to biology and chemistry are available. For example, microarray technology, a novel biotechnology, promises to monitor the whole genome at once, so that researchers can study the whole genome on the global level and have a better picture of the expressions among millions of genes simultaneously. Today, it is widely used in many fields- disease diagnosis, gene classification, gene regulatory network, and drug discovery. For example, designing organism specific microarray and analysis of experimental data require combining heterogeneous computational tools that usually differ in the data format; such as, GeneMark for ORF extraction, Promide for DNA probe selection, Chip for probe placement on microarray chip, BLAST to compare sequences, MEGA for phylogenetic analysis, and ClustalX for multiple alignments. Solution: Surprisingly enough, despite huge research efforts invested in DNA array applications, very few works are devoted to computer-aided optimization of DNA array design and manufacturing. Current design practices are dominated by ad-hoc heuristics incorporated in proprietary tools with unknown suboptimality. This will soon become a bottleneck for the new generation of high-density arrays, such as the ones currently being designed at Perlegen [109]. The goal of the already accomplished research was to develop highly scalable tools, with predictable runtime and quality, for cost-effective, computer-aided design and manufacturing of DNA probe arrays. We illustrate the utility of our approach by taking a concrete example of combining the design tools of microarray technology for Harpes B virus DNA data

Verifiable early-reply with C++

Concurrent programming can improve performance. However, it comes with two drawbacks. First, concurrent programs can be more difficult to design and reason about than their sequential counterparts. Second, error conditions that do not exist in sequential programs, such as data race conditions and deadlock, can make concurrent programs more unreliable. To make concurrent programming simpler and more reliable, while still providing sufficient performance gains, we present a concurrency framework based on an existing concurrency initiation mechanism called âÂÂEarly-ReplyâÂÂ. Early-Reply is based on the idea that some functions can produce final return values long before they terminate. Concurrent execution begins when return value of a function is returned to the caller, allowing the rest of the work of the function to be done on an auxiliary thread. The simpler sequential programming model can be used by the caller, because the concurrency is initiated and hidden within the function body. Pike and Sridhar recognized Early-Reply as a way for sequential programs to get the benefits of concurrent execution. They also discussed using object-oriented programming to serialize access to data that needs synchronization. Our work expands on their approach and provides an actual C++ implementation of an Early-Reply based framework. Our framework simplifies concurrent programming for both users and implementers by allowing developers to use sequential reasoning, and by providing a minimal framework interface. Concurrent programming is made more reliable by combining the concurrency synchronization and initiation into one mechanism within the framework, which isolates where race conditions and deadlock can occur. Furthermore, this isolation facilitates the development of a simple set of coding guidelines that can be used by developers (through inspection) or static analysis tools (through verification) to eliminate race conditions and deadlocks. As a motivating example, we parallelize an instructional compiler that processes multiple input source files. For each input file; the parsing and semantic analysis execute on the calling thread, while the code optimization and object code generation execute on an auxiliary thread. Speedups of 1.5 to 1.7 were observed on a dual processor confirming that sufficient performance gains are possible

Statically-analyzed stream monitoring for cyber-physical Systems

Cyber-physical systems are digital systems interacting with the physical world. Even though this induces an inherent complexity, they are responsible for safety-critical tasks like governing nuclear power plants or controlling autonomous vehicles. To preserve trust into the safety of such systems, this thesis presents a runtime verification approach designed to generate trustworthy monitors from a formal specification. These monitors are responsible for observing the cyber-physical system during runtime and ensuring its safety. As underlying language, I present the asynchronous real-time specification language RTLola. It contains primitives for arithmetic properties and grants precise control over the timing of the monitor. With this, it enables specifiers to express properties relevant to cyber-physical systems. The thesis further presents a static analysis that identifies inconsistencies in the specification and provides insights into the dynamic behavior of the monitor. As a result, the resource consumption of the monitor becomes predictable. The generation of the monitor produces either a hardware description synthesizable onto programmable hardware, or Rust code with verification annotation. These annotations allow for proving the correctness of the monitor with respect to the semantics of RTLola. Last, I present the construction of a conservative hybrid model of the underlying system using information extracted from the specification. This model enables further verification steps.Cyber-physische Systeme sind digitale Systeme, die mit der physischen Welt interagieren. Obwohl das zu einer inhärenten Komplexität führt, sind sie verantwortlich für sicherheitskritische Aufgaben wie der Steuerung von Kernkraftwerken oder autonomen Fahrzeugen. Umdas Vertrauen in deren Sicherheit zu wahren, präsentiert diese Doktorarbeit einen Ansatz zur Laufzeitverifikation, konzipiert, um vertrauenswürdige Monitore aus einer formalen Spezifikation zu generieren. Diese Monitore sind dafür verantwortlich, das cyber-physische System zur Laufzeit zu überwachen und dessen Sicherheit zu gewährleisten. Als zugrundeliegende Sprache präsentiere ich die asynchrone Echtzeit-Spezifikationssprache RTLola. Sie enthält Primitiven für arithmetische Eigenschaften und gewährt präzise Kontrolle über das Timing des Monitors. Damit wird es Spezifizierenden ermöglicht Eigenschaften auszudrücken, die für Cyber-physische Systeme relevant sind. Weiterhin präsentiert diese Doktorarbeit eine statische Analyse, die Unstimmigkeiten in der Spezifikation identifiziert und Einblicke in das dynamische Verhalten des Monitors liefert. Aufgrund dessen wird der Ressourcenverbrauch des Monitors vorhersehbar. Die Generierung des Monitors erzeugt entweder eine Hardwarebeschreibung, die auf programmierbarer Hardware synthetisiert werden kann, oder Rust Code mit Verifikationsannotationen. Diese Annotationen erlauben es, die Korrektheit des Monitors bezogen auf die Semantik von RTLola zu beweisen. Abschließend präsentiere ich die Konstruktion von einem konservativen hybriden Modell des zugrundeliegenden Systems anhand von Informationen, die aus der Spezifikation gewonnen wurden. Dieses Modell ermöglicht weitere Verifikationsschritte