A component-based framework for certification of components in a cloud of HPC services

HPC Shelfis a proposal of a cloud computing platform to provide component-oriented services for High Performance Computing (HPC) applications. This paper presents a Verification-as-a-Service (VaaS) framework for component certification onHPC Shelf. Certification is aimed at providing higher confidence that components of parallel computing systems ofHPC Shelfbehave as expected according to one or more requirements expressed in their contracts. To this end, new abstractions are introduced, starting with certifier components. They are designed to inspect other components and verify them for different types of functional, non-functional and behavioral requirements. The certification framework is naturally based on parallel computing techniques to speed up verification tasks.NORTE-01-0145- FEDER-000037

SAGA: A project to automate the management of software production systems

The Software Automation, Generation and Administration (SAGA) project is investigating the design and construction of practical software engineering environments for developing and maintaining aerospace systems and applications software. The research includes the practical organization of the software lifecycle, configuration management, software requirements specifications, executable specifications, design methodologies, programming, verification, validation and testing, version control, maintenance, the reuse of software, software libraries, documentation, and automated management

Automatically Leveraging MapReduce Frameworks for Data-Intensive Applications

MapReduce is a popular programming paradigm for developing large-scale, data-intensive computation. Many frameworks that implement this paradigm have recently been developed. To leverage these frameworks, however, developers must become familiar with their APIs and rewrite existing code. Casper is a new tool that automatically translates sequential Java programs into the MapReduce paradigm. Casper identifies potential code fragments to rewrite and translates them in two steps: (1) Casper uses program synthesis to search for a program summary (i.e., a functional specification) of each code fragment. The summary is expressed using a high-level intermediate language resembling the MapReduce paradigm and verified to be semantically equivalent to the original using a theorem prover. (2) Casper generates executable code from the summary, using either the Hadoop, Spark, or Flink API. We evaluated Casper by automatically converting real-world, sequential Java benchmarks to MapReduce. The resulting benchmarks perform up to 48.2x faster compared to the original.Comment: 12 pages, additional 4 pages of references and appendi

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.R.A.V. received support from the CIPRES project (NSF #EF-03314953 to W.P.M.), the FP7 Marie Curie Programme (Call FP7-PEOPLE-IEF-2008—Proposal No. 237046) and, for the NeXML implementation in TreeBASE, the pPOD project (NSF IIS 0629846); P.E.M. and J.S. received support from CIPRES (NSF #EF-0331495, #EF-0715370); M.T.H. was supported by NSF (DEB-ATOL-0732920); X.X. received support from NSERC (Canada) Discovery and RTI grants; W.P.M. received support from an NSERC (Canada) Discovery grant; J.C. received support from a Google Summer of Code 2007 grant; A.P. received support from a Google Summer of Code 2010 grant

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML

Ontological approach for DSL development

This paper presents a project whose main objective is to explore the Ontological based development of Domain Specific Languages (DSL), more precisely, of their underlying Grammar. After reviewing the basic concepts characterizing Ontologies and DSLs, we introduce a tool, Onto2Gra, that takes profit of the knowledge described by the ontology and automatically generates a grammar for a DSL that allows to discourse about the domain described by that ontology. This approach represents a rigorous method to create, in a secure and effective way, a grammar for a new specialized language restricted to a concrete domain. The usual process of creating a grammar from the scratch is, as every creative action, difficult, slow and error prone; so this proposal is, from a Grammar Engineering point of view, of uttermost importance. After the grammar generation phase, the Grammar Engineer can manipulate it to add syntactic sugar to improve the final language quality or even to add specific semantic actions. The Onto2Gra project is composed of three engines. The main one is OWL2DSL, the component that converts an OWL ontology into a complete Attribute Grammar for the construction of an internal representation of all the input data. The two additional modules are Onto2OWL, converts ontologies written in OntoDL into standard OWL, and DDesc2OWL, converts domain instances written in the new DSL into the initial OWL ontology.This work has been supported by FCT Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2013

A logic-based approach for the verification of UML timed models

This article presents a novel technique to formally verify models of real-time systems captured through a set of heterogeneous UML diagrams. The technique is based on the following key elements: (i) a subset of Unified Modeling Language (UML) diagrams, called Coretto UML (C-UML), which allows designers to describe the components of the system and their behavior through several kinds of diagrams (e.g., state machine diagrams, sequence diagrams, activity diagrams, interaction overview diagrams), and stereotypes taken from the UML Profile for Modeling and Analysis of Real-Time and Embedded Systems; (ii) a formal semantics of C-UML diagrams, defined through formulae of the metric temporal logic Tempo Reale ImplicitO (TRIO); and (iii) a tool, called Corretto, which implements the aforementioned semantics and allows users to carry out formal verification tasks on modeled systems. We validate the feasibility of our approach through a set of different case studies, taken from both the academic and the industrial domain

Towards Practical Graph-Based Verification for an Object-Oriented Concurrency Model

To harness the power of multi-core and distributed platforms, and to make the development of concurrent software more accessible to software engineers, different object-oriented concurrency models such as SCOOP have been proposed. Despite the practical importance of analysing SCOOP programs, there are currently no general verification approaches that operate directly on program code without additional annotations. One reason for this is the multitude of partially conflicting semantic formalisations for SCOOP (either in theory or by-implementation). Here, we propose a simple graph transformation system (GTS) based run-time semantics for SCOOP that grasps the most common features of all known semantics of the language. This run-time model is implemented in the state-of-the-art GTS tool GROOVE, which allows us to simulate, analyse, and verify a subset of SCOOP programs with respect to deadlocks and other behavioural properties. Besides proposing the first approach to verify SCOOP programs by automatic translation to GTS, we also highlight our experiences of applying GTS (and especially GROOVE) for specifying semantics in the form of a run-time model, which should be transferable to GTS models for other concurrent languages and libraries.Comment: In Proceedings GaM 2015, arXiv:1504.0244