Monitoring-Oriented Programming: A Tool-Supported Methodology for Higher Quality Object-Oriented Software

This paper presents a tool-supported methodological paradigm for object-oriented software development, called monitoring-oriented programming and abbreviated MOP, in which runtime monitoring is a basic software design principle. The general idea underlying MOP is that software developers insert specifications in their code via annotations. Actual monitoring code is automatically synthesized from these annotations before compilation and integrated at appropriate places in the program, according to user-defined configuration attributes. This way, the specification is checked at runtime against the implementation. Moreover, violations and/or validations of specifications can trigger user-defined code at any points in the program, in particular recovery code, outputting or sending messages, or raising exceptions. The MOP paradigm does not promote or enforce any specific formalism to specify requirements: it allows the users to plug-in their favorite or domain-specific specification formalisms via logic plug-in modules. There are two major technical challenges that MOP supporting tools unavoidably face: monitor synthesis and monitor integration. The former is heavily dependent on the specification formalism and comes as part of the corresponding logic plug-in, while the latter is uniform for all specification formalisms and depends only on the target programming language. An experimental prototype tool, called Java-MOP, is also discussed, which currently supports most but not all of the desired MOP features. MOP aims at reducing the gap between formal specification and implementation, by integrating the two and allowing them together to form a system

elPrep 4 : a multithreaded framework for sequence analysis

We present elPrep 4, a reimplementation from scratch of the elPrep framework for processing sequence alignment map files in the Go programming language. elPrep 4 includes multiple new features allowing us to process all of the preparation steps defined by the GATK Best Practice pipelines for variant calling. This includes new and improved functionality for sorting, (optical) duplicate marking, base quality score recalibration, BED and VCF parsing, and various filtering options. The implementations of these options in elPrep 4 faithfully reproduce the outcomes of their counterparts in GATK 4, SAMtools, and Picard, even though the underlying algorithms are redesigned to take advantage of elPrep's parallel execution framework to vastly improve the runtime and resource use compared to these tools. Our benchmarks show that elPrep executes the preparation steps of the GATK Best Practices up to 13x faster on WES data, and up to 7.4x faster for WGS data compared to running the same pipeline with GATK 4, while utilizing fewer compute resources

An All-in-One Debugging Approach: Java Debugging, Execution Visualization and Verification

We devise a widely applicable debugging approach to deal with the prevailing issue that bugs cannot be precisely reproduced in nondeterministic complex concurrent programs. A distinct efficient record-and-playback mechanism is designed to record all the internal states of execution including intermediate results by injecting our own bytecode, which does not affect the source code, and, through a two-step data processing mechanism, these data will be aggregated, structured and parallel processed for the purpose of replay in high fidelity while keeping the overhead at a satisfactory level. Docker and Git are employed to create a clean environment such that the execution will be undertaken repeatedly with a maximum precision of reproducing bugs. In our development, several other forefront technologies, such as MongoDB, Spark and Node.js are utilized and smoothly integrated for easy implementation. Altogether, we develop a system for Java Debugging Execution Visualization and Verification (JDevv), a debugging tool for Java although our debugging approach can apply to other languages as well. JDevv also offers an aggregated and interactive visualization for the ease of users’ code verification

Virtual Machine Support for Many-Core Architectures: Decoupling Abstract from Concrete Concurrency Models

The upcoming many-core architectures require software developers to exploit concurrency to utilize available computational power. Today's high-level language virtual machines (VMs), which are a cornerstone of software development, do not provide sufficient abstraction for concurrency concepts. We analyze concrete and abstract concurrency models and identify the challenges they impose for VMs. To provide sufficient concurrency support in VMs, we propose to integrate concurrency operations into VM instruction sets. Since there will always be VMs optimized for special purposes, our goal is to develop a methodology to design instruction sets with concurrency support. Therefore, we also propose a list of trade-offs that have to be investigated to advise the design of such instruction sets. As a first experiment, we implemented one instruction set extension for shared memory and one for non-shared memory concurrency. From our experimental results, we derived a list of requirements for a full-grown experimental environment for further research

Revisiting Actor Programming in C++

The actor model of computation has gained significant popularity over the last decade. Its high level of abstraction makes it appealing for concurrent applications in parallel and distributed systems. However, designing a real-world actor framework that subsumes full scalability, strong reliability, and high resource efficiency requires many conceptual and algorithmic additives to the original model. In this paper, we report on designing and building CAF, the "C++ Actor Framework". CAF targets at providing a concurrent and distributed native environment for scaling up to very large, high-performance applications, and equally well down to small constrained systems. We present the key specifications and design concepts---in particular a message-transparent architecture, type-safe message interfaces, and pattern matching facilities---that make native actors a viable approach for many robust, elastic, and highly distributed developments. We demonstrate the feasibility of CAF in three scenarios: first for elastic, upscaling environments, second for including heterogeneous hardware like GPGPUs, and third for distributed runtime systems. Extensive performance evaluations indicate ideal runtime behaviour for up to 64 cores at very low memory footprint, or in the presence of GPUs. In these tests, CAF continuously outperforms the competing actor environments Erlang, Charm++, SalsaLite, Scala, ActorFoundry, and even the OpenMPI.Comment: 33 page

Reconfigurable SCA Applications with the FraSCAti Platform

CORE A. Acceptance rate: 18% (35/189).International audienceThe Service Component Architecture (SCA) is a technology agnostic standard for developing and deploying distributed service-oriented applications. However, SCA does not define standard means for runtime manageability (including introspection and reconfiguration) of SOA applications and of their supporting environment. This paper presents the FraSCAti platform, which brings runtime management features to SCA, and discusses key principles in its design: the adoption of an extended SCA component model for the implementation of SOA applications and of the FraSCAti platform itself; the use of component-based interception techniques for dynamically weaving non-functional services such as transaction management with components. The paper presents micro-benchmarks that show that runtime manageability in the FraSCAti platform is achieved without hindering its performance relative to the de facto reference SCA implementation, Apache's Tuscany

Probabilistic Graphical Models on Multi-Core CPUs using Java 8

In this paper, we discuss software design issues related to the development of parallel computational intelligence algorithms on multi-core CPUs, using the new Java 8 functional programming features. In particular, we focus on probabilistic graphical models (PGMs) and present the parallelisation of a collection of algorithms that deal with inference and learning of PGMs from data. Namely, maximum likelihood estimation, importance sampling, and greedy search for solving combinatorial optimisation problems. Through these concrete examples, we tackle the problem of defining efficient data structures for PGMs and parallel processing of same-size batches of data sets using Java 8 features. We also provide straightforward techniques to code parallel algorithms that seamlessly exploit multi-core processors. The experimental analysis, carried out using our open source AMIDST (Analysis of MassIve Data STreams) Java toolbox, shows the merits of the proposed solutions.Comment: Pre-print version of the paper presented in the special issue on Computational Intelligence Software at IEEE Computational Intelligence Magazine journa