Agent-based management systems for many-core platforms : rigorous design and efficient implementation

Due to various advantages such as flexibility, scalability and updatability, software intensive systems are increasingly embedded in everyday life. The constantly growing number of functions executed by these systems requires a high level of performance from the underlying platform. The main approach to incrementing performance has been the increase of operating frequency of a chip. However, this has led to the problem of power dissipation, which has shifted the focus of research to parallel and distributed computing. Parallel many-core platforms can provide the required level of computational power along with low power consumption. On the one hand, this enables parallel execution of highly intensive applications. With their computational power, these platforms are likely to be used in various application domains: from home use electronics (e.g., video processing) to complex critical control systems. On the other hand, the utilization of the resources has to be efficient in terms of performance and power consumption. However, the high level of on-chip integration results in the increase of the probability of various faults and creation of hotspots leading to thermal problems. Additionally, radiation, which is frequent in space but becomes an issue also at the ground level, can cause transient faults. This can eventually induce a faulty execution of applications. Therefore, it is crucial to develop methods that enable efficient as well as resilient execution of applications. The main objective of the thesis is to propose an approach to design agentbased systems for many-core platforms in a rigorous manner. When designing such a system, we explore and integrate various dynamic reconfiguration mechanisms into agents functionality. The use of these mechanisms enhances resilience of the underlying platform whilst maintaining performance at an acceptable level. The design of the system proceeds according to a formal refinement approach which allows us to ensure correct behaviour of the system with respect to postulated properties. To enable analysis of the proposed system in terms of area overhead as well as performance, we explore an approach, where the developed rigorous models are transformed into a high-level implementation language. Specifically, we investigate methods for deriving fault-free implementations from these models into, e.g., a hardware description language, namely VHDL.

How computer programmers work : understanding software development in practise

Hur arbetar en framgångsrik programmerare? Uppgifterna att programmera datorspel och att programmera industriella, säkerhetskritiska system verkar tämligen olika. Genom en noggrann empirisk undersökning jämför och kontrasterar avhandlingen dessa två former av programmering och visar att programmering innefattar mer än teknisk förmåga. Med utgångspunkt i hermeneutisk och retorisk teori och med hjälp av både kulturvetenskap och datavetenskap visar avhandlingen att programmerarnas tradition och värderingar är grundläggande för deras arbete, och att båda sorter av programmering kan uppfattas och analyseras genom klassisk texttolkningstradition. Dessutom kan datorprogram betraktas och analyseras med hjälp av klassiska teorier om talproduktion i praktiken - program ses då i detta sammanhang som ett slags yttranden. Allt som allt förespråkar avhandlingen en återkomst till vetenskapens grunder, vilka innebär en ständig och oupphörlig cyklisk rörelse mellan att erfara och att förstå. Detta står i kontrast till en reduktionistisk syn på vetenskapen, som skiljer skarpt mellan subjektivt och objektivt, och på så sätt utgår från möjligheten att uppnå fullständigt vetande. Ofullständigt vetande är tolkandets och hermeneutikens domän. Syftet med avhandlingen är att med hjälp av exempel demonstrera programmeringens kulturella, hermeneutiska och retoriska natur.

Quantitative refinement of reaction-based biomodels

In the field of molecular biology, scientists adopted for decades a reductionist perspective in their inquiries, being predominantly concerned with the intricate mechanistic details of subcellular regulatory systems. However, integrative thinking was still applied at a smaller scale in molecular biology to understand the underlying processes of cellular behaviour for at least half a century. It was not until the genomic revolution at the end of the previous century that we required model building to account for systemic properties of cellular activity. Our system-level understanding of cellular function is to this day hindered by drastic limitations in our capability of predicting cellular behaviour to reflect system dynamics and system structures. To this end, systems biology aims for a system-level understanding of functional intraand inter-cellular activity. Modern biology brings about a high volume of data, whose comprehension we cannot even aim for in the absence of computational support. Computational modelling, hence, bridges modern biology to computer science, enabling a number of assets, which prove to be invaluable in the analysis of complex biological systems, such as: a rigorous characterization of the system structure, simulation techniques, perturbations analysis, etc. Computational biomodels augmented in size considerably in the past years, major contributions being made towards the simulation and analysis of large-scale models, starting with signalling pathways and culminating with whole-cell models, tissue-level models, organ models and full-scale patient models. The simulation and analysis of models of such complexity very often requires, in fact, the integration of various sub-models, entwined at different levels of resolution and whose organization spans over several levels of hierarchy. This thesis revolves around the concept of quantitative model refinement in relation to the process of model building in computational systems biology. The thesis proposes a sound computational framework for the stepwise augmentation of a biomodel. One starts with an abstract, high-level representation of a biological phenomenon, which is materialised into an initial model that is validated against a set of existing data. Consequently, the model is refined to include more details regarding its species and/or reactions. The framework is employed in the development of two models, one for the heat shock response in eukaryotes and the second for the ErbB signalling pathway. The thesis spans over several formalisms used in computational systems biology, inherently quantitative: reaction-network models, rule-based models and Petri net models, as well as a recent formalism intrinsically qualitative: reaction systems. The choice of modelling formalism is, however, determined by the nature of the question the modeler aims to answer. Quantitative model refinement turns out to be not only essential in the model development cycle, but also beneficial for the compilation of large-scale models, whose development requires the integration of several sub-models across various levels of resolution and underlying formal representations.

Sustainable Computer Science Education

As the world becomes more technologically advanced and economies become globalized, computer science evolution has become faster than ever before. With this evolution and globalization come the need for sustainable university curricula that adequately prepare graduates for life in the industry. Additionally, behavioural skills or “soft” skills have become just as important as technical abilities and knowledge or “hard” skills. The objective of this study was to investigate the current skill gap that exists between computer science university graduates and actual industry needs as well as the sustainability of current computer science university curricula by conducting a systematic literature review of existing publications on the subject as well as a survey of recently graduated computer science students and their work supervisors. A quantitative study was carried out with respondents from six countries, mainly Finland, 31 of the responses came from recently graduated computer science professionals and 18 from their employers. The observed trends suggest that a skill gap really does exist particularly with “soft” skills and that many companies are forced to provide additional training to newly graduated employees if they are to be successful at their jobs.

Model-based testing of software systems : functionality and performance

Software is a key component in many of our devices and products that we use every day. Most customers demand not only that their devices should function as expected but also that the software should be of high quality, reliable, fault tolerant, efficient, etc. In short, it is not enough that a calculator gives the correct result of a calculation, we want the result instantly, in the right form, with minimal use of battery, etc. One of the key aspects for succeeding in today's industry is delivering high quality. In most software development projects, high-quality software is achieved by rigorous testing and good quality assurance practices. However, today, customers are asking for these high quality software products at an ever-increasing pace. This leaves the companies with less time for development. Software testing is an expensive activity, because it requires much manual work. Testing, debugging, and verification are estimated to consume 50 to 75 per cent of the total development cost of complex software projects. Further, the most expensive software defects are those which have to be fixed after the product is released. One of the main challenges in software development is reducing the associated cost and time of software testing without sacrificing the quality of the developed software. It is often not enough to only demonstrate that a piece of software is functioning correctly. Usually, many other aspects of the software, such as performance, security, scalability, usability, etc., need also to be verified. Testing these aspects of the software is traditionally referred to as nonfunctional testing. One of the major challenges with non-functional testing is that it is usually carried out at the end of the software development process when most of the functionality is implemented. This is due to the fact that non-functional aspects, such as performance or security, apply to the software as a whole. In this thesis, we study the use of model-based testing. We present approaches to automatically generate tests from behavioral models for solving some of these challenges. We show that model-based testing is not only applicable to functional testing but also to non-functional testing. In its simplest form, performance testing is performed by executing multiple test sequences at once while observing the software in terms of responsiveness and stability, rather than the output. The main contribution of the thesis is a coherent model-based testing approach for testing functional and performance related issues in software systems. We show how we go from system models, expressed in the Unified Modeling Language, to test cases and back to models again. The system requirements are traced throughout the entire testing process. Requirements traceability facilitates finding faults in the design and implementation of the software. In the research field of model-based testing, many new proposed approaches suffer from poor or the lack of tool support. Therefore, the second contribution of this thesis is proper tool support for the proposed approach that is integrated with leading industry tools. We o er independent tools, tools that are integrated with other industry leading tools, and complete tool-chains when necessary. Many model-based testing approaches proposed by the research community suffer from poor empirical validation in an industrial context. In order to demonstrate the applicability of our proposed approach, we apply our research to several systems, including industrial ones.

Formal development of resilient distributed systems

Resilience is the property of a system to remain trustworthy despite changes. Changes of a different nature, whether due to failures of system components or varying operational conditions, significantly increase the complexity of system development. Therefore, advanced development technologies are required to build robust and flexible system architectures capable of adapting to such changes. Moreover, powerful quantitative techniques are needed to assess the impact of these changes on various system characteristics. Architectural flexibility is achieved by embedding into the system design the mechanisms for identifying changes and reacting on them. Hence a resilient system should have both advanced monitoring and error detection capabilities to recognise changes as well as sophisticated reconfiguration mechanisms to adapt to them. The aim of such reconfiguration is to ensure that the system stays operational, i.e., remains capable of achieving its goals. Design, verification and assessment of the system reconfiguration mechanisms is a challenging and error prone engineering task. In this thesis, we propose and validate a formal framework for development and assessment of resilient systems. Such a framework provides us with the means to specify and verify complex component interactions, model their cooperative behaviour in achieving system goals, and analyse the chosen reconfiguration strategies. Due to the variety of properties to be analysed, such a framework should have an integrated nature. To ensure the system functional correctness, it should rely on formal modelling and verification, while, to assess the impact of changes on such properties as performance and reliability, it should be combined with quantitative analysis. To ensure scalability of the proposed framework, we choose Event-B as the basis for reasoning about functional correctness. Event-B is a statebased formal approach that promotes the correct-by-construction development paradigm and formal verification by theorem proving. Event-B has a mature industrial-strength tool support { the Rodin platform. Proof-based verification as well as the reliance on abstraction and decomposition adopted in Event-B provides the designers with a powerful support for the development of complex systems. Moreover, the top-down system development by refinement allows the developers to explicitly express and verify critical system-level properties. Besides ensuring functional correctness, to achieve resilience we also need to analyse a number of non-functional characteristics, such as reliability and performance. Therefore, in this thesis we also demonstrate how formal development in Event-B can be combined with quantitative analysis. Namely, we experiment with integration of such techniques as probabilistic model checking in PRISM and discrete-event simulation in SimPy with formal development in Event-B. Such an integration allows us to assess how changes and di erent recon guration strategies a ect the overall system resilience. The approach proposed in this thesis is validated by a number of case studies from such areas as robotics, space, healthcare and cloud domain.

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Formal modelling for digital media distribution

Human beings have always strived to preserve their memories and spread their ideas. In the beginning this was always done through human interpretations, such as telling stories and creating sculptures. Later, technological progress made it possible to create a recording of a phenomenon; first as an analogue recording onto a physical object, and later digitally, as a sequence of bits to be interpreted by a computer. By the end of the 20th century technological advances had made it feasible to distribute media content over a computer network instead of on physical objects, thus enabling the concept of digital media distribution. Many digital media distribution systems already exist, and their continued, and in many cases increasing, usage is an indicator for the high interest in their future enhancements and enriching. By looking at these digital media distribution systems, we have identified three main areas of possible improvement: network structure and coordination, transport of content over the network, and the encoding used for the content. In this thesis, our aim is to show that improvements in performance, efficiency and availability can be done in conjunction with improvements in software quality and reliability through the use of formal methods: mathematical approaches to reasoning about software so that we can prove its correctness, together with the desirable properties. We envision a complete media distribution system based on a distributed architecture, such as peer-to-peer networking, in which different parts of the system have been formally modelled and verified. Starting with the network itself, we show how it can be formally constructed and modularised in the Event-B formalism, such that we can separate the modelling of one node from the modelling of the network itself. We also show how the piece selection algorithm in the BitTorrent peer-to-peer transfer protocol can be adapted for on-demand media streaming, and how this can be modelled in Event-B. Furthermore, we show how modelling one peer in Event-B can give results similar to simulating an entire network of peers. Going further, we introduce a formal specification language for content transfer algorithms, and show that having such a language can make these algorithms easier to understand. We also show how generating Event-B code from this language can result in less complexity compared to creating the models from written specifications. We also consider the decoding part of a media distribution system by showing how video decoding can be done in parallel. This is based on formally defined dependencies between frames and blocks in a video sequence; we have shown that also this step can be performed in a way that is mathematically proven correct. Our modelling and proving in this thesis is, in its majority, tool-based. This provides a demonstration of the advance of formal methods as well as their increased reliability, and thus, advocates for their more wide-spread usage in the future.

The role of business model in computer game development organizations

The computer game industry has grown steadily for years, and in revenues it can be compared to the music and film industries. The game industry has been moving to digital distribution. Computer gaming and the concept of business model are discussed among industrial practitioners and the scientific community. The significance of the business model concept has increased in the scientific literature recently, although there is still a lot of discussion going on on the concept. In the thesis, the role of the business model in the computer game industry is studied. Computer game developers, designers, project managers and organization leaders in 11 computer game companies were interviewed. The data was analyzed to identify the important elements of computer game business model, how the business model concept is perceived and how the growth of the organization affects the business model. It was identified that the importance of human capital is crucial to the business. As games are partly a product of creative thinking also innovation and the creative process are highly valued. The same applies to technical skills when performing various activities. Marketing and customer relationships are also considered as key elements in the computer game business model. Financing and partners are important especially for startups, when the organization is dependent on external funding and third party assets. The results of this study provide organizations with improved understanding on how the organization is built and what business model elements are weighted.

Energy aware software for many-core systems

Many-core systems provide a great potential in application performance with the massively parallel structure. Such systems are currently being integrated into most parts of daily life from high-end server farms to desktop systems, laptops and mobile devices. Yet, these systems are facing increasing challenges such as high temperature causing physical damage, high electrical bills both for servers and individual users, unpleasant noise levels due to active cooling and unrealistic battery drainage in mobile devices; factors caused directly by poor energy efficiency. Power management has traditionally been an area of research providing hardware solutions or runtime power management in the operating system in form of frequency governors. Energy awareness in application software is currently non-existent. This means that applications are not involved in the power management decisions, nor does any interface between the applications and the runtime system to provide such facilities exist. Power management in the operating system is therefore performed purely based on indirect implications of software execution, usually referred to as the workload. It often results in over-allocation of resources, hence power waste. This thesis discusses power management strategies in many-core systems in the form of increasing application software awareness of energy efficiency. The presented approach allows meta-data descriptions in the applications and is manifested in two design recommendations: 1) Energy-aware mapping 2) Energy-aware execution which allow the applications to directly influence the power management decisions. The recommendations eliminate over-allocation of resources and increase the energy efficiency of the computing system. Both recommendations are fully supported in a provided interface in combination with a novel power management runtime system called Bricktop. The work presented in this thesis allows both new- and legacy software to execute with the most energy efficient mapping on a many-core CPU and with the most energy efficient performance level. A set of case study examples demonstrate realworld energy savings in a wide range of applications without performance degradation.

Hierarchy and Expansiveness in Two-Dimensional Subshifts of Finite Type

Subshifts are sets of configurations over an infinite grid defined by a set of forbidden patterns. In this thesis, we study two-dimensional subshifts offinite type (2D SFTs), where the underlying grid is Z2 and the set of for-bidden patterns is finite. We are mainly interested in the interplay between the computational power of 2D SFTs and their geometry, examined through the concept of expansive subdynamics. 2D SFTs with expansive directions form an interesting and natural class of subshifts that lie between dimensions 1 and 2. An SFT that has only one non-expansive direction is called extremely expansive. We prove that in many aspects, extremely expansive 2D SFTs display the totality of behaviours of general 2D SFTs. For example, we construct an aperiodic extremely expansive 2D SFT and we prove that the emptiness problem is undecidable even when restricted to the class of extremely expansive 2D SFTs. We also prove that every Medvedev class contains an extremely expansive 2D SFT and we provide a characterization of the sets of directions that can be the set of non-expansive directions of a 2D SFT. Finally, we prove that for every computable sequence of 2D SFTs with an expansive direction, there exists a universal object that simulates all of the elements of the sequence. We use the so called hierarchical, self-simulating or fixed-point method for constructing 2D SFTs which has been previously used by Ga´cs, Durand, Romashchenko and Shen.

Examining human-centered design practice in the mobile apps era

Human-Centered Design (HCD) is a well-recognized approach to the design of interactive computing systems that supports everyday and professional lives of people. To that end, the HCD approach put central emphasis on the explicit understanding of users and context of use by involving users throughout the entire design and development process. With mobile computing, the diversity of users as well as the variety in the spatial, temporal, and social settings of the context of use has notably expanded, which affect the effort of interaction designers to understand users and context of use. The emergence of the mobile apps era in 2008 as a result of structural changes in the mobile industry and the profound enhanced capabilities of mobile devices, further intensify the embeddedness of technology in the daily life of people and the challenges that interaction designers face to cost-efficiently understand users and context of use. Supporting interaction designers in this challenge requires understanding of their existing practice, rationality, and work environment. The main objective of this dissertation is to contribute to interaction design theories by generating understanding on the HCD practice of mobile systems in the mobile apps era, as well as to explain the rationality of interaction designers in attending to users and context of use. To achieve that, a literature study is carried out, followed by a mixed-methods research that combines multiple qualitative interview studies and a quantitative questionnaire study. The dissertation contributes new insights regarding the evolving HCD practice at an important time of transition from stationary computing to mobile computing. Firstly, a gap is identified between interaction design as practiced in research and in the industry regarding the involvement of users in context; whereas the utilization of field evaluations, i.e. in real-life environments, has become more common in academic projects, interaction designers in the industry still rely, by large, on lab evaluations. Secondly, the findings indicate on new aspects that can explain this gap and the rationality of interaction designers in the industry in attending to users and context; essentially, the professional-client relationship was found to inhibit the involvement of users, while the mental distance between practitioners and users as well as the perceived innovativeness of the designed system are suggested in explaining the inclination to study users in situ. Thirdly, the research contributes the first explanatory model on the relation between the organizational context and HCD; essentially, innovation-focused organizational strategies greatly affect the cost-effective usage of data on users and context of use. Last, the findings suggest a change in the nature of HCD in the mobile apps era, at least with universal consumer systems; evidently, the central attention on the explicit understanding of users and context of use shifts from an early requirements phase and continual activities during design and development to follow-up activities. That is, the main effort to understand users is by collecting data on their actual usage of the system, either before or after the system is deployed. The findings inform both researchers and practitioners in interaction design. In particular, the dissertation suggest on action research as a useful approach to support interaction designers and further inform theories on interaction design. With regard to the interaction design practice, the dissertation highlights strategies that encourage a more cost-effective user- and context-informed interaction design process. With the continual embeddedness of computing into people’s life, e.g. with wearable devices and connected car systems, the dissertation provides a timely and valuable view on the evolving humancentered design.

Automated UI testing. WBCT, a computer-automated user test environment tool.

Today, the user experience and usability in software application are becoming a major design issue due to the adaptation of many processes using new technologies. Therefore, the study of the user experience and usability might be included in every software development project and, thus, they should be tested to get traceable results. As a result of different testing methods to evaluate the concepts, a non-expert on the topic might have doubts on which option he/she should opt for and how to interpret the outcomes of the process. This work aims to create a process to ease the whole testing methodology based on the process created by Seffah et al. and a supporting software tool to follow the procedure of these testing methods for the user experience and usability.