LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft

Algorithms and Software for the Analysis of Large Complex Networks

The work presented intersects three main areas, namely graph algorithmics, network science and applied software engineering. Each computational method discussed relates to one of the main tasks of data analysis: to extract structural features from network data, such as methods for community detection; or to transform network data, such as methods to sparsify a network and reduce its size while keeping essential properties; or to realistically model networks through generative models

Towards a Reference Architecture with Modular Design for Large-scale Genotyping and Phenotyping Data Analysis: A Case Study with Image Data

With the rapid advancement of computing technologies, various scientific research communities have been extensively using cloud-based software tools or applications. Cloud-based applications allow users to access software applications from web browsers while relieving them from the installation of any software applications in their desktop environment. For example, Galaxy, GenAP, and iPlant Colaborative are popular cloud-based systems for scientific workflow analysis in the domain of plant Genotyping and Phenotyping. These systems are being used for conducting research, devising new techniques, and sharing the computer assisted analysis results among collaborators. Researchers need to integrate their new workflows/pipelines, tools or techniques with the base system over time. Moreover, large scale data need to be processed within the time-line for more effective analysis. Recently, Big Data technologies are emerging for facilitating large scale data processing with commodity hardware. Among the above-mentioned systems, GenAp is utilizing the Big Data technologies for specific cases only. The structure of such a cloud-based system is highly variable and complex in nature. Software architects and developers need to consider totally different properties and challenges during the development and maintenance phases compared to the traditional business/service oriented systems. Recent studies report that software engineers and data engineers confront challenges to develop analytic tools for supporting large scale and heterogeneous data analysis. Unfortunately, less focus has been given by the software researchers to devise a well-defined methodology and frameworks for flexible design of a cloud system for the Genotyping and Phenotyping domain. To that end, more effective design methodologies and frameworks are an urgent need for cloud based Genotyping and Phenotyping analysis system development that also supports large scale data processing. In our thesis, we conduct a few studies in order to devise a stable reference architecture and modularity model for the software developers and data engineers in the domain of Genotyping and Phenotyping. In the first study, we analyze the architectural changes of existing candidate systems to find out the stability issues. Then, we extract architectural patterns of the candidate systems and propose a conceptual reference architectural model. Finally, we present a case study on the modularity of computation-intensive tasks as an extension of the data-centric development. We show that the data-centric modularity model is at the core of the flexible development of a Genotyping and Phenotyping analysis system. Our proposed model and case study with thousands of images provide a useful knowledge-base for software researchers, developers, and data engineers for cloud based Genotyping and Phenotyping analysis system development

Granularity in Large-Scale Parallel Functional Programming

This thesis demonstrates how to reduce the runtime of large non-strict functional programs using parallel evaluation. The parallelisation of several programs shows the importance of granularity, i.e. the computation costs of program expressions. The aspect of granularity is studied both on a practical level, by presenting and measuring runtime granularity improvement mechanisms, and at a more formal level, by devising a static granularity analysis. By parallelising several large functional programs this thesis demonstrates for the first time the advantages of combining lazy and parallel evaluation on a large scale: laziness aids modularity, while parallelism reduces runtime. One of the parallel programs is the Lolita system which, with more than 47,000 lines of code, is the largest existing parallel non-strict functional program. A new mechanism for parallel programming, evaluation strategies, to which this thesis contributes, is shown to be useful in this parallelisation. Evaluation strategies simplify parallel programming by separating algorithmic code from code specifying dynamic behaviour. For large programs the abstraction provided by functions is maintained by using a data-oriented style of parallelism, which defines parallelism over intermediate data structures rather than inside the functions. A highly parameterised simulator, GRANSIM, has been constructed collaboratively and is discussed in detail in this thesis. GRANSIM is a tool for architecture-independent parallelisation and a testbed for implementing runtime-system features of the parallel graph reduction model. By providing an idealised as well as an accurate model of the underlying parallel machine, GRANSIM has proven to be an essential part of an integrated parallel software engineering environment. Several parallel runtime- system features, such as granularity improvement mechanisms, have been tested via GRANSIM. It is publicly available and in active use at several universities worldwide. In order to provide granularity information this thesis presents an inference-based static granularity analysis. This analysis combines two existing analyses, one for cost and one for size information. It determines an upper bound for the computation costs of evaluating an expression in a simple strict higher-order language. By exposing recurrences during cost reconstruction and using a library of recurrences and their closed forms, it is possible to infer the costs for some recursive functions. The possible performance improvements are assessed by measuring the parallel performance of a hand-analysed and annotated program

Developing and Measuring Parallel Rule-Based Systems in a Functional Programming Environment

This thesis investigates the suitability of using functional programming for building parallel rule-based systems. A functional version of the well known rule-based system OPS5 was implemented, and there is a discussion on the suitability of functional languages for both building compilers and manipulating state. Functional languages can be used to build compilers that reflect the structure of the original grammar of a language and are, therefore, very suitable. Particular attention is paid to the state requirements and the state manipulation structures of applications such as a rule-based system because, traditionally, functional languages have been considered unable to manipulate state. From the implementation work, issues have arisen that are important for functional programming as a whole. They are in the areas of algorithms and data structures and development environments. There is a more general discussion of state and state manipulation in functional programs and how theoretical work, such as monads, can be used. Techniques for how descriptions of graph algorithms may be interpreted more abstractly to build functional graph algorithms are presented. Beyond the scope of programming, there are issues relating both to the functional language interaction with the operating system and to tools, such as debugging and measurement tools, which help programmers write efficient programs. In both of these areas functional systems are lacking. To address the complete lack of measurement tools for functional languages, a profiling technique was designed which can accurately measure the number of calls to a function , the time spent in a function, and the amount of heap space used by a function. From this design, a profiler was developed for higher-order, lazy, functional languages which allows the programmer to measure and verify the behaviour of a program. This profiling technique is designed primarily for application programmers rather than functional language implementors, and the results presented by the profiler directly reflect the lexical scope of the original program rather than some run-time representation. Finally, there is a discussion of generally available techniques for parallelizing functional programs in order that they may execute on a parallel machine. The techniques which are easier for the parallel systems builder to implement are shown to be least suitable for large functional applications. Those techniques that best suit functional programmers are not yet generally available and usable