Using Evolutionary Algorithms to Find Cache-Friendly Generalized Morton Layouts for Arrays

The layout of multi-dimensional data can have a significant impact on the efficacy of hardware caches and, by extension, the performance of applications. Common multi-dimensional layouts include the canonical row-major and column-major layouts as well as the Morton curve layout. In this paper, we describe how the Morton layout can be generalized to a very large family of multi-dimensional data layouts with widely varying performance characteristics. We posit that this design space can be efficiently explored using a combinatorial evolutionary methodology based on genetic algorithms. To this end, we propose a chromosomal representation for such layouts as well as a methodology for estimating the fitness of array layouts using cache simulation. We show that our fitness function correlates to kernel running time in real hardware, and that our evolutionary strategy allows us to find candidates with favorable simulated cache properties in four out of the eight real-world applications under consideration in a small number of generations. Finally, we demonstrate that the array layouts found using our evolutionary method perform well not only in simulated environments but that they can effect significant performance gains -- up to a factor ten in extreme cases -- in real hardware

Renewable Energy in Marine Environment

The effects of human-caused global warming are obvious, requiring new strategies and approaches. The concept of business-as-usual is now no longer beneficial. Extraction of renewable energy in marine environments represents a viable solution and an important path for the future. These huge renewable energy resources in seas and oceans can be harvested, including wind, tide, and waves. Despite the initial difficulties related mostly to the elevated operational risks in the harsh marine environment, newly developed technologies are economically effective or promising. Simultaneously, many challenges remain to be faced. These are the main issues targeted by the present book, which is associated with the Special Issue of Energies Journal entitled “Renewable Energy in Marine Environment”. Papers on innovative technical developments, reviews, case studies, and analytics, as well as assessments, and papers from different disciplines that are relevant to the topic are included. From this perspective, we hope that the results presented are of interest to for scientists and those in related fields such as energy and marine environments, as well as for a wider audience

Design and implementation of an array language for computational science on a heterogeneous multicore architecture

The packing of multiple processor cores onto a single chip has become a mainstream solution to fundamental physical issues relating to the microscopic scales employed in the manufacture of semiconductor components. Multicore architectures provide lower clock speeds per core, while aggregate floating-point capability continues to increase. Heterogeneous multicore chips, such as the Cell Broadband Engine (CBE) and modern graphics chips, also address the related issue of an increasing mismatch between high processor speeds, and huge latency to main memory. Such chips tackle this memory wall by the provision of addressable caches; increased bandwidth to main memory; and fast thread context switching. An associated cost is often reduced functionality of the individual accelerator cores; and the increased complexity involved in their programming. This dissertation investigates the application of a programming language supporting the first-class use of arrays; and capable of automatically parallelising array expressions; to the heterogeneous multicore domain of the CBE, as found in the Sony PlayStation 3 (PS3). The language is a pre-existing and well-documented proper subset of Fortran, known as the ‘F’ programming language. A bespoke compiler, referred to as E , is developed to support this aim, and written in the Haskell programming language. The output of the compiler is in an extended C++ dialect known as Offload C++, which targets the PS3. A significant feature of this language is its use of multiple, statically typed, address spaces. By focusing on generic, polymorphic interfaces for both the generated and hand constructed code, a number of interesting design patterns relating to the memory locality are introduced. A suite of medium-sized (100-700 lines), real-world benchmark programs are used to evaluate the performance, correctness, and scalability of the compiler technology. Absolute speedup values, well in excess of one, are observed for all of the programs. The work ultimately demonstrates that an array language can significantly reduce the effort expended to utilise a parallel heterogeneous multicore architecture, while retaining high performance. A substantial, related advantage in using standard ‘F’ is that any Fortran compiler can create debuggable, and competitively performing serial programs

Supporting Efficient Database Processing in Mapreduce

Ph.DDOCTOR OF PHILOSOPH

Advances in Modelling and Prediction on the Impact of Human Activities and Extreme Events on Environments

YesThis book is an edition of the Special Issue Advances in Modelling and Prediction on the Impact of Human Activities and Extreme Events on Environments that was published in Water journal

Signalling pathways in the regulation of gene expression by the proinflammatory cytokine interferon-gamma

The cytokine IFN-gamma regulates the expression of numerous genes in macrophages, including many that are implicated in atherosclerotic processes. Studying the signalling mechanisms involved in the mediation of IFN-gamma responses may lead to the identification of future therapeutic targets for the treatment of atherosclerosis. Previous work in our laboratory revealed a role for the kinase CK2 in modulating the expression of the LPL and ICER genes in response to IFN-gamma. Experiments detailed in this report show that the CK2 inhibitor apigenin inhibited the IFN-gamma-mediated induction of each gene in the group selected for study (ICER, MCP-1, SOCS-1, IP-10, Mig, l-TAC, CCR2), suggesting that there may be a common role for CK2 in the regulation of macrophage gene expression by the cytokine. The PI3K inhibitor LY294002 has also previously been found in our laboratory to prevent the IFN-gamma-mediated suppression of LPL expression. In this study LY294002 selectively inhibited the induction of MCP-1, IP-10, Mig, l-TAC, and CCR2 expression by IFN-gamma but not that of ICER or SOCS-1. Extension of this line of investigation through microarray analysis provided further evidence for a gene-specific requirement for PI3K in mediating IFN-gamma responses. The signalling pathways involved in the regulation of MCP-1 and ICER gene expression by IFN-gamma were chosen for more detailed study. The JAK-STAT pathway is the most widely accepted mechanism of IFN-gamma signalling. However, recent studies have suggested the existence of potential STATl-independent pathways. The functions of CK2 and PI3K were investigated, in relation to a STATl-dependent or - independent mechanism of IFN-gamma signalling, in the regulation of MCP-1 and ICER expression. A role for the JAK-STAT pathway in the regulation of MCP-1 expression by IFN-gamma was revealed, in macrophages, through co-transfection studies with inactive mutant forms of JAK1, JAK2 and STAT1. Promoter binding analyses demonstrated that IFN- y induced the binding of STAT1 to a GAS site in the MCP-1 promoter. PKB was found to act as a downstream effector for PI3K in the IFN-gamma-mediated induction of MCP-1. Both CK2 and PI3K/PKB were found to be involved in the IFN-gamma-mediated activation of STAT1 through phosphorylation at Serine 727. Additionally, constitutive Spl protein binding to the MCP-1 promoter was demonstrated. Co- immunoprecipitation revealed an IFN-gamma-inducible interaction between Spl and STAT1 that may function in the cytokine response. In our laboratory CK2 has previously been shown to phosphorylate CREB in response to IFN-gamma. A luciferase reporter construct containing four tandem CRE consensus elements, used to model the ICER promoter that contains four CRE-like sites, showed inducible activation by IFN-gamma, through CK2. The JAK2 inhibitor AG490, and dominant negative forms of JAK1, JAK2 and STAT1, did not attenuate increases in ICER expression in response to IFN-gamma. These findings indicate that CREs represent a novel class of IFN-gamma-responsive element and that the regulation of ICER expression may occur through CK2 in a JAK-STAT-independent pathway. Together these studies have demonstrated novel roles for the kinases CK2 and PI3K in the regulation of macrophage gene expression by IFNy