Astrophysical Supercomputing with GPUs: Critical Decisions for Early Adopters

General purpose computing on graphics processing units (GPGPU) is dramatically changing the landscape of high performance computing in astronomy. In this paper, we identify and investigate several key decision areas, with a goal of simplyfing the early adoption of GPGPU in astronomy. We consider the merits of OpenCL as an open standard in order to reduce risks associated with coding in a native, vendor-specific programming environment, and present a GPU programming philosophy based on using brute force solutions. We assert that effective use of new GPU-based supercomputing facilities will require a change in approach from astronomers. This will likely include improved programming training, an increased need for software development best-practice through the use of profiling and related optimisation tools, and a greater reliance on third-party code libraries. As with any new technology, those willing to take the risks, and make the investment of time and effort to become early adopters of GPGPU in astronomy, stand to reap great benefits.Comment: 13 pages, 5 figures, accepted for publication in PAS

Automatic Detection of Malware-Generated Domains with Recurrent Neural Models

Modern malware families often rely on domain-generation algorithms (DGAs) to determine rendezvous points to their command-and-control server. Traditional defence strategies (such as blacklisting domains or IP addresses) are inadequate against such techniques due to the large and continuously changing list of domains produced by these algorithms. This paper demonstrates that a machine learning approach based on recurrent neural networks is able to detect domain names generated by DGAs with high precision. The neural models are estimated on a large training set of domains generated by various malwares. Experimental results show that this data-driven approach can detect malware-generated domain names with a F_1 score of 0.971. To put it differently, the model can automatically detect 93 % of malware-generated domain names for a false positive rate of 1:100.Comment: Submitted to NISK 201

Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

Algopopulism and recursive conduct: grappling with fascism and the new populisms vis-à-vis Arendt, Deleuze and Guattari, and Stiegler

The continuing rise of right-wing populisms and fascism across the globe, mobilised by various factors such as the use of social technologies and the weaponisation of nationalism, xenophobia, sexism and racism – to name a few – provokes important questions in terms of resistance. Moreover, given that the lines between the new populisms and fascism are becoming increasingly nebulous, it is imperative that we at least attempt to better understand the conditions – including the more hauntological, which is to say historically and structurally invisibilised – from which algorithmic governmentality and its corollary, recursive conduct, are born. On that account, I unpack two understandings of fascism, first tracing it macropolitically through the work of Hannah Arendt and, thereafter, looking at its more micropolitical and libidinal aspects vis-à-vis the work of Deleuze and Guattari. I do so because it is my contention that there is a historical correlation between Arendt’s theorisation of a generalised espionage and our contemporary surveillance systems, as well as between Deleuze and Guattari’s theorisation of desire and the harnessing of affect through machine learning methods and their deployment via social media platforms, all of which aid the propagation of certain forms of populism – and even fascism. This is what I call algopopulism: algorithmically aided politics that transforms the ‘we’ into the ‘they’ through what can be thought of as recursive conduct or the digital exercise of power and its structuring of the field of possible action and thought. In turn, I link this to Stiegler’s understanding of negative sublimation, a paralysis of the human spirit which occurs due to, among other things, the generalised proletarianisation of knowledge, ultimately provoking the short-circuiting of processes of transindividuation. Finally, I offer some notes on resistance

Visualising biological data: a semantic approach to tool and database integration

<p>Abstract</p> <p>Motivation</p> <p>In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are <it>ad hoc </it>collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.</p> <p>Methods</p> <p>To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.</p> <p>Results</p> <p>The toolkit, named Utopia, is freely available from <url>http://utopia.cs.man.ac.uk/</url>.</p

Distributed texture-based terrain synthesis

Terrain synthesis is an important field of Computer Graphics that deals with the generation of 3D landscape models for use in virtual environments. The field has evolved to a stage where large and even infinite landscapes can be generated in realtime. However, user control of the generation process is still minimal, as well as the creation of virtual landscapes that mimic real terrain. This thesis investigates the use of texture synthesis techniques on real landscapes to improve realism and the use of sketch-based interfaces to enable intuitive user control

Hardware-accelerated algorithms in visual computing

This thesis presents new parallel algorithms which accelerate computer vision methods by the use of graphics processors (GPUs) and evaluates them with respect to their speed, scalability, and the quality of their results. It covers the fields of homogeneous and anisotropic diffusion processes, diffusion image inpainting, optic flow, and halftoning. In this turn, it compares different solvers for homogeneous diffusion and presents a novel \u27extended\u27 box filter. Moreover, it suggests to use the fast explicit diffusion scheme (FED) as an efficient and flexible solver for nonlinear and in particular for anisotropic parabolic diffusion problems on graphics hardware. For elliptic diffusion-like processes, it recommends to use cascadic FED or Fast Jacobi schemes. The presented optic flow algorithm represents one of the fastest yet very accurate techniques. Finally, it presents a novel halftoning scheme which yields state-of-the-art results for many applications in image processing and computer graphics.Diese Arbeit präsentiert neue parallele Algorithmen zur Beschleunigung von Methoden in der Bildinformatik mittels Grafikprozessoren (GPUs), und evaluiert diese im Hinblick auf Geschwindigkeit, Skalierungsverhalten, und Qualität der Resultate. Sie behandelt dabei die Gebiete der homogenen und anisotropen Diffusionsprozesse, Inpainting (Bildvervollständigung) mittels Diffusion, die Bestimmung des optischen Flusses, sowie Halbtonverfahren. Dabei werden verschiedene Löser für homogene Diffusion verglichen und ein neuer \u27erweiterter\u27 Mittelwertfilter präsentiert. Ferner wird vorgeschlagen, das schnelle explizite Diffusionsschema (FED) als effizienten und flexiblen Löser für parabolische nichtlineare und speziell anisotrope Diffusionsprozesse auf Grafikprozessoren einzusetzen. Für elliptische diffusionsartige Prozesse wird hingegen empfohlen, kaskadierte FED- oder schnelle Jacobi-Verfahren einzusetzen. Der vorgestellte Algorithmus zur Berechnung des optischen Flusses stellt eines der schnellsten und dennoch äußerst genauen Verfahren dar. Schließlich wird ein neues Halbtonverfahren präsentiert, das in vielen Bereichen der Bildverarbeitung und Computergrafik Ergebnisse produziert, die den Stand der Technik repräsentieren

Procedural Generation and Rendering of Realistic, Navigable Forest Environments: An Open-Source Tool

Simulation of forest environments has applications from entertainment and art creation to commercial and scientific modelling. Due to the unique features and lighting in forests, a forest-specific simulator is desirable, however many current forest simulators are proprietary or highly tailored to a particular application. Here we review several areas of procedural generation and rendering specific to forest generation, and utilise this to create a generalised, open-source tool for generating and rendering interactive, realistic forest scenes. The system uses specialised L-systems to generate trees which are distributed using an ecosystem simulation algorithm. The resulting scene is rendered using a deferred rendering pipeline, a Blinn-Phong lighting model with real-time leaf transparency and post-processing lighting effects. The result is a system that achieves a balance between high natural realism and visual appeal, suitable for tasks including training computer vision algorithms for autonomous robots and visual media generation.Comment: 14 pages, 11 figures. Submitted to Computer Graphics Forum (CGF). The application and supporting configuration files can be found at https://github.com/callumnewlands/ForestGenerato

Parallel and I/O-efficient randomisation of massive networks using global curveball trades

Graph randomisation is a crucial task in the analysis and synthesis of networks. It is typically implemented as an edge switching process (ESMC) repeatedly swapping the nodes of random edge pairs while maintaining the degrees involved [23]. Curveball is a novel approach that instead considers the whole neighbourhoods of randomly drawn node pairs. Its Markov chain converges to a uniform distribution, and experiments suggest that it requires less steps than the established ESMC [6]. Since trades however are more expensive, we study Curveball’s practical runtime by introducing the first efficient Curveball algorithms: the I/O-efficient EM-CB for simple undirected graphs and its internal memory pendant IM-CB. Further, we investigate global trades [6] processing every node in a single super step, and show that undirected global trades converge to a uniform distribution and perform superior in practice. We then discuss EM-GCB and EMPGCB for global trades and give experimental evidence that EM-PGCB achieves the quality of the state-of-the-art ESMC algorithm EM-ES [15] nearly one order of magnitude faster