Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Power and energy visualization for the micro-management of household electricity consumption

The paper describes a pilot system for the detailed management of domestic electricity consumption aimed at minimizing demand peaks and consumer cost. Management decisions are made both interactively by consumers themselves, and where practical, automatically by computer. These decisions are based on realtime pricing and availability information, as well as current and historic usage data. The benefits of the energy strategies implied by such a system are elaborated, showing the potential for significant peak demand reduction and slowing of the need for growth in generation capacity. An overview is provided of the component technologies and interaction methods we have designed, but the paper focuses on the communication of real-time information to the consumer through a combination of specific and ambient visualizations. There is a need for both overview information (eg how much power is being used right now; how much energy have we used so far today; what does it cost?) and information at the point-of-use (is it OK to turn this dryer on now, or should I wait until later?). To assist the design of these visualizations, a survey is underway aimed at establishing people's understanding of power and energy concepts

Fine-Grained Reliability for V2V Communications around Suburban and Urban Intersections

Safe transportation is a key use-case of the 5G/LTE Rel.15+ communications, where an end-to-end reliability of 0.99999 is expected for a vehicle-to-vehicle (V2V) transmission distance of 100-200 m. Since communications reliability is related to road-safety, it is crucial to verify the fulfillment of the performance, especially for accident-prone areas such as intersections. We derive closed-form expressions for the V2V transmission reliability near suburban corners and urban intersections over finite interference regions. The analysis is based on plausible street configurations, traffic scenarios, and empirically-supported channel propagation. We show the means by which the performance metric can serve as a preliminary design tool to meet a target reliability. We then apply meta distribution concepts to provide a careful dissection of V2V communications reliability. Contrary to existing work on infinite roads, when we consider finite road segments for practical deployment, fine-grained reliability per realization exhibits bimodal behavior. Either performance for a certain vehicular traffic scenario is very reliable or extremely unreliable, but nowhere in relatively proximity to the average performance. In other words, standard SINR-based average performance metrics are analytically accurate but can be insufficient from a practical viewpoint. Investigating other safety-critical point process networks at the meta distribution-level may reveal similar discrepancies.Comment: 27 pages, 6 figures, submitted to IEEE Transactions on Wireless Communication

Meeting the design challenges of nano-CMOS electronics: an introduction to an upcoming EPSRC pilot project

The years of ‘happy scaling’ are over and the fundamental challenges that the semiconductor industry faces, at both technology and device level, will impinge deeply upon the design of future integrated circuits and systems. This paper provides an introduction to these challenges and gives an overview of the Grid infrastructure that will be developed as part of a recently funded EPSRC pilot project to address them, and we hope, which will revolutionise the electronics design industry

Distributed Hybrid Simulation of the Internet of Things and Smart Territories

This paper deals with the use of hybrid simulation to build and compose heterogeneous simulation scenarios that can be proficiently exploited to model and represent the Internet of Things (IoT). Hybrid simulation is a methodology that combines multiple modalities of modeling/simulation. Complex scenarios are decomposed into simpler ones, each one being simulated through a specific simulation strategy. All these simulation building blocks are then synchronized and coordinated. This simulation methodology is an ideal one to represent IoT setups, which are usually very demanding, due to the heterogeneity of possible scenarios arising from the massive deployment of an enormous amount of sensors and devices. We present a use case concerned with the distributed simulation of smart territories, a novel view of decentralized geographical spaces that, thanks to the use of IoT, builds ICT services to manage resources in a way that is sustainable and not harmful to the environment. Three different simulation models are combined together, namely, an adaptive agent-based parallel and distributed simulator, an OMNeT++ based discrete event simulator and a script-language simulator based on MATLAB. Results from a performance analysis confirm the viability of using hybrid simulation to model complex IoT scenarios.Comment: arXiv admin note: substantial text overlap with arXiv:1605.0487

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor