OpenCL + OpenSHMEM Hybrid Programming Model for the Adapteva Epiphany Architecture

There is interest in exploring hybrid OpenSHMEM + X programming models to extend the applicability of the OpenSHMEM interface to more hardware architectures. We present a hybrid OpenCL + OpenSHMEM programming model for device-level programming for architectures like the Adapteva Epiphany many-core RISC array processor. The Epiphany architecture comprises a 2D array of low-power RISC cores with minimal uncore functionality connected by a 2D mesh Network-on-Chip (NoC). The Epiphany architecture offers high computational energy efficiency for integer and floating point calculations as well as parallel scalability. The Epiphany-III is available as a coprocessor in platforms that also utilize an ARM CPU host. OpenCL provides good functionality for supporting a co-design programming model in which the host CPU offloads parallel work to a coprocessor. However, the OpenCL memory model is inconsistent with the Epiphany memory architecture and lacks support for inter-core communication. We propose a hybrid programming model in which OpenSHMEM provides a better solution by replacing the non-standard OpenCL extensions introduced to achieve high performance with the Epiphany architecture. We demonstrate the proposed programming model for matrix-matrix multiplication based on Cannon's algorithm showing that the hybrid model addresses the deficiencies of using OpenCL alone to achieve good benchmark performance.Comment: 12 pages, 5 figures, OpenSHMEM 2016: Third workshop on OpenSHMEM and Related Technologie

Asynchronous In Situ Processing with Gromacs: Taking Advantage of GPUs

International audienceNumerical simulations using supercomputers are producing an ever growing amount of data. Efficient production and analysis of these data are the key to future discoveries. The in situ paradigm is emerging as a promising solution to avoid the I/O bottleneck encountered in the file system for both the simulation and the analytics by treating the data as soon as they are produced in memory. Various strategies and implementations have been proposed in the last years to support in situ treatments with a low impact on the simulation performance. Yet, little efforts have been made when it comes to perform in situ analytics with hybrid simulations supporting accelerators like GPUs. In this article, we propose a study of the in situ strategies with Gromacs, a molecular dynamic simulation code supporting multi-GPUs, as our application target. We specifically focus on the computational resources usage of the machine by the simulation and the in situ analytics. We finally extend the usual in situ placement strategies to the case of in situ analytics running on a GPU and study their impact on both Gromacs performance and the resource usage of the machine. We show in particular that running in situ analytics on the GPU can be a more efficient solution than on the CPU especially when the CPU is the bottleneck of the simulation

Magnetic excitations of the Cu2+^{2+} quantum spin chain in Sr3_3CuPtO6_6

We report the magnetic excitation spectrum as measured by inelastic neutron scattering for a polycrystalline sample of Sr$_3$CuPtO$_6$. Modeling the data by the 2+4 spinon contributions to the dynamical susceptibility within the chains, and with interchain coupling treated in the random phase approximation, accounts for the major features of the powder-averaged structure factor. The magnetic excitations broaden considerably as temperature is raised, persisting up to above 100 K and displaying a broad transition as previously seen in the susceptibility data. No spin gap is observed in the dispersive spin excitations at low momentum transfer, which is consistent with the gapless spinon continuum expected from the coordinate Bethe ansatz. However, the temperature dependence of the excitation spectrum gives evidence of some very weak interchain coupling.Comment: 9 pages, 5 figure

Contribution of thirdhand smoke to overall tobacco smoke exposure in pediatric patients: study protocol.

BackgroundThirdhand smoke (THS) is the persistent residue resulting from secondhand smoke (SHS) that accumulates in dust, objects, and on surfaces in homes where tobacco has been used, and is reemitted into air. Very little is known about the extent to which THS contributes to children's overall tobacco smoke exposure (OTS) levels, defined as their combined THS and SHS exposure. Even less is known about the effect of OTS and THS on children's health. This project will examine how different home smoking behaviors contribute to THS and OTS and if levels of THS are associated with respiratory illnesses in nonsmoking children.MethodsThis project leverages the experimental design from an ongoing pediatric emergency department-based tobacco cessation trial of caregivers who smoke and their children (NIHR01HD083354). At baseline and follow-up, we will collect urine and handwipe samples from children and samples of dust and air from the homes of smokers who smoke indoors, have smoking bans or who have quit smoking. These samples will be analyzed to examine to what extent THS pollution at home contributes to OTS exposure over and above SHS and to what extent THS continues to persist and contribute to OTS in homes of smokers who have quit or have smoking bans. Targeted and nontargeted chemical analyses of home dust samples will explore which types of THS pollutants are present in homes. Electronic medical record review will examine if THS and OTS levels are associated with child respiratory illness. Additionally, a repository of child and environmental samples will be created.DiscussionThe results of this study will be crucial to help close gaps in our understanding of the types, quantity, and clinical effects of OTS, THS exposure, and THS pollutants in a unique sample of tobacco smoke-exposed ill children and their homes. The potential impact of these findings is substantial, as currently the level of risk in OTS attributable to THS is unknown. This research has the potential to change how we protect children from OTS, by recognizing that SHS and THS exposure needs to be addressed separately and jointly as sources of pollution and exposure.Trial registrationClinicalTrials.gov Identifier: NCT02531594 . Date of registration: August 24, 2015

Predator-Induced Vertical Behavior of a Ctenophore

Although many studies have focused on Mnemiopsis leidyi predation, little is known about the role of this ctenophore as prey when abundant in native and invaded pelagic systems. We examined the response of the ctenophore M. leidyi to the predatory ctenophore Beroe ovata in an experiment in which the two species could potentially sense each other while being physically separated. On average, M. leidyi responded to the predator’s presence by increasing variability in swimming speeds and by lowering their vertical distribution. Such behavior may help explain field records of vertical migration, as well as stratified and near-bottom distributions of M. leidyi

Parallel processing area extraction and data transfer number reduction for automatic GPU offloading of IoT applications

For Open IoT, we have proposed Tacit Computing technology to discover the devices that have data users need on demand and use them dynamically and an automatic GPU offloading technology as an elementary technology of Tacit Computing. However, it can improve limited applications because it only optimizes parallelizable loop statements extraction. Thus, in this paper, to improve performances of more applications automatically, we propose an improved method with reduction of data transfer between CPU and GPU. We evaluate our proposed offloading method by applying it to Darknet and find that it can process it 3 times as quickly as only using CPU.Comment: 6 pages, 4 figures, in Japanese, IEICE Technical Report, SC2018-3

Batch solution of small PDEs with the OPS DSL

In this paper we discuss the challenges and optimisations opportunities when solving a large number of small, equally sized discretised PDEs on regular grids. We present an extension of the OPS (Oxford Parallel library for Structured meshes) embedded Domain Specific Language, and show how support can be added for solving multiple systems, and how OPS makes it easy to deploy a variety of transformations and optimisations. The new capabilities in OPS allow to automatically apply data structure transformations, as well as execution schedule transformations to deliver high performance on a variety of hardware platforms. We evaluate our work on an industrially representative finance simulation on Intel CPUs, as well as NVIDIA GPUs

Are lay people good at recognising the symptoms of schizophrenia?

©2013 Erritty, Wydell. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.This article has been made available through the Brunel Open Access Publishing Fund.Aim: The aim of this study was to explore the general public’s perception of schizophrenia symptoms and the need to seekhelp for symptoms. The recognition (or ‘labelling’) of schizophrenia symptoms, help-seeking behaviours and public awareness of schizophrenia have been suggested as potentially important factors relating to untreated psychosis. Method: Participants were asked to rate to what extent they believe vignettes describing classic symptoms (positive and negative) of schizophrenia indicate mental illness. They were also asked if the individuals depicted in the vignettes required help or treatment and asked to suggest what kind of help or treatment. Results: Only three positive symptoms (i.e., Hallucinatory behaviour, Unusual thought content and Suspiciousness) of schizophrenia were reasonably well perceived (above 70%) as indicating mental illness more than the other positive or negative symptoms. Even when the participants recognised that the symptoms indicated mental illness, not everyone recommended professional help. Conclusion: There may be a need to improve public awareness of schizophrenia and psychosis symptoms, particularly regarding an awareness of the importance of early intervention for psychosis

A social accounting matrix for Iraq

This paper deals with the challenges associated with the generation of a social accounting matrix (SAM) in conditions where up-to-date measured data are particularly scarce and provides future researchers of economic systems with the first SAM for Iraq. It delivers a unique and updated countrywide database for use in modeling and policy analysis and applies this database to the empirical investigation into the expected effects of economic diversification in Iraq as stated in the recent Iraq National Development Plan 2013-2017