Experiences in porting mini-applications to OpenACC and OpenMP on heterogeneous systems

This article studies mini-applications—Minisweep, GenASiS, GPP, and FF—that use computational methods commonly encountered in HPC. We have ported these applications to develop OpenACC and OpenMP versions, and evaluated their performance on Titan (Cray XK7 with K20x GPUs), Cori (Cray XC40 with Intel KNL), Summit (IBM AC922 with Volta GPUs), and Cori-GPU (Cray CS-Storm 500NX with Intel Skylake and Volta GPUs). Our goals are for these new ports to be useful to both application and compiler developers, to document and describe the lessons learned and the methodology to create optimized OpenMP and OpenACC versions, and to provide a description of possible migration paths between the two specifications. Cases where specific directives or code patterns result in improved performance for a given architecture are highlighted. We also include discussions of the functionality and maturity of the latest compilers available on the above platforms with respect to OpenACC or OpenMP implementations

On-the-fly memory compression for multibody algorithms.

Memory and bandwidth demands challenge developers of particle-based codes that have to scale on new architectures, as the growth of concurrency outperforms improvements in memory access facilities, as the memory per core tends to stagnate, and as communication networks cannot increase bandwidth arbitrary. We propose to analyse each particle of such a code to find out whether a hierarchical data representation storing data with reduced precision caps the memory demands without exceeding given error bounds. For admissible candidates, we perform this compression and thus reduce the pressure on the memory subsystem, lower the total memory footprint and reduce the data to be exchanged via MPI. Notably, our analysis and transformation changes the data compression dynamically, i.e. the choice of data format follows the solution characteristics, and it does not require us to alter the core simulation code

Contrasting the effects of intra-uterine smoking and one-carbon micronutrient exposures on offspring DNA methylation

Maternal smoking and micronutrient intake during pregnancy are two strong biological candidates for impacting the developing epigenome. The extent to which DNA methylation in offspring is modified by these intrauterine exposures has not been presented in parallel. In this review, we summarize human studies which have investigated genome-wide DNA methylation in the offspring in relation to maternal smoking and one-carbon micronutrient exposure during pregnancy. We contrast the primarily independent efforts for these two categories of exposure, and potential explanations for these differences. We emphasize methodological considerations such as power to detect methylation signals, exposure assessment, control of sources of variability, causal inference and the role of observed methylation changes in mediating downstream outcomes in the offspring

Inhalation therapy during acute asthma : the role of a combined steroid and beta-stimulant preparation

CITATION: Joubert, J. R., Burger, G. & Shephard, E. 1985. Inhalation therapy during acute asthma : the role of a combined steroid and beta-stimulant preparation. South African Medical Journal, 68:381-384.The original publication is available at http://www.samj.org.zaA compound consisting of a β-stimulant, salbutamol (100 μg/puff), and a steroid, beclomethasone diproprionate (50 μg/puff), was studied to test the hypothesis that the corticosteroid could enhance the bronchodilator proporties of the β-stimulant during chronic asthma and simulated acute attacks (antigen challenge). Conventional doses (200 μg and 100 μg of salbutamol and beclomethasone respectively) were compared using a schedule which included a second administration 1 hour later. The results obtained on the baseline bronchial responsiveness of chronic asthmatics and during the delayed asthmatic response (simulated acute asthma) were similar. The compound was as effective as salbutamol alone but not more so. A significantly greater bronchodilator response was recorded in all patients after the second administration of both the compound and salbutamol alone. The practical advantages of having one rather than two inhalers are evident, but the appropriate application of this compound agent, probably in a prophylactic role, must be defined.Publisher’s versio

Ensayo de una metodología innovadora para la detección de masas polimetálicas profundas: modelo geológico y exploración geotérmica preliminares de la Masa Valverde (Huelva).

Se presentan los resultados provisionales de los trabajos iniciales realizados para el Proyecto Innovative Geothermal Methodology to detect deep blind Polymetallic Ore Bodies, financiado por la CE Y co-financiado por DGICYT y organizaciones participantes. Los principales objetivos de este Proyecto son la cuantificación de los efectos térmicos "in situ" de masas polimetálicas profundas a fin de desarrollar nuevos métodos geotérmicos específicos que puedan detectar depósitos no aflorantes. Dichos métodos deberían proporcionar, previsiblemente, un procedimiento rápido y barato para la detección superficial de cuerpos profundos, midiendo perfiles térmicos en sondeos cortos. La exploración geotérmica permite, a diferencia de otros métodos (por ejemplo gravimetría), discriminar anomalías significativas. Para detectar pequeñas anomalías de temperatura (teniendo en cuenta que el efecto térmico decrece rápidamente hacia la superficie), la resolución térmica medida debe ser del orden de O,001ºC. Se han calibrado nuevos termistores muy sensibles en el Laboratoire National d'Essais (LNE) de París para obtener la máxima sensibilidad en el intervalo de temperaturas considerado (lO a 60ºC). Se miden conductividades térmicas sobre testigos con una precisión del 5% y una reproductibilidad del 2%, que permiten determinar las anomalías del gradiente de temperatura relacionadas con las litologías. Para poner a punto el método, se modelizarán las medidas y se compararán con la realidad de cuerpos conocidos, a fin de establecer un modelo fiable y de aplicación general. Esta metodología se ensaya en primer lugar en la MV (Masa Valverde, Huelva), descubierta y reconocida mediante sondeos por la E.N. Adaro, a fin de partir de un modelo suficientemente preciso para la modelización geotérmica. Los trabajos geológicos realizados integran observaciones de campo, examen y desmuestres de testigos de sondeos, geoquímica, geología estructural y estudio de testigos por diversas técnicas como petrografía, microscopía de menas, DRX, MEB, Microsonda Electrónica, etc. A pesar de la profundidad (en torno a los 600 m.l y de la complejidad de la estructura de MV puesta de manifiesto por el presente estudio, los resultados del primer año de investigación geológica -objeto de esta comunicación-, conducen a un modelo provisional que sirve de base a la interpretación de los datos térmicos. Dicho modelo difiere de los anteriormente conocidos en aspectos como: la posición, definición e interpretación de ciertos tramos litológicos; la demostración de muy frecuentes contactos tectónicos acompañados de procesos de deformación dúctil a veces muy intensa; la identificación de fallas o cabalgamientos que definen unidades independientes, entre las cuales los tramos litológicos, incluidos los cuerpos mineralizados, no son correlaciona bies; la estructura del cuerpo mineralizado, caracterizada por una superposición de escamas imbricadas con geometría antiformal, resultado de procesos tectónicos relacionados con la Tectónica de cabalgamientos de la región y recientemente demostrados -ITGE- en la parte española de la FPI (Faja Pirítica Ibérica). Los resultados provisionales arrojan, pues, un resultado coherente desde las diversas perspectivas de trabajo, particularmente por lo que respecta a los modelos geotérmico y geológico - geométrico, y permiten albergar fundadas esperanzas en una rápida puesta a punto del método, para su aplicación en exploración

Optimising allied health psychological treatments in primary health care: Piloting a randomised controlled trial of social worker training in focused psychological strategies (The SW-fps Study)

The SW-fps Study was part of a broader body of research which aims to improve access to evidence-based psychological treatments in primary health care. Over the last decade, major mental health reforms in Australia, such as the Better Outcomes and Better Access programs, have greatly increased community access to psychological treatments through a range of funding models designed to support provision of psychological treatments by allied health providers. More recently social workers, amongst other allied health professionals, are beginning to utilise the Medicare incentives to provide psychological treatments in primary mentalThe research reported in this paper is a project of the Australian Primary Health Care Research Institute, which is supported by a grant from the Australian Government Department of Health and Ageing under the Primary Health Care Research, Evaluation and Development Strategy

Structure Functions of the Nucleon in a Statistical Model

Deep inelastic scattering is considered in a statistical model of the nucleon. This incorporates certain features which are absent in the standard parton model such as quantum statistical correlations which play a role in the propagation of particles when considering Feynman diagrams containing internal lines. The inclusion of the ${\cal O}(\alpha_{s})$ corrections in our numerical calculations allows a good fit to the data for $x\geq 0.25$. The fit corresponds to values of temperature and chemical potential of approximately $T=0.067$ GeV and $\mu=0.133$ GeV. The latter values of parameters, however, give rise, for all $x$, to a large value for $R=\sigma_{L}/\sigma_{T}$.Comment: 16 pages TeX, 11 figures available as Postscript files, University of Bielefeld preprint BI-TP 93/3

Developing fencing policies in dryland ecosystems

The daily energy requirements of animals are determined by a combination of physical and physiological factors, but food availability may challenge the capacity to meet nutritional needs. Western gorillas (Gorilla gorilla) are an interesting model for investigating this topic because they are folivore-frugivores that adjust their diet and activities to seasonal variation in fruit availability. Observations of one habituated group of western gorillas in Bai-Hokou, Central African Republic (December 2004-December 2005) were used to examine seasonal variation in diet quality and nutritional intake. We tested if during the high fruit season the food consumed by western gorillas was higher in quality (higher in energy, sugar, fat but lower in fibre and antifeedants) than during the low fruit season. Food consumed during the high fruit season was higher in digestible energy, but not any other macronutrients. Second, we investigated whether the gorillas increased their daily intake of carbohydrates, metabolizable energy (KCal/g OM), or other nutrients during the high fruit season. Intake of dry matter, fibers, fat, protein and the majority of minerals and phenols decreased with increased frugivory and there was some indication of seasonal variation in intake of energy (KCal/g OM), tannins, protein/fiber ratio, and iron. Intake of non-structural carbohydrates and sugars was not influenced by fruit availability. Gorillas are probably able to extract large quantities of energy via fermentation since they rely on proteinaceous leaves during the low fruit season. Macronutrients and micronutrients, but not digestible energy, may be limited for them during times of low fruit availability because they are hind-gut fermenters. We discuss the advantages of seasonal frugivores having large dietary breath and flexibility, significant characteristics to consider in the conservation strategies of endangered species

Epigenetic memory in response to environmental stressors

Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors