A holistic scalable implementation approach of the lattice Boltzmann method for CPU/GPU heterogeneous clusters

This is the author accepted manuscript. The final version is available from MDPI via the DOI in this record.Heterogeneous clusters are a widely utilized class of supercomputers assembled from different types of computing devices, for instance CPUs and GPUs, providing a huge computational potential. Programming them in a scalable way exploiting the maximal performance introduces numerous challenges such as optimizations for different computing devices, dealing with multiple levels of parallelism, the application of different programming models, work distribution, and hiding of communication with computation. We utilize the lattice Boltzmann method for fluid flow as a representative of a scientific computing application and develop a holistic implementation for large-scale CPU/GPU heterogeneous clusters. We review and combine a set of best practices and techniques ranging from optimizations for the particular computing devices to the orchestration of tens of thousands of CPU cores and thousands of GPUs. Eventually, we come up with an implementation using all the available computational resources for the lattice Boltzmann method operators. Our approach shows excellent scalability behavior making it future-proof for heterogeneous clusters of the upcoming architectures on the exaFLOPS scale. Parallel efficiencies of more than 90% are achieved leading to 2,604.72 GLUPS utilizing 24,576 CPU cores and 2,048 GPUs of the CPU/GPU heterogeneous cluster Piz Daint and computing more than 6.8 · 109 lattice cells.This work was supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre “Invasive Computing” (SFB/TR 89). In addition, this work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under project ID d68. We further thank the Max Planck Computing & Data Facility (MPCDF) and the Global Scientific Information and Computing Center (GSIC) for providing computational resources

Restrictions and extensions of semibounded operators

We study restriction and extension theory for semibounded Hermitian operators in the Hardy space of analytic functions on the disk D. Starting with the operator zd/dz, we show that, for every choice of a closed subset F in T=bd(D) of measure zero, there is a densely defined Hermitian restriction of zd/dz corresponding to boundary functions vanishing on F. For every such restriction operator, we classify all its selfadjoint extension, and for each we present a complete spectral picture. We prove that different sets F with the same cardinality can lead to quite different boundary-value problems, inequivalent selfadjoint extension operators, and quite different spectral configurations. As a tool in our analysis, we prove that the von Neumann deficiency spaces, for a fixed set F, have a natural presentation as reproducing kernel Hilbert spaces, with a Hurwitz zeta-function, restricted to FxF, as reproducing kernel.Comment: 63 pages, 11 figure

Helping in humans and other animals: a fruitful interdisciplinary dialogue.

Humans are arguably unique in the extent and scale of cooperation with unrelated individuals. While pairwise interactions among non-relatives occur in some non-human species, there is scant evidence of the large-scale, often unconditional prosociality that characterizes human social behaviour. Consequently, one may ask whether research on cooperation in humans can offer general insights to researchers working on similar questions in non-human species, and whether research on humans should be published in biology journals. We contend that the answer to both of these questions is yes. Most importantly, social behaviour in humans and other species operates under the same evolutionary framework. Moreover, we highlight how an open dialogue between different fields can inspire studies on humans and non-human species, leading to novel approaches and insights. Biology journals should encourage these discussions rather than drawing artificial boundaries between disciplines. Shared current and future challenges are to study helping in ecologically relevant contexts in order to correctly interpret how payoff matrices translate into inclusive fitness, and to integrate mechanisms into the hitherto largely functional theory. We can and should study human cooperation within a comparative framework in order to gain a full understanding of the evolution of helping

On the Schoenberg Transformations in Data Analysis: Theory and Illustrations

The class of Schoenberg transformations, embedding Euclidean distances into higher dimensional Euclidean spaces, is presented, and derived from theorems on positive definite and conditionally negative definite matrices. Original results on the arc lengths, angles and curvature of the transformations are proposed, and visualized on artificial data sets by classical multidimensional scaling. A simple distance-based discriminant algorithm illustrates the theory, intimately connected to the Gaussian kernels of Machine Learning

Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia

<p>Abstract</p> <p>Background</p> <p>The effect of breed on Porcine Reproductive and Respiratory Syndrome Viremia (PRRSV) was tested using data collected in 17 Italian commercial pig farms and 1096 genotypes obtained by the PorcineSNP60 BeadChip. A binomial logistic model was used to investigate the relationship between breed-clusters and PRRSV susceptibility. Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.</p> <p>Results</p> <p>Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant. Sex, age and breed-cluster showed no statistically significant effect on PRRS viremia, although the Landrace and Cross breed-clusters showed the lowest Odds-Ratio</p> <p>Conclusions</p> <p>The model failed to detect a significant breed-cluster effect, highlighting the impact of environment and management on PRRS viremia incidence. Incomplete exposure over the observed period may have masked possible breed differences.</p

'I'm sorry to hear that'-Empathy and Empathic Dissonance : the Perspectives of PA Students

Context: Our understanding of clinical empathy could be enhanced through qualitative research-research currently under-represented in the field. Physician associates within the UK undergo an intensive 2-year postgraduate medical education. As a new group of health professionals, they represent a fresh pair of eyes through which to examine clinical empathy, its nature and teaching. Methods: Working with a constructivist paradigm, utilising grounded theory methodology, researchers studied 19 purposively sampled physician associate students in two UK medical schools. One-to-one semi-structured interviews were transcribed verbatim. Data were analysed using a grounded theory approach. Results: The global themes were the pathways to empathy, empathy modifiers and empathic dissonance a novel term to describe the discomfort students experience when pressurised into making empathic statements they don't sincerely feel. Students preferred using non-verbal over verbal expressions of empathy. A conceptual model is proposed. The more substantial empathic pathway, affective empathy, involves input from the heart. An alternative empathy, more constrained, comes from the head: cognitive empathy was considered a solution to time pressure and emotional burden. Formal teaching establishes empathic dissonance, a problem which stems from over-reliance on the empathic statement as the means to deliver clinical empathy. Conclusions: This study furthers our understanding of the construct and teaching of empathy. It identifies empathic barriers, especially time pressure. It proposes a novel concept-empathic dissonance-a concept that challenges medical educationalists to reframe future empathy teaching

Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium

<p>Abstract</p> <p>Background</p> <p>Understanding the role of host genetics in resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection, and the effects of PRRS on pig health and related growth, are goals of the PRRS Host Genetics Consortium (PHGC).</p> <p>Methods</p> <p>The project uses a nursery pig model to assess pig resistance/susceptibility to primary PRRSV infection. To date, 6 groups of 200 crossbred pigs from high health farms were donated by commercial sources. After acclimation, the pigs were infected with PRRSV in a biosecure facility and followed for 42 days post infection (dpi). Blood samples were collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi for serum and whole blood RNA gene expression analyses; weekly weights were recorded for growth traits. All data have been entered into the PHGC relational database. Genomic DNAs from all PHGC1-6 pigs were prepared and genotyped with the Porcine SNP60 SNPchip.</p> <p>Results</p> <p>Results have affirmed that all challenged pigs become PRRSV infected with peak viremia being observed between 4-21 dpi. Multivariate statistical analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories. Sera are now being compared for factors involved in recovery from infection, including speed of response and levels of immune cytokines. Genome-wide association studies (GWAS) are underway to identify genes and chromosomal locations that identify PRRS resistant/susceptible pigs and pigs able to maintain growth while infected with PRRSV.</p> <p>Conclusions</p> <p>Overall, the PHGC project will enable researchers to discover and verify important genotypes and phenotypes that predict resistance/susceptibility to PRRSV infection. The availability of PHGC samples provides a unique opportunity to continue to develop deeper phenotypes on every PRRSV infected pig.</p

"If only I had taken the other road...": Regret, risk and reinforced learning in informed route-choice

This paper presents a study of the effect of regret on route choice behavior when both descriptional information and experiential feedback on choice outcomes are provided. The relevance of Regret Theory in travel behavior has been well demonstrated in non-repeated choice environments involving decisions on the basis of descriptional information. The relation between regret and reinforced learning through experiential feedbacks is less understood. Using data obtained from a simple route-choice experiment involving different levels of travel time variability, discrete-choice models accounting for regret aversion effects are estimated. The results suggest that regret aversion is more evident when descriptional information is provided ex-ante compared to a pure learning from experience condition. Yet, the source of regret is related more strongly to experiential feedbacks rather than to the descriptional information itself. Payoff variability is negatively associated with regret. Regret aversion is more observable in choice situations that reveal risk-seeking, and less in the case of risk-aversion. These results are important for predicting the possible behavioral impacts of emerging information and communication technologies and intelligent transportation systems on travelers' behavior. © 2012 Springer Science+Business Media, LLC