A microstructural study of superconductive nanocrystalline diamond

A transmission electron microscopy (TEM) study of superconducting nanocrystalline diamond (NCD) continuous layers is reported. The high resolution transmission electron microscopy (HREM) and the diffraction contrast modes of observations are used to reveal the nanograins configuration. Three types of them are observed: first, close to the interface with the Si/SiO2 substrate, 10 to 20 nm-sized diamond 16 seeds resulting from the 5nm size diamond powder deposition before growth that show some regrowth during CVD process, second a diamond overgrown layer, quasi-epitaxially by coalesced columnar NCD grains, and finally, up to the free surface, a thin disordered region composed of nanocrystallites smaller than 6 nm. This last layer was not nominally expected and is attributed to a renucleated-like (RND) diamond layer embedding ultra nanocrystalline grains. Diffraction contrast observations confirm this HREM observed behaviour.6 page

Arbitration policies for on-demand user-level I/O forwarding on HPC platforms

I/O forwarding is a well-established and widely-adopted technique in HPC to reduce contention in the access to storage servers and transparently improve I/O performance. Rather than having applications directly accessing the shared parallel file system, the forwarding technique defines a set of I/O nodes responsible for receiving application requests and forwarding them to the file system, thus reshaping the flow of requests. The typical approach is to statically assign I/O nodes to applications depending on the number of compute nodes they use, which is not always necessarily related to their I/O requirements. Thus, this approach leads to inefficient usage of these resources. This paper investigates arbitration policies based on the applications I/O demands, represented by their access patterns. We propose a policy based on the Multiple-Choice Knapsack problem that seeks to maximize global bandwidth by giving more I/O nodes to applications that will benefit the most. Furthermore, we propose a user-level I/O forwarding solution as an on-demand service capable of applying different allocation policies at runtime for machines where this layer is not present. We demonstrate our approach's applicability through extensive experimentation and show it can transparently improve global I/O bandwidth by up to 85% in a live setup compared to the default static policy.This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Supenor - Brasil (CAPES) - Finance Code 001. It has also received support from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. It is also partially supported by the Spanish Ministry of Economy and Competitiveness (MINECO) under grants PID2019-107255GB; and the Generalitat de Catalunya under contract 2014-SGR-1051. The authors thankfully acknowledge the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center. Experiments presented in this paper were carried out using the Grid’5000 testbed, supported by a scientific interest group hosted by Inria and including CNRS, RENATER and several Universities as well as other organizations (see https://www.grid5000.fr).Peer ReviewedPostprint (author's final draft

Enhancing Energy Production with Exascale HPC Methods

High Performance Computing (HPC) resources have become the key actor for achieving more ambitious challenges in many disciplines. In this step beyond, an explosion on the available parallelism and the use of special purpose processors are crucial. With such a goal, the HPC4E project applies new exascale HPC techniques to energy industry simulations, customizing them if necessary, and going beyond the state-of-the-art in the required HPC exascale simulations for different energy sources. In this paper, a general overview of these methods is presented as well as some specific preliminary results.The research leading to these results has received funding from the European Union's Horizon 2020 Programme (2014-2020) under the HPC4E Project (www.hpc4e.eu), grant agreement n° 689772, the Spanish Ministry of Economy and Competitiveness under the CODEC2 project (TIN2015-63562-R), and from the Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP). Computer time on Endeavour cluster is provided by the Intel Corporation, which enabled us to obtain the presented experimental results in uncertainty quantification in seismic imagingPostprint (author's final draft

Leveraging Cloud Heterogeneity for Cost-Efficient Execution of Parallel Applications

Public cloud providers offer a wide range of instance types, with different processing and interconnection speeds, as well as varying prices. Furthermore, the tasks of many parallel applications show different computational demands due to load imbalance. These differences can be exploited for improving the cost efficiency of parallel applications in many cloud environments by matching application requirements to instance types. In this paper, we introduce the concept of heterogeneous cloud systems consisting of different instance types to leverage the different computational demands of large parallel applications for improved cost efficiency. We present a mechanism that automatically suggests a suitable combination of instances based on a characterization of the application and the instance types. With such a heterogeneous cloud, we are able to improve cost efficiency significantly for a variety of MPI-based applications, while maintaining a similar performance.Peer ReviewedPostprint (author's final draft

Seismic Wave Propagation Simulations on Low-power and Performance-centric Manycores

International audienceThe large processing requirements of seismic wave propagation simulations make High Performance Computing (HPC) architectures a natural choice for their execution. However, to keep both the current pace of performance improvements and the power consumption under a strict power budget, HPC systems must be more energy e than ever. As a response to this need, energy-e and low-power processors began to make their way into the market. In this paper we employ a novel low-power processor, the MPPA-256 manycore, to perform seismic wave propagation simulations. It has 256 cores connected by a NoC, no cache-coherence and only a limited amount of on-chip memory. We describe how its particular architectural characteristics influenced our solution for an energy-e implementation. As a counterpoint to the low-power MPPA-256 architecture, we employ Xeon Phi, a performance-centric manycore. Although both processors share some architectural similarities, the challenges to implement an e seismic wave propagation kernel on these platforms are very di↵erent. In this work we compare the performance and energy e of our implementations for these processors to proven and optimized solutions for other hardware platforms such as general-purpose processors and a GPU. Our experimental results show that MPPA-256 has the best energy e consuming at least 77 % less energy than the other evaluated platforms, whereas the performance of our solution for the Xeon Phi is on par with a state-of-the-art solution for GPUs

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection are often non-specific, and there is no definitive test for the accurate diagnosis of infection. The 'omics' approaches to identifying biomarkers from the host-response to bacterial infection are promising. In this study, lipidomic analysis was carried out with plasma samples obtained from febrile children with confirmed bacterial infection (n = 20) and confirmed viral infection (n = 20). We show for the first time that bacterial and viral infection produces distinct profile in the host lipidome. Some species of glycerophosphoinositol, sphingomyelin, lysophosphatidylcholine and cholesterol sulfate were higher in the confirmed virus infected group, while some species of fatty acids, glycerophosphocholine, glycerophosphoserine, lactosylceramide and bilirubin were lower in the confirmed virus infected group when compared with confirmed bacterial infected group. A combination of three lipids achieved an area under the receiver operating characteristic (ROC) curve of 0.911 (95% CI 0.81 to 0.98). This pilot study demonstrates the potential of metabolic biomarkers to assist clinicians in distinguishing bacterial from viral infection in febrile children, to facilitate effective clinical management and to the limit inappropriate use of antibiotics

Accuracy Assessment of the ESA CCI 20M Land Cover Map: Kenya, Gabon, Ivory Coast and South Africa

This working paper presents the overall and spatial accuracy assessment of the European Space Agency (ESA) 20 m prototype land cover map for Africa for four countries: Kenya, Gabon, Ivory Coast and South Africa. This accuracy assessment was undertaken as part of the ESA-funded CrowdVal project. The results varied from 44% (for South Africa) to 91% (for Gabon). In the case of Kenya (56% overall accuracy) and South Africa, these values are largely caused by the confusion between grassland and shrubland. However, if a weighted confusion matrix is used, which diminishes the importance of the confusion between grassland and shrubs, the overall accuracy for Kenya increases to 79% and for South Africa, 75%. The overall accuracy for Ivory Coast (47%) is a result of a highly fragmented land cover, which makes it a difficult country to map with remote sensing. The exception was Gabon with a high overall accuracy of 91%, but this can be explained by the high amount of tree cover across the country, which is a relatively easy class to map

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection ar

Centrality evolution of the charged-particle pseudorapidity density over a broad pseudorapidity range in Pb-Pb collisions at root s(NN)=2.76TeV

Peer reviewe