The Mont-Blanc prototype: an alternative approach for high-performance computing systems

High-performance computing (HPC) is recognized as one of the pillars for further advance of science, industry, medicine, and education. Current HPC systems are being developed to overcome emerging challenges in order to reach Exascale level of performance,which is expected by the year 2020. The much larger embedded and mobile market allows for rapid development of IP blocks, and provides more flexibility in designing an application-specific SoC, in turn giving possibility in balancing performance, energy-efficiency and cost. In the Mont-Blanc project, we advocate for HPC systems be built from such commodity IP blocks, currently used in embedded and mobile SoCs. As a first demonstrator of such approach, we present the Mont-Blanc prototype; the first HPC system built with commodity SoCs, memories, and NICs from the embedded and mobile domain, and off-the-shelf HPC networking, storage, cooling and integration solutions. We present the system’s architecture, and evaluation including both performance and energy efficiency. Further, we compare the system’s abilities against a production level supercomputer. At the end, we discuss parallel scalability, and estimate the maximum scalability point of this approach across a set of HPC applications.Postprint (published version

Follicle-Stimulating Hormone Receptor: Advances and Remaining Challenges

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The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer, studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory, a versatile observatory designed to address the Hot and Energetic Universe science theme, selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), it aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over an hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR, browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters. Finally we briefly discuss on the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, and touch on communication and outreach activities, the consortium organisation, and finally on the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. (abridged).Comment: 48 pages, 29 figures, Accepted for publication in Experimental Astronomy with minor editin

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory. Athena is a versatile observatory designed to address the Hot and Energetic Universe science theme, as selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), X-IFU aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over a hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR (i.e. in the course of its preliminary definition phase, so-called B1), browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters, such as the instrument efficiency, spectral resolution, energy scale knowledge, count rate capability, non X-ray background and target of opportunity efficiency. Finally, we briefly discuss the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, touch on communication and outreach activities, the consortium organisation and the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. The X-IFU will be provided by an international consortium led by France, The Netherlands and Italy, with ESA member state contributions from Belgium, Czech Republic, Finland, Germany, Poland, Spain, Switzerland, with additional contributions from the United States and Japan.The French contribution to X-IFU is funded by CNES, CNRS and CEA. This work has been also supported by ASI (Italian Space Agency) through the Contract 2019-27-HH.0, and by the ESA (European Space Agency) Core Technology Program (CTP) Contract No. 4000114932/15/NL/BW and the AREMBES - ESA CTP No.4000116655/16/NL/BW. This publication is part of grant RTI2018-096686-B-C21 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. This publication is part of grant RTI2018-096686-B-C21 and PID2020-115325GB-C31 funded by MCIN/AEI/10.13039/501100011033

Introducing group-sparsity and orthogonality constraints in RGCCA

International audienceRGCCA-a fast and flexible method-generalizes many other well-known methods in order to analyze data-sets comprising multiple blocks of variables. Here we extend RGCCA by adding two new constraints to the RCCCA optimization problem: 1) group sparsity and 2) orthogonality of the block weight vectors. These two constraints facilitate the interpretability of the results when analyzing high dimensional data with a group structure. We illustrate this new method-called gSGCCA-with the analysis of pediatric high-grade glioma data: a set comprising three data blocks. This analysis shows that these new constraints greatly improve the interpretability of the statistical analysis.RGCCA est une méthode flexible et rapide qui-généralisant de nombreuses méthodes existantes-permet l'analyse de données structurées en plusieurs blocs hétérogènes. Nous présentons l'ajout dans RGCCA de deux nouvelles contraintes : une contrainte de parcimonie de groupes et une contrainte d'orthogonalité sur les poids de RGCCA. Ces deux contraintes ont pour but d'augmenter l'interprétabilité de l'analyse de données de grande dimension qui possèdent une structure de groupe. Nous appliquons cette nouvelle méthode-abrégée en gSGCCA-à l'analyse de données de gliome malin pédiatrique structurées en trois blocs. Nous montrons sur ces données le gain en interprétabilité apporté par les contraintes de parcimonie et d'orthogonalité

Bioactive capsular polysaccharide from the thermophilic Cyanophyte/Cyanobacterium Mastigocladus laminosus-cytotoxic properties

1 - ArticleThe capsular polysaccharide produced by the thermophilic blue green alga/cyanobacterium Mastigocladus laminosus was tested for its cytotoxic activity against the A431 human epidermoid carcinoma cell line. This polysaccharide inhibited the proliferation of A431 cells in a dose-dependent manner with an IC50 value of 50 mu g mL(-1). In addition, this polysaccharide strongly inhibited A431 cell migration and invasion. Preliminary experiments showing that secretion of metalloproteinases MMP2 and MMP9 by A431 tumour cells was inhibited by this polysaccharide suggest that this mechanism of action could play a role in its anti-migration and anti-invasive properties. Acid hydrolysis of the polysaccharide produced specific oligosaccharides which conserved - at similar concentrations - their cytotoxic, anti-migration and anti-invasion properties; in this case, the mechanism of action was nevertheless uncorrelated to the decrease of metalloproteinase expression

Adsorption of fulvic and humic acids on surfaces of clays: relation with SUVA index and acidity

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Adsorption of fulvic and humic like acids on surfaces of clays: Relation with SUVA index and acidity

International audienceIn the context of sustainable development, economic and environmental issues encourage the valorization of local materials such as clay and agro-industrial waste. One of the major problems nowadays is the management of municipal waste. The degradation of this waste produces leachate rich in humic-like substances which can be valued for the consolidation of earth bricks. The characterization of the interaction between humic-like substances with clay minerals could provide a better understanding of the consolidation mechanism. In this respect, the adsorption behavior of fulvic and humic like acids on surfaces of distinctive raw clays has been studied. Five types of products were tested: green waste extract, municipal solid waste extract, two commercial products and one product synthetised from xylose. The quantities of fulvic acids adsorbed by the surfaces of raw clays (expressed in mg per g of clay) are greater than the quantities of humic acids. A raw clay with a large specific surface area and a large amount of iron compounds adsorbs a higher quantity (expressed in mg per g of clay) of fulvic acid than a raw clay, rich in kaolinite, containing less iron compounds and with a lower specific surface area. In alkaline conditions, the adsorbed quantities are lower than in alkaline conditions, and the surface area or the presence or iron compounds influence less the adsorption capacity than in acid conditions. It is interesting to note that if the adsorbed quantities are expressed in mg divided by the specific surface area of the clay, it appears that a kaolinite rich clay adsorbs more fulvic or humic like substances than a lateritic clay which is rich in iron oxides. Lastly, in acid (resp. alkaline) conditions, the parameter which governs the adsorption is the acidity (resp. the Specific Ultra-Violet Absorbance, SUVA index): the lower (resp. the higher) the parameter, the greater is the adsorption capacity. The interest in these adsorption reactions is the possibility to use these acids in the building sector for the manufacture of clay bricks at low temperature (compared to fired clay bricks)

A constrained singular value decomposition method that integrates sparsity and orthogonality

International audienceWe propose a new sparsification method for the singular value decomposition—called the constrained singular value decomposition (CSVD)—that can incorporate multiple constraints such as sparsification and orthogonality for the left and right singular vectors. The CSVD can combine different constraints because it implements each constraint as a projection onto a convex set, and because it integrates these constraints as projections onto the intersection of multiple convex sets. We show that, with appropriate sparsification constants, the algorithm is guaranteed to converge to a stable point. We also propose and analyze the convergence of an efficient algorithm for the specific case of the projection onto the balls defined by the norms L1 and L2. We illustrate the CSVD and compare it to the standard singular value decomposition and to a non-orthogonal related sparsification method with: 1) a simulated example, 2) a small set of face images (corresponding to a configuration with a number of variables much larger than the number of observations), and 3) a psychometric application with a large number of observations and a small number of variables. The companion R-package, csvd, that implements the algorithms described in this paper, along with reproducible examples, are available for download from https://github.com/vguillemot/csvd

Analyse des Correspondances Multiples Parcimonieuse

International audienceMultiple Correspondence Analysis (MCA) is the method of choicefor themultivariate analysis of categorical data. In MCA each qualitative variable is representedby a group of binary variables (with a coding scheme called “complete disjunctive coding”)and each binary variable has a weight inversely proportional to its frequency. The datamatrix concatenates all these binary variables, and once normalized and centered thisdata matrix is analyzed with a generalized singular value decomposition (GSVD) thatincorporates the variable weights as constraints (or “metric”). The GSVD is, of course,based on the plain SVD and so MCA can be sparsified by extending algorithms designedto sparsify the SVD. To do so requires two additional features: to include weights andto be able to sparsify entire groups of variables at once. Another important feature ofsuch a sparsification should be to preserve the orthogonality of the components, Here, weintegrate all these constraints by using an exact projection scheme onto the intersectionof subspaces (i.e., balls) where each ball represents a specific type of constraints. Weillustrate our procedure with the data from a questionnaire survey on the perception ofcheese in two French cities