Computing Double Precision Euclidean Distances using GPU Tensor Cores

Tensor cores (TCs) are a type of Application-Specific Integrated Circuit (ASIC) and are a recent addition to Graphics Processing Unit (GPU) architectures. As such, TCs are purposefully designed to greatly improve the performance of Matrix Multiply-Accumulate (MMA) operations. While TCs are heavily studied for machine learning and closely related fields, where their high efficiency is undeniable, MMA operations are not unique to these fields. More generally, any computation that can be expressed as MMA operations can leverage TCs, and potentially benefit from their higher computational throughput compared to other general-purpose cores, such as CUDA cores on Nvidia GPUs. In this paper, we propose the first double precision (FP64) Euclidean distance calculation algorithm, which is expressed as MMA operations to leverage TCs on Nvidia GPUs, rather than the more commonly used CUDA cores. To show that the Euclidean distance can be accelerated in a real-world application, we evaluate our proposed TC algorithm on the distance similarity self-join problem, as the most computationally intensive part of the algorithm consists of computing distances in a multi-dimensional space. We find that the performance gain from using the tensor core algorithm over the CUDA core algorithm depends weakly on the dataset size and distribution, but is strongly dependent on data dimensionality. Overall, TCs are a compelling alternative to CUDA cores, particularly when the data dimensionality is low ($\leq{4}$), as we achieve an average speedup of $1.28\times$ and up to $2.23\times$ against a state-of-the-art GPU distance similarity self-join algorithm. Furthermore, because this paper is among the first to explore the use of TCs for FP64 general-purpose computation, future research is promising.Comment: Accepted for publicatio

UML Based Specifications of PDM Product Structure and Workflow

The paper deals with the use of UML approach for the specification of a PDM system. A PDM enables the management of the product data about its entire lifecycle. The main goal of the paper is to highlight the added value of in using an object-oriented approach to modelling and implementing a PDM in a business case study

UML Based Specifications of PDM Product Structure and Workflow

International audienceThe paper deals with the use of UML approach for the specification of a PDM system. A PDM enables the management of the product data about its entire lifecycle. The main goal of the paper is to highlight the added value of in using an object-oriented approach to modelling and implementing a PDM in a business case study. The chosen object-oriented approach and the used UML diagrams for themodelling and integration of product, process, and resource data is detailed for a turboprop aircraft project

UML Based Specifications of PDM Product Structure and Workflow

The paper deals with the use of UML approach for the specification of a PDM system. A PDM enables the management of the product data about its entire lifecycle. The main goal of the paper is to highlight the added value of in using an object-oriented approach to modelling and implementing a PDM in a business case study

L’activité métallurgique à l’abbaye de Morimond (Haute-Marne) : nouvel éclairage de la fouille à partir de l’analyse archéomagnétique de deux foyers

Une étude archéomagnétique à des fins de datation a été menée sur deux foyers en carreaux de terre cuite mis au jour sur le site de l’ancienne abbaye cistercienne de Morimond (Haute-Marne). La désaimantation thermique complète des échantillons prélevés a permis de définir pour chacun des deux foyers une direction archéomagnétique moyenne précise, acquise lors de leur dernière utilisation. Pour dater cet instant, les directions archéomagnétiques ont été comparées à une courbe des variations directionnelles du champ géomagnétique construite à partir de données obtenues en France et dans des pays voisins. Nous obtenons, à 95% de confiance, une datation comprise entre 1585 et 1615 après J.-C. pour le premier foyer et entre 1525 et 1605 après J.-C. pour le second foyer. Bien que leurs deux intervalles d'âge se recouvrent partiellement, les deux directions archéomagnétiques moyennes ne sont pas compatibles à 95% ce qui indique que les arrêts de fonctionnement des deux foyers ne sont pas contemporains. Ces résultats archéomagnétiques confirment deux phases métallurgiques observées indépendamment lors des fouilles. Ils précisent les datations issues des radiocarbones qui ne permettaient pas de discriminer chronologiquement les deux phases. Les datations envisagées se calent avant l’abandon du bâtiment suite à plusieurs saccages évoqués dans les sources écrites.This paper presents the archeomagnetic dating results obtained from two brick fireplaces excavated inside the ancient Cistercian Abbey of Morimond (Haute-Marne). Complete thermal demagnetization of the collected samples allowed us to define a precise mean archeomagnetic direction acquired during the last cooling of each of the two structures. The dating of the last use of the two fireplaces was derived from the statistical comparison between a reference geomagnetic field directional variation curve constructed using the available French data set together with other data from nearby countries and the two directions obtained in this study. The two dating results lie, with a 95% confidence level, between 1585 and 1615 AD and between 1525 and 1605 AD. Although these dates partially overlap, the two mean archeomagnetic directions are not compatible at the 95% confidence level, indicating a chronology in the abandonment of the two structures. These archeomagnetic results therefore confirm the existence of two metallurgical phases, which were independently observed during the excavations. They further refine the radiocarbon dating unable to discriminate the two phases. The two time intervals defined by archeomagnetism pre-date the abandonment of the building due to severe damages mentioned in written sources

Plastid thylakoid architecture optimizes photosynthesis in diatoms

Photosynthesis is a unique process that allows independent colonization of the land by plants and of the oceans by phytoplankton. Although the photosynthesis process is well understood in plants, we are still unlocking the mechanisms evolved by phytoplankton to achieve extremely efficient photosynthesis. Here, we combine biochemical, structural and in vivo physiological studies to unravel the structure of the plastid in diatoms, prominent marine eukaryotes. Biochemical and immunolocalization analyses reveal segregation of photosynthetic complexes in the loosely stacked thylakoid membranes typical of diatoms. Separation of photosystems within subdomains minimizes their physical contacts, as required for improved light utilization. Chloroplast 3D reconstruction and in vivo spectroscopy show that these subdomains are interconnected, ensuring fast equilibration of electron carriers for efficient optimum photosynthesis. Thus, diatoms and plants have converged towards a similar functional distribution of the photosystems although via different thylakoid architectures, which likely evolved independently in the land and the ocean.ISSN:2041-172

Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae

Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition

The Use of Adenovirus Dodecahedron in the Delivery of an Enzymatic Activity in the Cell

Penton-dodecahedron (Pt-Dd) derived from adenovirus type 3 is a symmetric complex of pentameric penton base plus fiber which can be produced in the baculovirus system at a high concentration. The size of Pt-Dd is smaller than the virus, but this virus-like particle (VLP) has the major proteins recognized by specific receptors on the surface of almost all types of cell. In this study, by direct observation with fluorescence microscopy on a fixed and living cell, the intracellular trafficking and localization of Pt-Dd labeled with fluorescence dyes in the cytoplasm of HeLa Tub-GFP showed a rapid internalization characteristic. Subsequently, the linkage of horseradish peroxidase (HRP) with Pt-Dd as the vector demonstrated an efficient system to deliver this enzyme into the cell without interfering its enzymatic activity as shown by biochemical and cellular experiments. These results were supported by additional studies using Bs-Dd or free form of the HRP used as the control. Overall, this study strengthens the potential role of Pt-Dd as an alternative vector for delivering therapeutic agents

Automated high-throughput process for site-directed mutagenesis, production, purification, and kinetic characterization of enzymes.

Site-directed mutagenesis followed by functional characterization is a widely used approach to obtain information on the structure-function relationship of proteins. Due to time and cost considerations, the number of amino acids studied is frequently reduced. To address the need for convenient parallel production of numerous point mutants of a protein, we developed an automated method to perform classical site-directed mutagenesis, protein purification, and characterization in a high-throughput manner. The process consists of a succession of six fully automated protocols that can be adapted to any automated liquid handling systems. Our procedure allows construction, validation, and characterization of hundreds of site-directed mutants of a given protein in just 4 days. The method is especially adapted to projects aiming at the study of unique or multiple mutants without the need to construct and screen large libraries of random mutants. The usefulness of the technique is illustrated by the construction and characterization of tens of single mutants of the penicillin-binding protein 2x (PBP2x) from Streptococcus pneumoniae. Moreover, seven mutations of PBP2x were obtained simultaneously in a single experiment with efficiency close to 90%

Computing the throughput of replicated workflows on heterogeneous platforms

International audienceIn this paper, we focus on computing the throughput of replicated workflows. Given a streaming application whose dependence graph is a linear chain, and a mapping of this application onto a fully heterogeneous platform, how can we compute the optimal throughput, or equivalently the minimal period? The problem is easy when workflow stages are not replicated, i.e., assigned to a single processor: in that case the period is dictated by the critical hardware resource. But when stages are replicated, i.e., assigned to several processors, the problem gets surprisingly complicated, and we provide examples where the optimal period is larger than the largest cycle-time of any resource. We then show how to model the problem as a timed Petri net to compute the optimal period in the general case, and we provide a polynomial algorithm for the one-port communication model with overlap. Finally, we report comprehensive simulation results on the gap between the optimal period and the largest resource cycle-time