CuDB : a Relational Database Engine Boosted by Graphics Processing Units

Proceedings of the First PhD Symposium on Sustainable Ultrascale Computing Systems (NESUS PhD 2016) Timisoara, Romania. February 8-11, 2016.GPUs benefit from much more computation power with the same order of energy consumption than CPUs. Thanks to their massive data parallel architecture, GPUs can outperform CPUs, especially on Single Program Multiple Data (SPMD) programming paradigm on a large amount of data. Database engines are now everywhere, from different sizes and complexities, for multiple usages, embedded or distributed; in 2012, 500 million of SQLite active instances were estimated over the world. Our goal is to exploit the computation power of GPUs to improve performance of SQLite, which is a key software component of many applications and systems. In this paper, we introduce CuDB, a GPU-boosted in-memory database engine (IMDB) based on SQLite. The SQLite API remains unchanged, allowing developers to easily upgrade database engine from SQlite to CuDB even on already existing applications. Preliminary results show significant speedups of 70x with join queries on datasets of 1 million records. We also demonstrate the "memory bounded" character of GPU-databases and show the energy efficiency of our approach.European Cooperation in Science and Technology. COS

Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization

Comparative genomic in situ hybridization (CGH) provides a new possibility for searching genomes for imbalanced genetic material. Labeled genomic test DNA, prepared from clinical or tumor specimens, is mixed with differently labeled control DNA prepared from cells with normal chromosome complements. The mixed probe is used for chromosomal in situ suppression (CISS) hybridization to normal metaphase spreads (CGH-metaphase spreads). Hybridized test and control DNA sequences are detected via different fluorochromes, e.g., fluorescein isothiocyanate (FITC) and tetraethylrhodamine isothiocyanate (TRITC). The ratios of FITC/TRITC fluorescence intensities for each chromosome or chromosome segment should then reflect its relative copy number in the test genome compared with the control genome, e.g., 0.5 for monosomies, 1 for disomies, 1.5 for trisomies, etc. Initially, model experiments were designed to test the accuracy of fluorescence ratio measurements on single chromosomes. DNAs from up to five human chromosome-specific plasmid libraries were labeled with biotin and digoxigenin in different hapten proportions. Probe mixtures were used for CISS hybridization to normal human metaphase spreads and detected with FITC and TRITC. An epifluorescence microscope equipped with a cooled charge coupled device (CCD) camera was used for image acquisition. Procedures for fluorescence ratio measurements were developed on the basis of commercial image analysis software. For hapten ratios 4/1, 1/1 and 1/4, fluorescence ratio values measured for individual chromosomes could be used as a single reliable parameter for chromosome identification. Our findings indicate (1) a tight correlation of fluorescence ratio values with hapten ratios, and (2) the potential of fluorescence ratio measurements for multiple color chromosome painting. Subsequently, genomic test DNAs, prepared from a patient with Down syndrome, from blood of a patient with Tcell prolymphocytic leukemia, and from cultured cells of a renal papillary carcinoma cell line, were applied in CGH experiments. As expected, significant differences in the fluorescence ratios could be measured for chromosome types present in different copy numbers in these test genomes, including a trisomy of chromosome 21, the smallest autosome of the human complement. In addition, chromosome material involved in partial gains and losses of the different tumors could be mapped to their normal chromosome counterparts in CGH-metaphase spreads. An alternative and simpler evaluation procedure based on visual inspection of CCD images of CGH-metaphase spreads also yielded consistent results from several independent observers. Pitfalls, methodological improvements, and potential applications of CGH analyses are discussed

3D-Voronoi Diagramme zur quantitativen Bildanalyse in der Interphase-Cytogenetik

Um die Anordnung von Chromosomen in Zellkernen der Interphase zu untersuchen, wurde ein Verfahren aus der Computergeometrie adaptiert. Dieser Ansatz basiert auf der Zerlegung von dreidimensionalen Bildvolumen mithilfe des Voronoi-Diagramms in konvexe Polyeder. Die graphenorientierte, geometrische Struktur dieses Verfahrens ermöglicht sowohl eine schnelle Extraktion von Objekten im Bildraum als auch die Berechnung morphologischer Parameter wie Volumina, Oberflächen und Rundheitsfaktoren. In diesem Beitrag wird exemplarisch die dreidimensionale Morphologie von XChromosomen in weiblichen Interphasezellkernen mithilfe dieser drei Parameter untersucht. Um diese Zellkerne mit lichtoptischen Methoden zu untersuchen, wurden die Territorien der X-Chromosomen mit einem molekularcytogenetischen Verfahren fluoreszierend dargestellt. Zur Unterscheidung des aktiven und inaktiven X-Chromosoms wurde das Barr-Körperchen zusätzlich markiert und mithilfe eines Epifluoreszenzmikroskops, ausgerüstet mit einer CCD-Kamera, aufgenommen. Anschließend wurden 1 2 - 2 5 äquidistante, lichtoptische Schnitte der X-Chromosomenterritorien mit einem konfokalen Laser Scanning Mikroskop (CLSM) aufgenommen. Diese lichtoptischen Schnitte wurden mithilfe des Voronoi-Verfahrens segmentiert und analysiert. Methoden aus der Computergraphik wurden zur Visualisierung der Ergebnisse eingesetzt. Es konnte gezeigt werden, daß mithilfe des Voronoi-Verfahrens Chromosomen- Territorien anhand der morphologischen Parameter zuverlässig beschrieben werden können

Inestabilidades y deformación en la cubierta sedimentaria de la parte superior del talud del margen continental de Aquitania, norte del cañon del Capbreton (Golfo de Vizcaya)

Acoustic and core data have recently been collected on the shelf break and the upper part of the slope of the south Aquitaine continental margin. They reveal the major role played by mass-flow gravity processes in deposit erosion and redistribution, modelling of the sea-bed, and transfer of sediment toward the deep-sea. The study region is bounded in the south by the Capbreton canyon. The northern area, which shows a smooth morphology, is characterised by small-scale deformations due to sediment creep or low-amplitude slide processes. The deformations are associated with mini listric-like faults that bound packets of sediments in which the deposit geometry is typical of constructional sediment waves. These sediment waves result from the interaction of depositional and gravity deformation processes. In the southern area, closer to the canyon, wave-like structures are still present but mostly of smaller size. They only result from gravity deformation processes without any evidence of constructional processes. In the vicinity of the Capbreton canyon, the shelf break and upper slope have a much more uneven morphology with sedimentary reliefs, escarpments and depressions directed toward the canyon thalweg. The depressions look like slide scars, and could be the result of regressive slides initiated at the top of the canyon flank. The age of the sliding event responsible for the formation of the depression observed today could be middle to upper Quaternary. Since their formation, these depressions act as conduits that channel the transfer of shelf sediment into the canyon, as demonstrated by the occurrence of a meandering channel on the sea-floor of one depression.Se recogieron datos acústicos y de testigos (cores) en el límite de la plataforma y la parte superior del talud en el margen continental del sur de Aquitania. Estos datos revelan el importante papel que juegan los procesos de flujos en masa por gravedad en la erosión y redistribución de los depósitos, el modelado del lecho marino y la transferencia de sedimentos hacia el fondo del océano. La región de estudio está limitada al sur por el cañón de Capbreton. El área norte, que presenta una morfología suave, está caracterizada por deformaciones de pequeña escala debidas al arrastre de sedimentos o procesos de deslizamiento de baja amplitud. Las deformaciones están asociadas a mini fallas de tipo lístrico que delimitan bolsas de sedimentos en las cuales la geometría del depósito es típica de ondas de sedimento constructivas. Estas ondas sedimentarias resultan de la interacción de los procesos de deformación deposicionales y por gravedad. En el área sur, cerca del cañón, están todavía presentes estructuras similares a ondas, pero la mayor parte son de pequeño tamaño. Estas estructuras son el resultado de los procesos de deformación por gravedad sin ninguna evidencia de procesos constructivos. En las proximidades del cañón de Capbreton, el margen continental y el talud superior tienen una morfología mucho más desigual con relieves sedimentarios, escarpaduras y depresiones dirigidas hacia el talweg del cañón. Las depresiones semejan marcas de deslizamientos y pueden ser el resultado de deslizamientos regresivos iniciados en la parte superior de los flancos del cañón. Los eventos de deslizamiento responsables de la formación de las depresiones observadas actualmente podrían datarse en el Cuaternario medio o superior. Desde su formación, estas depresiones funcionan como conductos que canalizan la transferencia de sedimentos de plataforma hacia el cañón, tal y como demuestra la presencia de un canal con meandros en el fondo de una de estas depresiones

Amélioration des performances d'un moteur de base de données relationnelle embarqué par l'utilisation de GPU

International audienceConcomitamment à la montée en puissance des systèmes de type « Big Data », les systèmes de gestion de base de données relationnelle (SGBDR) restent toujours largement utilisés. Dans cet article, nous présentons une solution capable d'améliorer la rapidité et la consommation énergétique d'un SGBDR embarqué SQLite. Notre solution, nommée CuDB, tente d'exploiter au mieux les spécificités des architectures modernes CPU/GPU. Nous combinons des traite-ments massivement parallèles avec un placement stratégique des données au plus près des unités de calculs. CuDB est un SGBDR embarqué de type « In-Memory » (IMDB). En fonction du contenu, de la sélectivité et du poids des échanges, nos mesures révèlent des facteurs d'ac-célération allant jusqu'à 90x sur GPU GTX770 par rapport à une implémentation classique de SQLite sur CPU Core i7. L'accélération des traitements fournis par notre solution engendre de surcroît une nette amélioration de l'efficience énergétique globale du système

3-[2-(1H-Benzimidazol-2-ylsulfan­yl)eth­yl]-1,3-oxazolidin-2-one

In the title compound, C12H13N3O2S, the oxazolidin ring displays an envelope conformation. The dihedral angle between the benzimidazole ring and the 1,3-oxazolidin-2-one mean plane is 69.85 (13)°. In the crystal, mol­ecules are linked by inter­molecular N—H⋯N hydrogen bonds, forming a chain parallel to the b axis

Ethyl 5-cyano-8-nitro-2,3,4,4a,5,6-hexahydro-1H-pyrido[1,2-a]quinoline-5-carboxylate

In the title compound, C17H19N3O4, the piperidine ring adopts a chair conformation. The crystal structure features inversion dimers linked by pairs of weak C—H⋯N hydrogen bonds

Benthic and planktic foraminiferal distributions in the Bay of Biscay during the Holocene - Evaluation of hydrological patterns

The southeastern part of the Bay of Biscay is under the combined influence of the eastern branch of the North Atlantic Current (NAC) and coastal river plumes. The objective of this study is to use foraminiferal distribution from a 3 m high resolution record (SE Bay of Biscay; 550 m water depth) as proxies to evaluate the hydrological pattern of the Bay of Biscay during the Holocene; a period of rapid climatic change. Faunal distributions coupled to grain size variability suggest a rapid evolution of the sedimentary structuring of the basin. Major changes are recorded in benthic and planktic foraminiferal communities suggesting important fluctuations of primary and exported productivity during the Holocene. These rapid changes could be related to variations of the oceanic hydrology of the basin and/or to the coastal rivers hydrological regimes