Etude de l'adéquation des machines Exascale pour les algorithmes implémentant la méthode du Reverse Time Migation

As we are expecting Exascale systems for the 2018-2020 time frame, performance analysis and characterization of applications for new processor architectures and large scale systems are important tasks that permit to anticipate the required changes to efficiently exploit the future HPC systems. This thesis focuses on seismic imaging applications used for modeling complex physical phenomena, in particular the depth imaging application called Reverse Time Migration (RTM). My first contribution consists in characterizing and modeling the performance of the computational core of RTM which is based on finite-difference time-domain (FDTD) computations. I identify and explore the major tuning parameters influencing performance and the interaction between the architecture and the application. The second contribution is an analysis to identify the challenges for a hybrid and heterogeneous implementation of FDTD for manycore architectures. We target Intel’s first Xeon Phi co-processor, the Knights Corner. This architecture is an interesting proxy for our study since it contains some of the expected features of an Exascale system: concurrency and heterogeneity.My third contribution is an extension of the performance analysis and modeling to the full RTM. This adds communications and IOs to the computation part. RTM is a data intensive application and requires the storage of intermediate values of the computational field resulting in expensive IO accesses. My fourth contribution is the final measurement and model validation of my hybrid RTM implementation on a large system. This has been done on Stampede, a machine of the Texas Advanced Computing Center (TACC), which allows us to test the scalability up to 64 nodes each containing one 61-core Xeon Phi and two 8-core CPUs for a total close to 5000 heterogeneous coresLa caractérisation des applications en vue de les préparer pour les nouvelles architectures et les porter sur des systèmes très étendus est une étape importante pour pouvoir anticiper les modifications nécessaires. Comme les machines Exascale sont prévues pour la période 2018-2020, l'étude des applications et leur préparation pour ces machines s'avèrent donc essentielles. Nous nous intéressons aux applications d'imagerie sismique et en particulier à l'application Reverse Time Migration (RTM) car elle est très utilisée par les pétroliers dans le cadre de l'exploration sismique.La première partie de nos travaux a porté sur l'étude du cœur de calcul de l'application RTM qui consiste en un calcul de différences finies dans le domaine temporel (FDTD). Nous avons caractérisé cette partie de l'application en soulevant les aspects architecturaux des machines actuelles ayant un fort impact sur la performance, notamment les caches, les bandes passantes et le prefetching. Cette étude a abouti à l'élaboration d'un modèle de performance permettant de prédire le trafic DRAM des FDTD. La deuxième partie de la thèse se focalise sur l'impact de l'hétérogénéité et le parallélisme sur la FDTD et sur RTM. Nous avons choisi l'architecture manycore d’Intel, Xeon Phi, et nous avons étudié une implémentation "native" et une implémentation hétérogène et hybride, la version "symmetric". Enfin, nous avons porté l'application RTM sur un cluster hétérogène, Stampede du Texas Advanced Computing Center (TACC), où nous avons effectué des tests de scalabilité allant jusqu'à 64 nœuds contenant des coprocesseurs Xeon Phi et des processeurs Sandy Bridge ce qui correspond à presque 5000 cœur

Electronic structure, spectroscopy, cold ion-atom elastic collision properties and photoassociation formation prediction of (MgCs)+^+ molecular ion

Studies on the interactions between an alkali atom and an alkaline earth ion at low energy are important in the field of cold chemistry. In this paper we, extensively, study the structure, interactions, and dynamics of (MgCs)$^+$ molecular ion. We use an ab initio approach based on the formalism of non-empirical pseudo-potential for Mg$^{2+}$ and Cs$^+$ cores, large Gaussian basis sets and full valence configuration interaction. In this context, the (MgCs)$^+$ cation is treated as an effective two-electron system. Potential energy curves and their spectroscopic constants for the ground and the first 41 excited states of $^{1,3}\Sigma^+$, $^{1,3}\Pi$ and $^{1,3}\Delta$ symmetries are determined. Furthermore, we identify the avoided crossings between the electronic states of $^{1,3}\Sigma^+$ and $^{1,3}\Pi$ symmetries. These crossings are related to the charge transfer process between the two ionic limits Mg/Cs$^+$ and Mg$^+$/Cs. In addition, vibrational-level spacings, the transition and permanent dipole moments are presented and analysed. Using the produced potential energy data, the ground-state scattering wave functions and elastic cross sections for a wide range of energies are performed. Furthermore, we predict the formation of translationally and rotationally cold molecular ion (MgCs) + in the ground state electronic potential energy by stimulated Raman type process aided by ion-atom cold collision. In the low energy limit (< 1 mK), elastic scattering cross sections exhibit Wigner law threshold behaviour; while in the high energy limit the cross sections as a function of energy E go as E$^{-1/3}$. A qualitative discussion about the possibilities of forming the cold (MgCs)$^+$ molecular ions by photoassociative spectroscopy is presented

A MEASURE OF POLITICAL INSTITUTIONS INSTABILITY AND ITS IMPACT ON THE ECONOMIC GROWTH: EVIDENCE FROM MENA

We examine the multidimensionality of political institutions instability using 22 political institutions instability indicators in Principal components analysis (PCA). We find that political institutions instability has five dimensions:  Largest Government Party Seats, Number of Government Seats, Legislative Index of Political Competitiveness, Executive Index of Political Competitiveness and Largest Opposition Party Seats. By using the GMM system estimator for linear dynamic panel data models on a sample covering up to 19 countries from 1980 to 2012, we find that the five dimensions of political institutions instability have significant negative effect on economic growth

Structure, spectroscopy and cold collisions of the (SrNa)+^+ ionic system

We perform a study on extended adiabatic potential energy curves of nearly 38 states of 1,3$\Sigma^+$, 1,3$\Pi$ and 1,3$\Delta$ symmetries for the (SrNa)$^+$ ion, though only the ground and first two excited states are used for the study of scattering processes. Full Interaction Configuration (CI) calculations are carried out for this molecule using the pseudopotential approach. In this context, it is considered that two active electrons interact with the ionic cores and all single and double excitations were included in the CI calculations. A correction including the core-core electron interactions is also considered. Using the accurate potential energy data, the ground state scattering wave functions and cross sections are obtained for a wide range of energies. We find that, in order to get convergent results for the total scattering cross sections for energies of the order 1 K, one need to take into account at least 87 partial waves. In the low energy limit ( < 1 mK), elastic scattering cross sections exhibit Wigner law threshold law behavior while in the high energy limit the cross sections go as $E^{-1/3}$. A qualitative discussion about the possibility of forming the cold molecular ion by photoassociative spectroscopy is presented.Comment: accepted in EPJ

Effect of melatonin ingestion on physical performance, metabolic responses, and recovery after an intermittent training session

Objectives Fatigue is a limiting factor for sport performance. For this reason, optimal recovery after training is just as critical as the training program itself, if not more. Indeed, there is a need for strategies that can facilitate recovery after training, and one such strategy is the ingestion of supplements like melatonin (MEL). This study aimed to evaluate if MEL intake could improve recovery of athletes after an intermittent training session (ITS). Methods Fifteen elite female athletes (17.4 ± 0.4 years, 76.4 ± 5.6 kg, 1.76 ± 0.04 m; mean ± standard deviation) participated in two testing campaigns. During each period, they performed a battery of physical and cognitive tests before and after an ITS, as well as after ingesting MEL (6 mg tablet) or placebo in a randomized design. The ITS comprised the modified agility T-test, squat jump, counter movement jump, maximum standing ball-throw velocity test, maximum jump ball-throw velocity test, and 20-m sprint. Oral temperature (OT) and vigilance were evaluated before and after the ITS. Rating of perceived exertion (RPE), blood lactate [La], and glucose [Gl] were recorded after each ITS. Results Short-term performance, recovery of physical performance, and OT were not affected by MEL ingestion after the ITS. Moreover, MEL did not affect cognitive performance or RPE scores after the ITS. However, [La] and [Gl] (p < 0.05 for both) were decreased after MEL ingestion. Conclusion: MEL has no effect on the recovery of physical performance but may affect glucose utilization and lactate metabolism during the team-handball training session

Adaptive Radiation within Marine Anisakid Nematodes: A Zoogeographical Modeling of Cosmopolitan, Zoonotic Parasites

Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area

First molecular identification of the zoonotic parasite Anisakis pegreffii (Nematoda: Anisakidae) in a paraffin-embedded granuloma taken from a case of human intestinal anisakiasis in Italy

<p>Abstract</p> <p>Background</p> <p>Anisakiasis is an important fish-borne zoonosis provoked by larval stages of nematodes belonging to the genus <it>Anisakis</it>. The detection and identification of human infections is difficult. This is due to: a) the low specificity of the clinical features and symptomatology related to human infections; b) the paucity of diagnostic features of larvae found in granulomatous lesions characteristic of "invasive anisakiasis"; and c) the lack morphological characters diagnostic at the specific level when larvae of <it>Anisakis </it>are detected. Thus, molecular-based diagnostic approaches are warranted.</p> <p>Method</p> <p>We have developed a PCR method that amplifies the DNA of <it>Anisakis </it>spp. in fixed paraffin-embedded tissues. This method was applied to a granuloma removed from a human case of intestinal anisakiasis in Italy. Specific primers of the mtDNA <it>cox2 </it>gene were used and sequence analysis was performed according to the procedures already established for species of <it>Anisakis</it>.</p> <p>Results</p> <p>The sequence obtained (629 bp) was compared with those of the other species of <it>Anisakis </it>which have so far been genetically characterized and with sequences obtained from larval stages of <it>Anisakis </it>collected from the Mediterranean fish <it>Engraulis encrasicolus</it>. This enabled the genetic identification of the larva in the human tissue as <it>A. pegreffii</it>. This is the first instance of human intestinal anisakiasis diagnosed using PCR of DNA purified from a fixed eosinophilic granuloma embedded in paraffin.</p> <p>Conclusion</p> <p>The case of human anisakiasis presented reinforces the pathological significance of the species <it>A. pegreffii </it>to humans. The molecular/genetic methodological approach based on mtDNA <it>cox2 </it>sequence analysis, described here, can allow easy and rapid identification of <it>Anisakis </it>spp. in formalin-fixed and paraffin embedded tissues removed from cases of either gastric or intestinal human anisakiasis.</p