742 research outputs found

    Optimizing the Performance of Parallel and Concurrent Applications Based on Asynchronous Many-Task Runtimes

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    Nowadays, High-performance Computing (HPC) scientific applications often face per- formance challenges when running on heterogeneous supercomputers, so do scalability, portability, and efficiency issues. For years, supercomputer architectures have been rapidly changing and becoming more complex, and this challenge will become even more com- plicated as we enter the exascale era, where computers will exceed one quintillion cal- culations per second. Software adaption and optimization are needed to address these challenges. Asynchronous many-task (AMT) systems show promise against the exascale challenge as they combine advantages of multi-core architectures with light-weight threads, asynchronous executions, smart scheduling, and portability across diverse architectures. In this research, we optimize the performance of a highly scalable scientific application using HPX, an AMT runtime system, and address its performance bottlenecks on super- computers. We use DCA++ (Dynamical Cluster Approximation) as a research vehicle for studying the performance bottlenecks in parallel and concurrent applications. DCA++ is a high-performance research software application that provides a modern C++ imple- mentation to solve quantum many-body problems with a Quantum Monte Carlo (QMC) kernel. QMC solver applications are widely used and are mission-critical across the US Department of Energy’s (DOE’s) application landscape. Throughout the research, we implement several optimization techniques. Firstly, we add HPX threading backend support to DCA++ and achieve significant performance speedup. Secondly, we solve a memory-bound challenge in DCA++ and develop ring- based communication algorithms using GPU RDMA technology that allow much larger scientific simulation cases. Thirdly, we explore a methodology for using LLVM-based tools to tune the DCA++ that targets the new ARM A64Fx processor. We profile all imple- mentations in-depth and observe significant performance improvement throughout all the implementations

    Application and Optimization of Contact-Guided Replica Exchange Molecular Dynamics

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    Proteine sind komplexe Makromoleküle, die in lebenden Organismen eine große Vielfalt an wichtigen Aufgaben erfüllen. Proteine können beispielsweise Gene regulieren, Struktur stabilisieren, Zellsignale übertragen, Substanzen transportieren und vieles mehr. Typischerweise sind umfassende Kenntnisse von Struktur und Dynamik eines Proteins erforderlich um dessen physiologische Funktion und Interaktionsmechanismen vollständig zu verstehen. Gewonnene Erkenntnisse sind für Biowissenschaften unerlässlich und können auf viele Bereiche angewendet werden, wie z.B. für Arzneimitteldesign oder zur Krankheitsbehandlung. Trotz des unfassbaren Fortschritts experimenteller Techniken bleibt die Bestimmung einer Proteinstruktur immer noch eine herausfordernde Aufgabe. Außerdem können Experimente nur Teilinformationen liefern und Messdaten können mehrdeutig und schwer zu interpretieren sein. Aus diesem Grund werden häufig Computersimulationen durchgeführt um weitere Erkenntnisse zu liefern und die Lücke zwischen Theorie und Experiment zu schließen. Heute sind viele in-silico Methoden in der Lage genaue Protein Strukturmodelle zu erzeugen, sei es mit einem de novo Ansatz oder durch Verbesserung eines anfänglichen Modells unter Berücksichtigung experimenteller Daten. In dieser Dissertation erforsche ich die Möglichkeiten von Replica Exchange Molekulardynamik (REX MD) als ein physikbasierter Ansatz zur Erzeugung von physikalisch sinnvollen Proteinstrukturen. Dabei lege ich den Fokus darauf möglichst nativähnliche Strukturen zu erhalten und untersuche die Stärken und Schwächen der angewendeten Methode. Ich erweitere die Standardanwendung, indem ich ein kontaktbasiertes Bias-Potential integriere um die Leistung und das Endergebnis von REX zu verbessern. Die Einbeziehung nativer Kontaktpaare, die sowohl aus theoretischen als auch aus experimentellen Quellen abgeleitet werden können, treibt die Simulation in Richtung gewünschter Konformationen und reduziert dementsprechend den notwendigen Rechenaufwand. Während meiner Arbeit führte ich mehrere Studien durch mit dem Ziel, die Anreicherung von nativ-ähnlichen Strukturen zu maximieren, wodurch der End-to-End Prozess von geleitetem REX MD optimiert wird. Jede Studie zielt darauf ab wichtige Aspekte der verwendeten Methode zu untersuchen und zu verbessern: 1) Ich studiere die Auswirkungen verschiedener Auswahlen von Bias-Kontakten, insbesondere die Reichweitenabhängigkeit und den negativen Einfluss von fehlerhaften Kontakten. Dadurch kann ich ermitteln, welche Art von Bias zu einer signifikanten Anreicherung von nativ-ähnlichen Konformationen führen im Vergleich zu regulärem REX. 2) Ich führe eine Parameteroptimierung am verwendeten Bias-Potential durch. Der Vergleich von Ergebnissen aus REX-Simulationen unter Verwendung unterschiedlicher sigmoidförmiger Potentiale weist mir sinnvolle Parameter Bereiche auf, wodurch ich ein ideales Bias-Potenzial für den allgemeinen Anwendungsfall ableiten kann. 3) Ich stelle eine de novo Faltungsmethode vor, die möglichst schnell viele einzigartige Startstrukturen für REX generieren kann. Dabei untersuche ich ausführlich die Leistung dieser Methode und vergleiche zwei verschiedene Ansätze zur Auswahl der Startstruktur. Das Ergebnis von REX wird stark verbessert, falls Strukturen bereits zu Beginn eine große Bandbreite des Konformationsraumes abdecken und gleichzeitig eine geringe Distanz zum angestrebten Zustand aufweisen. 4) Ich untersuche vier komplexe Algorithmusketten, die in der Lage sind repräsentative Strukturen aus großen biomolekularen Ensembles zu extrahieren, welche durch REX erzeugt wurden. Dabei studiere ich ihre Robustheit und Zuverlässigkeit, vergleiche sie miteinander und bewerte ihre erbrachte Leistung numerisch. 5) Basierend auf meiner Erfahrung mit geleitetem REX MD habe ich ein Python-Paket entwickelt um REX-Projekte zu automatisieren und zu vereinfachen. Es ermöglicht einem Benutzer das Entwerfen, Ausführen, Analysieren und Visualisieren eines REX-Projektes in einer interaktiven und benutzerfreundlichen Umgebung

    Two-Phase Flows With Dynamic Contact Angle Effects For Fuel Cell Applications

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    Liquid water management is still a very critical challenge in the commercialization of proton exchange membrane fuel cell (PEMFC). Fundamental understanding of two-phase flow behaviors is of crucial importance to the investigation of water management issues. Recently, it has been noted that the dynamic contact angle (DCA) plays a critical role in the two-phase flow simulations and the conventional static contact angle (SCA) model has obvious limitations in the prediction of droplet behaviors. This thesis mainly focuses on the numerical modeling and simulation of two-phase flow problems with dynamic contact angle (DCA) and is presented by four papers. The first paper proposes and validates an advancing-and-receding DCA (AR-DCA) model that is able to predict both advancing and receding dynamic contact angles using Hoffman function (Chapter 2). In the second paper, the AR-DCA model is further applied to simulate droplet behaviors on inclined surfaces with different impact velocities, impact angles and droplet viscosities (Chapter 3). The third paper introduces a methodology to improve the evaluation method of contact line velocity in the AR-DCA model and an improved-AR-DCA (i-AR-DCA) model is developed (Chapter 4). The last paper presents different flow regimes in a single straight microchannel under various air and water inlet flow rates (Chapter 5)

    Investigation of age-related protein changes in the human lens by quasi-elastic light scattering

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    The health and viability of cells and tissues in the human body depend on the functional integrity of proteins. A small number of long-lived proteins, including the crystallins in the lens of the eye, evade protein turnover, a typical cellular mechanism for repair and regeneration, and remain extant throughout life. The cumulative effect of post-translational modifications on the structure, function, and conformation of these long-lived proteins records the history of molecular aging in an individual. Along with absence of protein turnover, the optical accessibility, transparency, and age-related spatial order make the lens an ideal target for in vivo assessment of molecular aging. Accordingly, this doctoral thesis investigated the hypothesis that age-related perturbations that alter the protein environment in the human lens can be detected and monitored as a quantitative biomarker of molecular aging detectable by quasi-elastic light scattering (QLS). To test this hypothesis, QLS was applied in vitro and in vivo to study time-dependent changes in lens proteins. Water-soluble human lens protein extract was used in vitro as a model system that mimics the lens fiber cell cytoplasm. The effects of long-term incubation (nearly one year, proxy for aging), oxidative stress, ionizing radiation, metal-protein and pathogenic protein-protein interactions were investigated by QLS as a function of time. In vitro results were validated by protein gel electrophoresis and transmission electron microscopy. In vivo, age-dependent changes in lens proteins were assessed in healthy subjects across a broad age-range (5–61 years of age). Pathogenic protein aggregation in the lens was examined in vivo using Down syndrome (DS) subjects, a common chromosomal disease associated with an age-related Alzheimer’s disease (AD)-linked lens phenotype. Results obtained from the in vitro studies noted, for the first time, QLS detection of long-term supramolecular changes in a complex lens protein model system. Our FDA-approved QLS device was successful in assessing age-dependent lens protein changes in a clinical study at Boston Children’s Hospital (BCH). In two landmark studies conducted at BCH, we detected statistically significant AD-related lens protein changes in DS subjects aged 10–20 years, when compared with age-matched controls. These studies are the first clinical application of QLS in DS, and demonstrate protein changes in DS earlier than any previously reported studies. Due to the discrepancy in chronological and biological age and the lack of an objective index for the latter, we propose the application of QLS in the human lens as a quantitative biomarker of molecular aging

    Nonlocal Graph-PDEs and Riemannian Gradient Flows for Image Labeling

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    In this thesis, we focus on the image labeling problem which is the task of performing unique pixel-wise label decisions to simplify the image while reducing its redundant information. We build upon a recently introduced geometric approach for data labeling by assignment flows [ APSS17 ] that comprises a smooth dynamical system for data processing on weighted graphs. Hereby we pursue two lines of research that give new application and theoretically-oriented insights on the underlying segmentation task. We demonstrate using the example of Optical Coherence Tomography (OCT), which is the mostly used non-invasive acquisition method of large volumetric scans of human retinal tis- sues, how incorporation of constraints on the geometry of statistical manifold results in a novel purely data driven geometric approach for order-constrained segmentation of volumetric data in any metric space. In particular, making diagnostic analysis for human eye diseases requires decisive information in form of exact measurement of retinal layer thicknesses that has be done for each patient separately resulting in an demanding and time consuming task. To ease the clinical diagnosis we will introduce a fully automated segmentation algorithm that comes up with a high segmentation accuracy and a high level of built-in-parallelism. As opposed to many established retinal layer segmentation methods, we use only local information as input without incorporation of additional global shape priors. Instead, we achieve physiological order of reti- nal cell layers and membranes including a new formulation of ordered pair of distributions in an smoothed energy term. This systematically avoids bias pertaining to global shape and is hence suited for the detection of anatomical changes of retinal tissue structure. To access the perfor- mance of our approach we compare two different choices of features on a data set of manually annotated 3 D OCT volumes of healthy human retina and evaluate our method against state of the art in automatic retinal layer segmentation as well as to manually annotated ground truth data using different metrics. We generalize the recent work [ SS21 ] on a variational perspective on assignment flows and introduce a novel nonlocal partial difference equation (G-PDE) for labeling metric data on graphs. The G-PDE is derived as nonlocal reparametrization of the assignment flow approach that was introduced in J. Math. Imaging & Vision 58(2), 2017. Due to this parameterization, solving the G-PDE numerically is shown to be equivalent to computing the Riemannian gradient flow with re- spect to a nonconvex potential. We devise an entropy-regularized difference-of-convex-functions (DC) decomposition of this potential and show that the basic geometric Euler scheme for inte- grating the assignment flow is equivalent to solving the G-PDE by an established DC program- ming scheme. Moreover, the viewpoint of geometric integration reveals a basic way to exploit higher-order information of the vector field that drives the assignment flow, in order to devise a novel accelerated DC programming scheme. A detailed convergence analysis of both numerical schemes is provided and illustrated by numerical experiments

    Information Theory in Molecular Evolution: From Models to Structures and Dynamics

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    This Special Issue collects novel contributions from scientists in the interdisciplinary field of biomolecular evolution. Works listed here use information theoretical concepts as a core but are tightly integrated with the study of molecular processes. Applications include the analysis of phylogenetic signals to elucidate biomolecular structure and function, the study and quantification of structural dynamics and allostery, as well as models of molecular interaction specificity inspired by evolutionary cues

    Exploring manycore architectures for next-generation HPC systems through the MANGO approach

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    [EN] The Horizon 2020 MANGO project aims at exploring deeply heterogeneous accelerators for use in High-Performance Computing systems running multiple applications with different Quality of Service (QoS) levels. The main goal of the project is to exploit customization to adapt computing resources to reach the desired QoS. For this purpose, it explores different but interrelated mechanisms across the architecture and system software. In particular, in this paper we focus on the runtime resource management, the thermal management, and support provided for parallel programming, as well as introducing three applications on which the project foreground will be validated.This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 671668.Flich Cardo, J.; Agosta, G.; Ampletzer, P.; Atienza-Alonso, D.; Brandolese, C.; Cappe, E.; Cilardo, A.... (2018). Exploring manycore architectures for next-generation HPC systems through the MANGO approach. Microprocessors and Microsystems. 61:154-170. https://doi.org/10.1016/j.micpro.2018.05.011S1541706
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