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  • ddc:004  (10)
  • English  (10)
  • 1
    Publication Date: 2016-06-30
    Description: Executing applications in the Grid often requires access to multiple geographically distributed resources. In a Grid environment, these resources belong to different administrative domains, each employing its own scheduling policy. That is, at which time an activity (e.g., compute job, data transfer) is started, is decided by the resource's local management system. In such an environment, the coordinated execution of distributed applications requires guarantees on the quality of service (QoS) of the needed resources. Reserving resources in advance is an accepted means to obtain QoS guarantees from a single provider. The challenge, however, is to coordinate advance reservations of multiple resources. This work presents a system architecture and mechanisms to coordinate multiple advance reservations -- called co-reservations -- for delivering QoS guarantees to complex applications. We formally define the co-reservation problem as an optimization problem. The presented model supports three dimensions of freedom: the start time, the duration and the service level of a reservation. Requests and resources are described in a simple language. After matching the static properties and requirements of either side in a mapping, the reservation mechanism probes information about the future status of the resources. The versatile design of the probing step allows the efficient processing of requests, but also lets the resources express their preferences among the myriads of reservation candidates. Next, the best mapping is found through an implementation of the formal co-reservation model. Then, the mapping has to be secured, i.e., resources need to be allocated to a co-reservation candidate with all-or-nothing semantics. We study several goal-driven sequential and concurrent allocation mechanisms and define schemes for handling allocation failures. Finally, we introduce the concept of virtual resources for seamlessly embedding co-reservations into Grid resource management.
    Description: Die Ausführung von Anwendungen erfordert oft mehrere, geographisch verteilte Ressourcen. In Grid-Umgebungen gehören diese Ressourcen zu verschiedenen administrativen Organisationen, wobei jede ihre eigene Schedulingregeln verwendet. Das bedeutet, zu welcher Zeit eine Aktivität gestartet wird (z.B. ein Rechenjob), wird vom lokalen Ressourcenmanagementsystem entschieden. Die koordinierte Ausführung von verteilten Anwendungen erfordert Dienstgütegarantien für die benötigten Ressourcen. Das Reservieren von Ressourcen im Voraus ist ein Mittel, um Dienstgütegarantien von einem einzelnen Ressourcenanbieter zu erhalten. Die Herausforderung in dieser Arbeit ist, Vorausreservierungen von mehreren Ressourcen zu koordinieren. Es wird ein System für die Koordinierung mehrerer Vorausreservierungen -- Co-Reservierungen genannt -- für die Bereitstellung von Dienstgütegarantien vorgestellt. Wir definieren das Co-Reservierungsproblem als Optimierungsproblem. Das vorgestellte Modell unterstützt drei Freiheitsgrade: die Startzeit, die Dauer und die Dienstgüte einer Reservierung. Anfragen und Ressourcen werden in einer einfachen Sprache beschrieben. Nachdem statische Eigenschaften und Anforderungen beider Seiten überprüft wurden, ermittelt der Reservierungsmechanismus Informationen über den zukünftigen Zustand der Ressourcen. Dieser Schritt ist so allgemein gehalten, daß er sowohl ein effizientes Bearbeiten der Anfragen erlaubt als auch den Ressourcen ermöglicht ihre Präferenzen auszudrücken. Im Anschluss wird die optimale Zuweisung von Anfragen zu Ressourcen ermittelt. Im letzten Schritt muss diese Zuweisung umgesetzt werden, d.h., entweder alle oder keine Ressource wird allokiert. Es werden mehrere sequentielle und parallele Allokationsverfahren vorgestellt sowie deren Auswirkung auf verschiedene Metriken untersucht. Die Einbettung von Co-Reservierungen in das Grid-Ressourcenmanagement wird anhand des Konzeptes der virtuellen Ressource dargestellt.
    Keywords: ddc:004
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
    Format: application/pdf
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  • 2
    Publication Date: 2017-11-02
    Description: One of the biggest impacts on the performance of a Distributed Hash Table (DHT), once established, is its ability to balance load among its nodes. DHTs supporting range queries for example suffer from a potentially huge skew in the distribution of their items since techniques such as consistent hashing can not be applied. Thus explicit load balancing schemes need to be deployed. Several such schemes have been developed and are part of recent research, most of them using only information locally available in order to scale to arbitrary systems. Gossiping techniques however allow the retrieval of fairly good estimates of global information with low overhead. Such information can then be added to existing load balancing algorithms that can use the additional knowledge to improve their performance. Within this thesis several schemes are developed that use global information like the average load and the standard deviation of the load among the nodes to primarily reduce the number of items an algorithm moves to achieve a certain balance. Two novel load balancing algorithms have then been equipped with implementations of those schemes and have been simulated on several scenarios. Most of these variants show better balance results and move far less items than the algorithms they are based on. The best of the developed algorithms achieves a 15-30% better balance and moves only about 50-70% of the number of items its underlying algorithm moves. This variation is also very robust to erroneous estimates and scales linearly with the system size and system load. Further experiments with self-tuning algorithms that set an algorithm’s parameter according to the system’s state show that even more improvements can be gained if additionally applied. Such a variant based on the algorithm described by Karger and Ruhl shows the same balance improvements of 15-30% as the variant above but reduces the number of item movements further to 40-65%.
    Keywords: ddc:004
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 3
    Publication Date: 2021-01-22
    Description: We present a framework for transactional data access on data stored in a DHT. It allows to atomically read and write items and to run distributed transactions consisting of a sequence of read and write operations on the items. Items are symmetrically replicated in order to achieve durability of data stored in the SON. To provide availability of items despite the unavailability of some replicas, operations on items are quorum-based. They make progress as long as a majority of replicas can be accessed. Our framework processes transactions optimistically with an atomic commit protocol that is based on Paxos atomic commit. We present algorithms for the whole framework with an event based notation. Additionally we discuss the problem of lookup inconsistencies and its implications on the one-copy serializability property of the transaction processing in our framework.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 4
    Publication Date: 2020-12-11
    Description: When planning teams for projects with specific goals, employees of a company have to group together so well, that all necessary knowledge for conquering the project’s challenges are met within the member’s skills. A tool that facilitates semantic web technologies can support the team recruiter, who is responsible for chosing the members of the team, in terms of finding the most efficient combinations of the company’s employees based on their expertises.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 5
    Publication Date: 2021-01-22
    Description: Key/value stores which are built on structured overlay networks often lack support for atomic transactions and strong data consistency among replicas. This is unfortunate, because consistency guarantees and transactions would allow a wide range of additional application domains to benefit from the inherent scalability and fault-tolerance of DHTs. The Scalaris key/value store supports strong data consistency and atomic transactions. It uses an enhanced Paxos Commit protocol with only four communication steps rather than six. This improvement was possible by exploiting information from the replica distribution in the DHT. Scalaris enables implementation of more reliable and scalable infrastructure for collaborative Web services that require strong consistency and atomic changes across multiple items.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 6
    Publication Date: 2016-06-30
    Description: We study performance and scaling of the Berlin Quantum Chromodynamics Program (BQCD) on the SGI Altix 4700 at Leibniz Supercomputing Centre (LRZ). We employ different communication methods (MPI, MPI with two OpenMP threads per process, as well as the shmem library) and run the MPI version on the two types of nodes of that machine. For comparison with other machines we made performance measurements on an IBM p690 cluster and a Cray XT4.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 7
    Publication Date: 2022-07-19
    Description: This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces.
    Description: In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 8
    Publication Date: 2022-07-19
    Description: For medical diagnosis, visualization, and model-based therapy planning three-dimensional geometric reconstructions of individual anatomical structures are often indispensable. Computer-assisted, model-based planning procedures typically cover specific modifications of “virtual anatomy” as well as numeric simulations of associated phenomena, like e.g. mechanical loads, fluid dynamics, or diffusion processes, in order to evaluate a potential therapeutic outcome. Since internal anatomical structures cannot be measured optically or mechanically in vivo, three-dimensional reconstruction of tomographic image data remains the method of choice. In this work the process chain of individual anatomy reconstruction is described which consists of segmentation of medical image data, geometrical reconstruction of all relevant tissue interfaces, up to the generation of geometric approximations (boundary surfaces and volumetric meshes) of three-dimensional anatomy being suited for finite element analysis. All results presented herein are generated with amira ® – a highly interactive software system for 3D data analysis, visualization and geometry reconstruction.
    Keywords: ddc:004
    Language: English
    Type: reportzib , doc-type:preprint
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  • 9
    Publication Date: 2022-07-19
    Description: This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation.
    Description: Die vorliegende Arbeit führt I/O-effiziente Algorithmen und Standard-Algorithmen zur Berechnung von Voxel-Skeletten aus großen Voxel-Objekten mit komplexer, netzwerkartiger Struktur und zur Umwandlung solcher Voxel-Skelette in stückweise-lineare Geometrie ein. Die vorgestellten Techniken werden zur Visualisierung und Analyse komplexer drei-dimensionaler Bilddaten, beispielsweise aus Biologie und Medizin, eingesetzt. Abschnitt 2.3.1 leistet mit der Diskussion von topologischem Thinning im Grid-Cell-Modell einen Beitrag zu den theoretischen Grundlagen von Thinning-Algorithmen. Im Grid-Cell-Modell wird ein Voxel-Objekt als Zellkomplex dargestellt, der aus den Ecken, Kanten, Flächen und den eingeschlossenen Volumina der Voxel gebildet wird. Topologisch unklare Situationen an Verzweigungen und blockierte Voxel-Kombinationen werden aufgelöst. Die Charakterisierung von Zellpaaren, die im Thinning-Prozess entfernt werden dürfen, ist einfacher als bekannte Charakterisierungen von so genannten "Simple Voxels". Eine wesentliche Schlussfolgerung ist, dass das Grid-Cell-Modell atomaren Voxeln überlegen ist, wenn Algorithmen detaillierte Kontrolle über Topologie benötigen. Abschnitt 2.3.2 präsentiert ein rauschunempfindliches Maß, das den geodätischen Abstand entlang der Oberfläche verwendet, um zweidimensionale Skelette zu berechnen, welche dünne, aber geometrisch bedeutsame, Strukturen des Objekts rauschunempfindlich abbilden. Das Maß wird im weiteren mit Thinning kombiniert, um die Erosion von Voxeln auf Linien zuzusteuern, die zentriert in plattenförmigen Strukturen liegen. Maße, die auf dem geodätischen Abstand aufbauen, scheinen sehr geeignet zu sein, um ein- und zwei-dimensionale Skelette bei vorhandenem Rauschen zu identifizieren. Eine theoretische Begründung für diese Beobachtung steht noch aus. In Abschnitt 6 werden die diskutierten Methoden zur Visualisierung von Knochenfeinstruktur eingesetzt. Abschnitt 3 beschreibt eine Methode, um Voxel-Skelette durch kontrollierte Retraktion in eine stückweise-lineare geometrische Darstellung umzuwandeln, die als Eingabe für Geometrieverarbeitung und effizientes Rendering von Voxel-Skeletten dient. Es zeigt sich, dass eine detaillierte Betrachtung der topologischen Eigenschaften eines Voxel-Skeletts einer Betrachtung von allgemeinen Voxel-Konfigurationen für die Umwandlung zu einer geometrischen Darstellung überlegen ist. Die diskutierte Methode bildet die Grundlage für die Anwendungen, die in Abschnitt 6 diskutiert werden. Abschnitt 5 führt einen I/O-effizienten Algorithmus für Thinning ein. Die vorgestellte Methode erweitert bekannte Algorithmen zur Berechung von Chamfer-Distanztransformationen und Thinning so, dass diese effizient ausführbar sind, wenn die Eingabedaten den verfügbaren Hauptspeicher übersteigen. Der Einfluss der Blockgrenzen auf die Algorithmen wurde analysiert, um global korrekte Ergebnisse sicherzustellen. Eine detaillierte Analyse ist einer naiven Zerlegung, die die Einflüsse von Blockgrenzen vernachlässigt, überlegen. In Abschnitt 6 wird, aufbauend auf den I/O-effizienten Algorithmen, ein Verfahren zur quantitativen Analyse von Mikrogefäßnetzwerken diskutiert.
    Keywords: ddc:004
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
    Format: application/pdf
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  • 10
    Publication Date: 2022-07-19
    Description: One crucial step in virtual drug design is the identification of new lead structures with respect to a pharmacological target molecule. The search for new lead structures is often done with the help of a pharmacophore, which carries the essential structural as well as physico-chemical properties that a molecule needs to have in order to bind to the target molecule. In the absence of the target molecule, such a pharmacophore can be established by comparison of a set of active compounds. In order to identify their common features,a multiple alignment of all or most of the active compounds is necessary. Moreover, since the “outer shape” of the molecules plays a major role in the interaction between drug and target, an alignment algorithm aiming at the identification of common binding properties needs to consider the molecule’s “outer shape”, which can be approximated by the solvent excluded surface. In this thesis, we present a new approach to molecular surface alignment based on a discrete representation of shape as well as physico-chemical properties by points distributed on the solvent excluded surface. We propose a new method to distribute points regularly on a surface w.r.t. a smoothly varying point density given on that surface. Since the point distribution algorithm is not restricted to molecular surfaces, it might also be of interest for other applications. For the computation of pairwise surface alignments, we extend an existing point matching scheme to surface points, and we develop an efficient data structure speeding up the computation by a factor of three. Moreover, we present an approach to compute multiple alignments from pairwise alignments, which is able to handle a large number of surface points. All algorithms are evaluated on two sets of molecules: eight thermolysin inhibitors and seven HIV-1 protease inhibitors. Finally, we compare the results obtained from surface alignment with the results obtained by applying an atom alignment approach.
    Description: Die Identifizierung neuer Leitstrukturen (lead structures) zur Entwicklung optimierter Wirkstoffe ist ein äußerst wichtiger Schritt in der virtuellen Wirkstoffentwicklung (virtual drug design). Die Suche nach neuen Leitstrukturen wird oft mit Hilfe eines Pharmakophor-Modells durchgeführt, welches die wichtigsten strukturellen wie auch physiko-chemischen Eigenschaften eines bindenden Moleküls in sich vereint. Ist das Zielmolekül (target) nicht bekannt, kann das Pharmakophor-Modell mit Hilfe des Vergleiches aktiver Moleküle erstellt werden. Hier ist insbesondere die gleichzeitige Überlagerung (multiple alignment) aller oder nahezu aller Moleküle notwendig. Da bei der Interaktion zweier Moleküle die "äußere Form" der Moleküle eine besondere Rolle spielt, sollte diese von jedem Überlagerungsalgorithmus, der sich mit der Identifizierung von Bindungseigenschaften befasst, berücksichtigt werden. Dabei kann die "äußere Form" durch eine bestimmte Art von molekularer Oberfläche approximiert werden, die man als solvent excluded surface bezeichnet. In dieser Arbeit stellen wir einen neuen Ansatz zur Überlagerung molekularer Oberflächen dar, der auf einer diskreten Repräsentation sowohl der Form als auch der molekularen Eigenschaften mittels Punkten beruht. Um die Punkte auf der molekularen Oberfläche möglichst regulär entsprechend einer gegebenen Punktdichte zu verteilen, entwickeln wir eine neue Methode. Diese Methode ist nicht auf Moleküloberflächen beschränkt und könnte daher auch für andere Anwendungen von Interesse sein. Basierend auf einem bekannten Point-Matching Verfahren entwickeln wir einen Point-Matching Algorithmus für Oberflächenpunkte. Dazu erarbeiten wir u.a. eine effiziente Datenstruktur, die den Algorithmus um einen Faktor von drei beschleunigt. Darüberhinaus stellen wir einen Ansatz vor, der Mehrfachüberlagerungen (multiple alignments) aus paarweisen Überlagerungen berechnet. Die Herausforderung besteht hierbei vor allem in der großen Anzahl von Punkten, die berücksichtigt werden muss. Die vorgestellten Algorithmen werden an zwei Gruppen von Molekülen evaluiert, wobei die erste Gruppe aus acht Thermolysin Inhibitoren besteht, die zweite aus sieben HIV-1 Protease Inhibitoren. Darüberhinaus vergleichen wir die Ergebnisse der Oberflächenüberlagerung mit denen einer Atommittelpunktüberlagerung.
    Keywords: ddc:004
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
    Format: application/pdf
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