TY - THES A1 - Kruber, Nico T1 - DHT Load Balancing with Estimated Global Information N2 - 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%. KW - Peer-to-Peer KW - Verteilte Hashtabelle (DHT) KW - Lastverteilung KW - Gossiping KW - Peer-to-Peer KW - Distributed Hash Table (DHT) KW - Load Balancing KW - Gossiping Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11514 ER - TY - GEN A1 - Moser, Monika A1 - Haridi, Seif A1 - Shafaat, Tallat A1 - Schütt, Thorsten A1 - Högqvist, Mikael A1 - Reinefeld, Alexander T1 - Transactional DHT Algorithms N2 - 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. T3 - ZIB-Report - 09-34 KW - Distributed System KW - DHT KW - Paxos KW - Algorithms KW - Storage Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11532 SN - 1438-0064 ER - TY - THES A1 - Mauter, Daniel T1 - Ein eingebettetes Hauptspeicher-Datenbanksystem mit Snapshot-Reads T1 - An embedded main memory database with snapshot-reads N2 - Entwurf und Entwicklung eines eingebetteten Hauptspeicher-Datenbanksystems mit Snapshot-Reads. N2 - Design and implementation of an embedded main memory database with snapshot reads. KW - Datenbank KW - Hauptspeicher KW - Snapshot-Reads KW - database KW - main memory KW - snapshot-read Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11552 ER - TY - GEN A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Haridi, Seif A1 - Schütt, Thorsten T1 - Enhanced Paxos Commit for Transactions on DHTs N2 - 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. T3 - ZIB-Report - 09-28 KW - Paxos KW - Transaktionen KW - DHT KW - strenge Konsistenz KW - Paxos KW - transactions KW - DHT KW - strong consistency Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11448 SN - 1438-0064 ER - TY - THES A1 - Tuschl, Roland T1 - Ein Userspace-Dateisystem zur Verwaltung von Grid-Daten T1 - A Userspace Filesystem for the Management of Grid Data N2 - Das Ziel dieser Arbeit ist die Schaffung einer Zugriffs-Komponente für das Grid-Datenmanagement-System ZIB-DMS, das dessen transparente Einbindung in den Verzeichnisbaum eines Linux-Systems erlaubt. Dazu wird unter Verwendung des FUSE-Rahmenwerkes ein Userspace-Dateisystem mit Anbindung an das ZIB-DMS konzipiert und implementiert. Im Fokus stehen dabei die Abbildung der erweiterten Verwaltungsmechanismen des Systems auf die limitierte Schnittstelle hierarchischer Dateisysteme und die dazu notwendigen Änderungen am ZIB-DMS. N2 - The goal of this work is to create an access component for the Grid data management system ZIB-DMS, that allows a transparent integration into the directory tree of a Linux system. For this purpose the FUSE framework is used to design and implement a userspace file system with connections to the ZIB-DMS. The focus is on the mapping of the extended management mechanisms of the system to the limited interface of hierarchical file systems and the therefore necessary changes to ZIB-DMS. KW - Dateisystem KW - Grid KW - Datenmanagement KW - filesystem KW - Grid KW - data management Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11483 ER - TY - THES A1 - Prollius, Christian von T1 - Ein Peer-to-Peer System mit Bereichsabfragen in PlanetLab T1 - A Peer-to-Peer System with Range Queries in PlanetLab N2 - Aktuelle Entwicklungen zeigen, dass Peer-to-Peer (P2P) Anwendungen wie Skype oder Bittorrent im Internet immer mehr an Bedeutung gewinnen. In den letzten Jahren hat es einen explosionsartigen Anstieg an Nutzern und Daten in solchen Netzen gegeben. Dabei stellt der eigentliche Dateitransfer zwischen zwei Rechnern kein großes Problem mehr dar und auch der Speicherbedarf für die große Menge an Daten kann durch die Weiterentwicklung der Hardware gut gedeckt werden. Das eigentliche Problem liegt vielmehr darin, den Rechner zu finden, der die gewünschten Daten hat. Client-Server Architekturen, wie zum Beispiel Napster, haben sich als ungünstig herausgestellt. Wenige Server, die eine große Anzahl an Clients bedienen müssen, sind einerseits sehr anfällig gegenüber Angriffen und Ausfällen (Single Point of Failure)und kommen auch nicht mit der ständig wachsenden Anzahl an Nutzern zurecht. Verteilte Hashtabellen (DHT) bieten hier einen guten Lösungsansatz, der mit einer großen Anzahl an Nutzern skaliert und ausfallsicher ist. Andere dezentrale Lösungen, wie zum Beispiel das P2P Netzwerk Gnutella haben zwar das Problem des Single Point of Failure gelöst, jedoch haben sie starke Nachteile bei der Suche nach Keys. Bei einer Suche wird ein Broadcast verwendet (jeder schickt die Anfrage an jeden weiter) und damit ein enormer Netzwerkverkehr erzeugt. In "Why Gnutella Can't Scale. No, Really" wird erklärt, dass eine Suchanfrage bei Standardeinstellungen in der Clientsoftware einen Netzwerkverkehr von 17MB erzeugt. Deswegen wird zusätzlich eine Lösung benötigt, die Keys und Values geordnet verteilt, damit sie gezielt gesucht werden können. Aus diesem Grund beschäftigt sich die folgende Arbeit mit einer völlig dezentralen Architektur, die außerdem eine sinnvolle Platzierung der Keys vornimmt. Die dezentrale Architektur hat den Vorteil, dass die Endgeräte den Hauptteil des Dienstes selbst erbringen und damit jeder zusätzliche Teilnehmer seine eigenen Ressourcen beisteuert. Diese Arbeit präsentiert Chord#, eine dezentrale, skalierbare und selbstorganisierende verteilte Hashtabelle. Chord# wurde ausgewählt, da in dieser Arbeit auch Wert auf Bereichsabfragen gelegt wurde. Diese sind zum Beispiel bei dem Chord Algorithmus nicht möglich, da dieser eine Hashfunktion für die Keys verwendet und somit die Daten zwar gleichmäßig aber unsortiert auf die Teilnehmer verteilt. Es wird in dieser Arbeit gezeigt, dass mit Hilfe von Chord# auch ohne die Hashfunktion gute Ergebnisse erzielt werden. Außerdem können durch den Verzicht auf die Hashfunktion Bereichsabfragen ermöglicht werden. Dafür wird der Chord# Algorithmus in Java implementiert (ca. 1500 Zeilen Code) und in dem Forschungsnetz PlanetLab ausführlich auf Laufzeiten, Instandhaltungskosten und Skalierung getestet. N2 - Recent developments show that peer-to-peer (p2p) applications, such as Skype or Bittorrent have become increasingly important in the internet. Over the last years there has been a rapid growth of both users and data in such networks. However, the actual file transfer between two peers is not really an issue anymore. The same holds true for data storage, since the new hardware grants users enough space to store their data. The real problem is finding the peers that possess the desired data. Client-server architectures like Napster have proven to be ineffective addressing that problem. One or few servers being responsible for many peers are vulnerable to attacks or failures (single point of failure). Additionally, they are unable to cope with the rapidly growing number of peers. Distributed hashtables (DHT) are a good approach to solve these problems, since they scale nicely with large numbers of peers and provide a high tolerance for errors. Other decentralized solutions like the p2p network Gnutella solved the problem of Single Point of Failure but show considerable disadvantages when searching for keys. The peers in Gnutella use a broadcast (sending the message to all peers they know)resulting in massive traffic. According to "Why Gnutella Can't Scale. No, Really.", each search using standard client settings yields 17MB traffc. This calls for a different solution, distributing keys and values to peers quickly and efficiently so they can be found fast. For that reason this thesis focuses on a fully distributed architecture using organized key placement. One major advantage of distributed architecture is the fact, that the peers do most of the work themselves. This way, new peers joining the network add resources to it. This thesis presents Chord#, a scalable, self-organizing and completely decentralized DHT. It has been chosen due to its capability to allow range queries. The regular Chord algorithm does not support range queries, because of the hashfunction it uses to evenly distribute the keys among the peers. This results in similar or logical coherent keys most likely not being close together in the network. This thesis shows Chord# achieving same results as Chord - regarding performance costs - without the hashfunction. In dropping the hashfunction this algorithm allows the use of range queries. The Chord# algorithm is implemented in Java (about 1500 lines of code) and thoroughly tested in the research network PlanetLab. The results are evaluated regarding performance, maintenance and scalability. KW - Peer-to-Peer KW - Bereichsabfragen KW - peer-to-peer KW - range queries Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11492 ER - TY - GEN A1 - Allalen, Mohammed A1 - Brehm, Matthias A1 - Stüben, Hinnerk T1 - Performance of Quantum Chromodynamics (QCD) Simulations on the SGI Altix N2 - 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. T3 - ZIB-Report - 08-54 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11086 SN - 1438-0064 ER - TY - GEN A1 - Streuer, Thomas A1 - Stüben, Hinnerk T1 - Simulations of QCD in the Era of Sustained Tflop/s Computing N2 - The latest machine generation installed at supercomputer centres in Germany offers a peak performance in the tens of Tflop/s range. We study performance and scaling of our quantum chromodynamics simulation programme BQCD that we obtained on two of these machines, an IBM Blue Gene/L and an SGI Altix 4700. We compare the performance of Fortran/MPI code with assembler code. The latter allows to exploit concurrency at more levels, in particular in overlapping communication and computation as well as prefetching data from main memory. T3 - ZIB-Report - 07-48 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10623 SN - 1438-0064 ER - TY - THES A1 - Röblitz, Thomas T1 - Co-Reservation of Resources in the Grid N2 - 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. N2 - 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. KW - Ressourcen-Verwaltung KW - Reservierung KW - Verteilte Systeme KW - Grid Computing KW - resource management KW - reservation KW - distributed systems KW - grid computing Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11626 SN - 978-3-86853-137-4 ER - TY - GEN A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Stender, Jan A1 - Hupfeld, Felix T1 - Fault-Tolerant and Decentralized Lease Coordination in Distributed Systems N2 - Applications which need exclusive access to a shared resource in distributed systems require a fault-tolerant and scalable mechanism to coordinate this exclusive access. Examples of such applications include distributed file systems and master/slave data replication. We present Flease, an algorithm for decentralized and fault-tolerant lease coordination in distributed systems. Our algorithm allows the processes competing for a resource to coordinate exclusive access through leases among themselves without a central component. The resulting system easily scales with an increasing number of nodes and resources. We prove that Flease ensures exclusive access, i.e. guarantees that there is at most one valid lease at any time. T3 - ZIB-Report - 10-02 Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11658 SN - 1438-0064 ER - TY - THES A1 - Plantikow, Stefan T1 - Transaktionen für verteilte Wikis auf strukturierten Overlay Netzwerken T1 - Transactions for Distributed Wikis on Structured Overlay Networks N2 - Die Diplomarbeit präsentiert ein Transaktionsverfahren für strukturierte Overlay-Netzwerke, das an die Erfordernisse verteilter Informationssysteme mit relationalem Datenmodell angepasst ist. Insbesondere wird der Einsatz von Transaktionen für verteilte Wikis betrachtet, die moderne Funktionalitäten, wie Metadaten und zusätzliche Indexe für die Navigation, unterstützen. Konsistenz und Dauerhaftigkeit der gespeicherten Daten erfordert die Behandlung von Knotenausfällen. Die Arbeit schlägt dafür das Zellenmodell vor: Das Overlay wird aus replizierten Zustandsmaschinen gebildet, um Verfügbarkeit zu gewährleisten. Das Transaktionsverfahren baut darauf auf und verwendet Two-Phase-Commit mit Fehlererkennung und Widerherstellung von ausgefallenen Transaktionsmanagern. Anwendungen wird eine Auswahl an pessimistischen und hybrid-optimistischen Nebenläufigkeitskontrollverfahren geboten, die die Minimierung von Latenzeffekten und die schnelle Ausführung von Nur-Lese-Transaktionen ermöglichen. Für die Beispielanwendung Wiki wird der erforderliche Pseudocode angegeben und die verschiedenen Nebenläufigkeitskontrollverfahren hinsichtlich ihrer Nachrichtenkomplexität verglichen. N2 - The diploma thesis presents a transaction processing scheme for structured overlay networks and uses it to develop a distributed Wiki application based on a relational data model. The Wiki supports rich metadata and additional indexes for navigation purposes. Ensuring consistency and durability requires handling of node failures. Such failures are masked by providing high availability of nodes. This in turn is achieved by constructing the overlay from replicated state machines (cell model). Atomicity is realized using two phase commit with additional support for failure detection and restoration of the transaction manager. The developed transaction processing scheme provides the application with a mixture of pessimistic, hybrid optimistic and multiversioning concurrency control techniques to minimize the impact of replication on latency and optimize for read operations. The pseudocode of the relevant Wiki functions is presented and the different concurrency control techniques are evaluated in terms of message complexity. KW - Verteilte Transaktionen KW - Content Management Systeme KW - Strukturierte Overlay-Netzwerke KW - Konsistenz KW - Nebenläufigkeitskontrolle KW - distributed transactions KW - content management systems KW - structured overlay networks KW - consistency KW - concurrency control Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10176 ER - TY - GEN A1 - May, Patrick A1 - Bauer, Markus A1 - Köberle, Christian A1 - Klau, Gunnar T1 - A computational approach to microRNA detection N2 - During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures. T3 - ZIB-Report - 06-44 KW - microRNA Smith-Waterman RNA folding Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9383 ER - TY - GEN A1 - May, Patrick A1 - Steinke, Thomas T1 - THESEUS - Protein Structure Prediction at ZIB N2 - THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004. T3 - ZIB-Report - 06-24 KW - Protein Structure Prediction KW - Bioinformatics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9184 ER - TY - GEN A1 - Golas, Ulrike T1 - A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version N2 - Attributes are an important concept for modeling data in practical applications. Up to now there is no adequate way to define attributes for different kinds of models used in M-adhesive transformation systems, which are a special kind of graph transformation systems based on M-adhesive categories. Especially a proper representation and definition of attributes and their values as well as a suitable handling of the data does not fit well with other graph transformation formalisms. In this paper, we propose a new method to define attributes in a natural, but still formally precise and widely applicable way. We define a new kind of adhesive category, called W-adhesive, that can be used for transformations of attributes, while the underlying models are still M-adhesive ones. As a result, attributed models can be used as they are intended to be, but with a formal background and proven well-behavior. T3 - ZIB-Report - 12-22 KW - graph transformation KW - attribution KW - adhesive categories Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15547 SN - 1438-0064 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - A Novel Hybrid Approach to Automatically Determine Kernel Interface Data Volumes N2 - Scheduling algorithms for heterogeneous platforms make scheduling decisions based on several metrics. One of these metrics is the amount of data to be transferred from and to the accelerator. However, the automated determination of this metric is not a simple task. A few schedulers and runtime systems solve this problem by using regression models, which are imprecise though. Our novel approach for the determination of data volumes removes this limitation and thus provides a solution to obtain exact information. T3 - ZIB-Report - 12-23 KW - function parameter analysis KW - function parameter sizes KW - heterogeneous systems KW - scheduling metrics KW - tool flow Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15569 SN - 1438-0064 ER - TY - THES A1 - Wende, Florian T1 - Simulation of Spin Models on Nvidia Graphics Cards using CUDA N2 - This thesis reports on simulating spin models on Nvidia graphics cards using the CUDA programming model; a particular approach for making GPGPU (General Purpose Computation on Graphics Processing Units) available for a wide range of software developers not necessarily acquainted with (massively) parallel programming. By comparing program execution times for simulations of the Ising model and the Ising spin glass by means of the Metropolis algorithm on Nvidia Tesla C1060 graphics cards and an Intel Core i7-920 quad-core x86 CPU (we used OpenMP to make our simulations run on all 4 execution units of the CPU), we noticed that the Tesla C1060 performed about a factor 5-10 faster than the Core i7-920, depending on the particular model and the accuracy of the calculations (32-bit or 64-bit). We also investigated the reliability of GPGPU computations, especially with respect to the occurrence of soft-errors as suggested in [23]. We noticed faulty program outputs during long-time simulations of the Ising model on ''large'' lattices. We were able to link these problems to overheating of the corresponding graphics cards. Doing Monte Carlo simulations on parallel computer architectures, as was the case in this thesis, suggests to also generate random numbers in a parallel manner. We present implementations of the random number generators Ranlux and Mersenne Twister. In addition, we give an alternative and very efficient approach for producing parallel random numbers on Nvidia graphics cards. We successfully tested all random number generators used in this thesis for their quality by comparing Monte Carlo estimates against exact calculations. N2 - Vorliegende Diplomarbeit befasst sich mit der Simulation von Spin-Modellen auf Nvidia Grafikkarten. Hierbei wird das Programmiermodell CUDA verwendet, welches einer breiten Masse von Softwareentwicklern den Zugang zu GPGPU (General Purpose Computation on Graphics Processing Units) gestattet ohne dass diese notwendigerweise mit (massiv) paralleler Programmierung vertraut sein müssen. Im Rahmen von Vergleichen der Programmlaufzeiten für Simulationen des Ising- Modells sowie des Ising-Spin-Glases auf Nvidia Tesla C1060 Grafikkarten und einer Intel Core i7-920 x86 Quad-Core-CPU war zu vermerken, dass, abhängig vom konkreten Modell und der Rechengenauigkeit (32-bit oder 64-bit), die Tesla C1060 zwischen 5-10 mal schneller arbeitete als die Core i7-920 Quad-Core-CPU. Wir haben uns ebenfalls mit der Zuverlässigkeit von GPGPU-Rechnungen befasst, gerade in Hinblick auf das Auftreten von Soft-Errors, wie es in [23] angedeutet wird. Wir beobachteten falsche Programmausgaben bei langen Simulationen des Ising-Modells auf ,,großen'''' Gittern. Es gelang uns die auftretenden Probleme mit Überhitzung der entsprechenden Grafikkarten in Verbindung zu bringen. Für die Durchführung von Monte-Carlo-Simulationen auf Parallelrechnerarchitekturen, wie es in vorliegender Arbeit der Fall ist, liegt es nahe auch Zufallszahlen parallel zu erzeugen. Wir präsentieren Implementierungen der Zufallszahlengeneratoren Ranlux und Mersenne Twister. Zusätzlich stellen wir eine alternative und sehr effiziente Möglichkeit vor parallele Zufallszahlen auf Nvidia Grafikkarten zu erzeugen. Alle verwendeten Zufallszahlengeneratoren wurden erfolgreich auf ihre Qualität getestet indem Monte-Carlo-Schätzer exakten Rechnungen gegenübergestellt wurden. Y1 - 2010 UR - http://edoc.hu-berlin.de/master/wende-florian-2010-10-20/PDF/wende.pdf ER - TY - THES A1 - Wende, Florian T1 - Dynamic Load Balancing on Massively Parallel Computer Architectures N2 - This thesis reports on using dynamic load balancing methods on massively parallel computers in the context of multithreaded computations. In particular we investigate the applicability of a randomized work stealing algorithm to ray tracing and breadth-first search as representatives of real-world applications with dynamic work creation. For our considerations we made use of current massively parallel hardware accelerators: Nvidia Tesla M2090, and Intel Xeon Phi. For both of the two we demonstrate the suitability of the work stealing scheme for the said real-world applications. Also the necessity of dynamic load balancing for irregular computations on such hardware is illustrated. N2 - Vorliegende Bachelorarbeit befasst sich mit Methoden der dynamischen Lastbalancierung auf massiv parallelen Computern im Rahmen von mehrprozess gestützten Ausführungen von Programmen. Im einzelnen wird die Eignung eines randomisierten Work-Stealing Algorithmus für die Ausführung realer Anwendungen mit dynamischer Arbeitserzeugung, wie Ray-Tracing und Breitensuche, untersucht. Für die entsprechenden Betrachtungen wer den aktuelle massiv parallele Hardwarebeschleuniger vom Typ Nvidia Tesla M2090 und Intel Xeon Phi verwendet. Für beide Beschleunigertypen konnte die Tauglichkeit des Work-Stealing Schemas für die genannten Anwendungen gezeigt werden. Ebenfalls wird die Notwendigkeit der Verwendung dynamischer Lastausgleichsmethoden für irreguläre Berechnungen auf der genannten Hardware verdeutlicht. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42166 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU N2 - Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated. T3 - ZIB-Report - 13-44 KW - Swendsen-Wang Multi-Cluster Algorithm KW - Ising Model KW - Xeon Phi KW - GPGPU KW - Connected Component Labeling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42187 SN - 1438-0064 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects N2 - Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces. T3 - ZIB-Report - 13-46 KW - memory footprint KW - non-linear objects KW - static analysis KW - dynamic analysis Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42224 SN - 1438-0064 ER - TY - THES A1 - Maier, Robert T1 - Massiv-parallele Suche und effiziente Heuristiken N2 - Pattern Datenbanken (PDBs) werden in der heuristischen Suche eingesetzt, um irrelevante Pfade in der Suche auszuschließen. Da die Leistung einer PDB mit ihrer Größe steigt und für die effektive heuristische Suche in großen Zustandsräumen große PDBs nötig sind, ist ein paralleler Ansatz notwendig, um sehr große PDBs zu erzeugen. Diese Arbeit erweitert einen, auf MapReduce basierenden, Algorithmus von Reinefeld und Schütt (2009) zur massiv-parallelen Breitensuche so, dass damit sehr große PDBs erzeugt werden können. So entsteht die erste vollständige 8+8+8 PDB für das 24er-Puzzle. Reinefeld und Schütt implementieren ebenfalls das heuristische Suchverfahren BFIDA* für MapReduce. In dieser Arbeit wird dieser Implementation ein Speedup von 857 bei 2039 Kernen nachgewiesen. Weiterhin führt diese Arbeit ein Schema ein, mit dem PDBs bei der Suche direkt von der Festplatte gelesen werden können. Des Weiteren wird der Nutzen von großen PDBs in einer Gruppe von PDBs untersucht, deren Heuristikwerte maximiert werden. Dazu wird analysiert, wie sich Gruppen von PDBs mit unterschiedlicher Größe verhalten und welche Faktoren bei solchen Konstellationen zum Erfolg der Gruppe beitragen. Es wird gezeigt, dass der Einsatz von großen PDBs effizient ist, wenn der zur Verfügung stehende Hauptspeicher ausreicht, eine Gruppe zusammen mit einigen kleineren PDBs zu bilden. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42448 ER - TY - THES A1 - Müller, Magnus T1 - Flexible Routing Tables in a Distributed Key-Value Store N2 - We present our implementation of Flexible Routing Tables (FRT) in the distributed key-value store Scalaris. Classic routing table generators like Chord structure routing tables by considering node identifiers only. Secondary requirements such as latency properties are considered after the general structure, eliminating potential performance gains. FRT aims to allow multiple requirements when creating routing tables. The concept is based on lazy routing table entries learning and filtering entries when a routing table is full. Entries are filtered such that the resulting table is best among all other possible tables where one node was filtered. FRT uses a total order to define which of the possible routing tables is best. We implemented two instances of FRT, namely FRT-Chord and grouped FRT-Chord (GFRT-Chord). We compare our implementation with the existing implementation of Chord in Scalaris and evaluate the advantages and disadvantages of more flexible routing schemes. KW - FRT KW - FRT-Chord KW - GFRT-Chord KW - Routing KW - DHT KW - Scalaris Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42742 ER - TY - THES A1 - Dillmann, Johannes T1 - Konsistentes Hinzufügen und Entfernen von Replikaten in XtreemFS N2 - In replizierten Systemen muss es möglich sein ausgefallene Server zu ersetzen und Replikate dynamisch hinzuzufügen oder zu entfernen. Veränderungen an der Menge der eingesetzten Replikate können zu inkonsistenten Daten führen. In dieser Arbeit wird ein Algorithmus für das konsistente Hinzufügen und Entfernen von Replikaten für das verteilte Dateisystem XtreemFS vorgestellt. Der Algorithmus nutzt einen fehlertoleranten Service, der die Replikatliste speichert sowie Veränderungen koordiniert und diese aus globaler Sicht atomar ausführt. KW - replication KW - dynamic reconfiguration KW - distributed storage systems Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43109 ER - TY - THES A1 - Kairies, Lukas T1 - Leistungsanalyse von XtreemFS als Ersatz für HDFS in Hadoop N2 - In dieser Arbeit wird die Leistungsfähigkeit des MapReduce-Framework Hadoop mit XtreemFS als verteiltes und POSIX-konformes Dateisystem bestimmt. Damit wird XtreemFS das für die Nutzung mit Hadoop entwickelte Dateisystem HDFS ersetzen. HDFS und XtreemFS werden verglichen und XtreemFS für Nutzung unter Hadoop konfiguriert. Zudem werden Optimierungen an der Hadoop-Schnittstelle von XtreemFS vorgenommen. Die Leistung von Hadoop mit XtreemFS wird mittels synthetischer Benchmarks und realer Hadoop Anwendungen gemessen und mit der Leistung von Hadoop mit HDFS verglichen. KW - XtreemFS KW - HDFS KW - Hadoop KW - Benchmark Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43130 ER - TY - GEN A1 - Pyszkalski, Wolfgang T1 - Übersicht über die Datenhaltung im ZIB und die Möglichkeiten einer Nutzung durch Projekte N2 - Dieser Bericht beschreibt in allgemein verständlicher Form die Struktur der Datenhaltung im Zuse‐Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer stärker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten über im Grunde unbegrenzte Zeit. T3 - ZIB-Report - 13-16 KW - Langfristige Datenhaltung KW - Speichersysteme KW - Magnetband KW - Vertrauenswürdigkeit des Langzeitspeichers KW - Sicherstellung der Lesbarkeit des Bandmaterials Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42060 SN - 1438-0064 ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle T2 - Workshop on Computer Games Y1 - 2013 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Outgassing induced acceleration of comet 67P/Churyumov-Gerasimenko JF - Astronomy & Astrophysics N2 - Cometary activity affects the orbital motion and rotation state due to sublimation induced forces. The availability of precise rotation-axis orientation and position data from the Rosetta mission allows one to accurately determine the outgassing of comet Churyumov-Gerasimenko/67P (67P). We derive the observed non-gravitational acceleration of 67P directly from the Rosetta spacecraft trajectory. From the non-gravitational acceleration we recover the diurnal outgassing variations and study a possible delay of the sublimation response with respect to the peak solar illumination. This allows us to compare the non-gravitational acceleration of 67P with expectations based on empirical models and common assumptions about the sublimation process. We use an iterative orbit refinement and Fourier decomposition of the diurnal activity to derive the outgassing induced non-gravitational acceleration. The uncertainties of the data reduction are established by a sensitivity analysis of an ensemble of best-fit orbits for comet 67P. We find that the Marsden non-gravitational acceleration parameters reproduce part of the non-gravitational acceleration but need to be augmented by an analysis of the nucleus geometry and surface illumination to draw conclusions about the sublimation process on the surface. The non-gravitational acceleration follows closely the subsolar latitude (seasonal illumination), with a small lag angle with respect to local noon around perihelion. The observed minor changes of the rotation axis do not favor forced precession models for the non-gravitational acceleration. In contrast to the sublimation induced torques, the non-gravitational acceleration does not put strong constraints on localized active areas on the nucleus. We find a close agreement of the orbit deduced non-gravitational acceleration and the water production independently derived from Rosetta in-situ measurement. Y1 - 2019 U6 - https://doi.org/10.1051/0004-6361/201935229 VL - 630 SP - A4 ER - TY - JOUR A1 - Delle Site, Luigi A1 - Krekeler, Christian A1 - Whittaker, John A1 - Agarwal, Animesh A1 - Klein, Rupert A1 - Höfling, Felix T1 - Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir JF - Advanced Theory and Simulations N2 - The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed. Y1 - 2019 U6 - https://doi.org/10.1002/adts.201900014 VL - 2 SP - 1900014 ER - TY - JOUR A1 - Wende, Florian A1 - Marsman, Martijn A1 - Kim, Jeongnim A1 - Vasilev, Fedor A1 - Zhao, Zhengji A1 - Steinke, Thomas T1 - OpenMP in VASP: Threading and SIMD JF - International Journal of Quantum Chemistry N2 - The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version, as well as a 2x increased performance of collective operations using the multiple-endpoint MPI feature. The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9x performance gain on AVX512 platforms with the Intel compiler. Y1 - 2018 U6 - https://doi.org/10.1002/qua.25851 IS - Emerging Architectures in Computational Chemistry SP - e25851 PB - Wiley Online Library ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Data-flow scheduling for a scalable FLESnet JF - CBM Progress Report 2017 Y1 - 2018 SN - 978-3-9815227-5-4 U6 - https://doi.org/10.15120/GSI-2018-00485 SP - 130 EP - 131 ER - TY - JOUR A1 - Rodríguez, Mirta A1 - Kramer, Tobias T1 - Machine Learning of Two-Dimensional Spectroscopic Data JF - Chemical Physics N2 - Two-dimensional electronic spectroscopy has become one of the main experimental tools for analyzing the dynamics of excitonic energy transfer in large molecular complexes. Simplified theoretical models are usually employed to extract model parameters from the experimental spectral data. Here we show that computationally expensive but exact theoretical methods encoded into a neural network can be used to extract model parameters and infer structural information such as dipole orientation from two dimensional electronic spectra (2DES) or reversely, to produce 2DES from model parameters. We propose to use machine learning as a tool to predict unknown parameters in the models underlying recorded spectra and as a way to encode computationally expensive numerical methods into efficient prediction tools. We showcase the use of a trained neural network to efficiently compute disordered averaged spectra and demonstrate that disorder averaging has non-trivial effects for polarization controlled 2DES. Y1 - 2019 U6 - https://doi.org/10.1016/j.chemphys.2019.01.002 VL - 520 SP - 52 EP - 60 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Hviid, Stubbe A1 - Jorda, Laurent A1 - Keller, Horst Uwe A1 - Kührt, Ekkehard T1 - Comet 67P/Churyumov-Gerasimenko rotation changes derived from sublimation induced torques JF - Astronomy & Astrophysics N2 - Context. The change of the rotation period and the orientation of the rotation axis of comet 67P/Churyumov-Gerasimenko (67P/C-G) is deducible from images taken by the scientific imaging instruments on-board the Rosetta mission with high precision. Non gravitational forces are a natural explanation for these data. Aims. We describe observed changes for the orientation of the rotation axis and the rotation period of 67P/C-G. For these changes we give an explanation based on a sublimation model with a best-fit for the surface active fraction (model P). Torque effects of periodically changing gas emissions on the surface are considered. Methods. We solve the equation of state for the angular momentum in the inertial and the body- fixed frames and provide an analytic theory of the rotation changes in terms of Fourier coefficients, generally applicable to periodically forced rigid body dynamics. Results. The torque induced changes of the rotation state constrain the physical properties of the surface, the sublimation rate and the local active fraction of the surface. Conclusions. We determine a distribution of the local surface active fraction in agreement with the rotation properties, period and orientation, of 67P/C-G. The torque movement confirms that the sublimation increases faster than the insolation towards perihelion. The derived relatively uniform activity pattern is discussed in terms of related surface features. Y1 - 2019 U6 - https://doi.org/10.1051/0004-6361/201834349 VL - 630 SP - A3 ER - TY - GEN A1 - Schneck, Jakob A1 - Weiser, Martin A1 - Wende, Florian T1 - Impact of mixed precision and storage layout on additive Schwarz smoothers N2 - The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth- bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage. T3 - ZIB-Report - 18-62 KW - higher order finite elements KW - mixed precision KW - overlapping Schwarz smoother Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71305 SN - 1438-0064 ER - TY - THES A1 - Deppisch, Daniel T1 - Advancing the Heterogeneous Active Messages Approach Y1 - 2019 ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Checkpoint Scheduling for Shared Usage of Burst-Buffers in Supercomputers T2 - Proceedings of the 47th International Conference on Parallel Processing Companion; SRMPDS 2018: The 14th International Workshop on Scheduling and Resource Management for Parallel and Distributed Systems N2 - User-defined and system-level checkpointing have contrary properties. While user-defined checkpoints are smaller and simpler to recover, system-level checkpointing better knows the global system's state and parameters like the expected mean time to failure (MTTF) per node. Both approaches lead to non-optimal checkpoint time, intervals, sizes, or I/O bandwidth when concurrent checkpoints conflict and compete for it. We combine user-defined and system-level checkpointing to exploit the benefits and avoid the drawbacks of each other. Thus, applications frequently offer to create checkpoints. The system accepts such offers according to the current status and implied costs to recalculate from the last checkpoint or denies them, i.e., immediately lets continue the application without checkpoint creation. To support this approach, we develop economic models for multi-application checkpointing on shared I/O resources that are dedicated for checkpointing (e.g. burst-buffers) by defining an appropriate goal function and solving a global optimization problem. Using our models, the checkpoints of applications on a supercomputer are scheduled to effectively use the available I/O bandwidth and minimize the failure overhead (checkpoint creations plus recalculations). Our simulations show an overall reduction in failure overhead of all nodes of up to 30% for a typical supercomputer workload (HLRN). We can also derive the most cost effective burst-buffer bandwidth for a given node's MTTF and application workload. Y1 - 2018 U6 - https://doi.org/10.1145/3229710.3229755 SP - 44:1 EP - 44:10 ER - TY - GEN A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Modeling Checkpoint Schedules for Concurrent HPC Applications T2 - CoSaS 2018 International Symposium on Computational Science at Scale Y1 - 2018 ER - TY - CHAP A1 - Schmidtke, Robert A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - From Application to Disk: Tracing I/O Through the Big Data Stack T2 - High Performance Computing ISC High Performance 2018 International Workshops, Frankfurt/Main, Germany, June 24 - 28, 2018, Revised Selected Papers, Workshop on Performance and Scalability of Storage Systems (WOPSSS) N2 - Typical applications in data science consume, process and produce large amounts of data, making disk I/O one of the dominating — and thus worthwhile optimizing — factors of their overall performance. Distributed processing frameworks, such as Hadoop, Flink and Spark, hide a lot of complexity from the programmer when they parallelize these applications across a compute cluster. This exacerbates reasoning about I/O of both the application and the framework, through the distributed file system, such as HDFS, down to the local file systems. We present SFS (Statistics File System), a modular framework to trace each I/O request issued by the application and any JVM-based big data framework involved, mapping these requests to actual disk I/O. This allows detection of inefficient I/O patterns, both by the applications and the underlying frameworks, and builds the basis for improving I/O scheduling in the big data software stack. Y1 - 2018 U6 - https://doi.org/10.1007/978-3-030-02465-9_6 SP - 89 EP - 102 ER - TY - THES A1 - Steininger, Lennart T1 - Atomarer Datenzugriff auf verteilten persistenten Arbeitsspeicher N2 - Nicht flüchtiger Arbeitsspeicher bzw. Non-volatile Random Access Memory oder auch Persistent Memory befindet sich im frühen Markteintritt. Diese Art von Speicher nimmt eine Stellung zwischen bisherigem flüchtigen Arbeitsspeicher (Memory) und bisherigem Permanentspeicher (Storage) ein. Im Zusammenspiel mit verteilten Algorithmen und Systemen sowie dem Zugriff auf entfernte Speicherbereiche durch die Netzwerkinterfaces per Remote Direct Memory Access sind die Konzepte zum Umgang mit Durability und allen einhergehenden Herausforderungen bisher nicht ausgereift. Diese Arbeit untersucht, wie sich in Rechnernetzen mit persistentem Speicher und möglichst passivem Zugriff auf entfernten Speicher performante verteilte Systeme implementieren lassen. Es werden Anforderungen und Voraussetzungen eines solchen Systems bestimmt und daraufhin Lösungsmöglichkeiten aufgezeigt, wie sich diese Anforderungen mit Nutzung nicht flüchtigen Arbeitsspeichers umsetzen lassen. Die notwendigen Eigenschaften der Hard- und Software sowie der eingesetzten Netzwerkprotokolle werden beschrieben. Y1 - 2018 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Surface localization of gas sources on comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data JF - Monthly Notices of the Royal Astronomical Society N2 - We reconstruct the temporal evolution of the source distribution for the four major gas species H2O, CO2, CO, and O2 on the surface of comet 67P/Churyumov-Gerasimenko during its 2015 apparition. The analysis applies an inverse coma model and fits to data between August 6th 2014 and September 5th 2016 measured with the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS). The spatial distribution of gas sources with their temporal variation allows one to construct surface maps for gas emissions and to evaluate integrated productions rates. For all species peak production rates and integrated productions rates per orbit are evaluated separately for the northern and the southern hemisphere. The nine most active emitting areas on the comet’s surface are defined and their correlation to emissions for each of the species is discussed. Y1 - 2018 U6 - https://doi.org/10.1093/mnras/sty3103 VL - 483 SP - 852 EP - 861 PB - Monthly Notices of the Royal Astronomical Society ER - TY - JOUR A1 - Stoop, Ralph L. A1 - Straube, Arthur A1 - Johansen, Tom H. A1 - Tierno, Pietro T1 - Collective directional locking of colloidal monolayers on a periodic substrate JF - Phys. Rev. Lett. N2 - We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.058002 VL - 124 SP - 058002 ER - TY - CHAP A1 - Weinhold, Carsten A1 - Lackorzynski, Adam A1 - Bierbaum, Jan A1 - Küttler, Martin A1 - Planeta, Maksym A1 - Weisbach, Hannes A1 - Hille, Matthias A1 - Härtig, Hermann A1 - Margolin, Alexander A1 - Sharf, Dror A1 - Levy, Ely A1 - Gak, Pavel A1 - Barak, Amnon A1 - Gholami, Masoud A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Lieber, Matthias A1 - Nagel, Wolfgang T1 - FFMK: A Fast and Fault-Tolerant Microkernel-Based System for Exascale Computing T2 - Software for Exascale Computing - SPPEXA 2016-2019 Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-47956-5_16 SP - 483 EP - 516 PB - Springer ER - TY - JOUR A1 - Abbott, Joshua L. A1 - Straube, Arthur A1 - Aarts, Dirk G. A. L. A1 - Dullens, Roel P. A. T1 - Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape JF - New J. Phys. N2 - A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking. Y1 - 2019 U6 - https://doi.org/10.1088/1367-2630/ab3765 VL - 21 SP - 083027 ER - TY - JOUR A1 - Straube, Arthur A1 - Pagès, Josep M. A1 - Tierno, Pietro A1 - Ignés-Mullol, Jordi A1 - Sagués, Francesc T1 - Collective dynamics and conformal ordering in electrophoretically driven nematic colloids JF - Phys. Rev. Research N2 - We present a theoretical framework to understand the collective dynamics of an ensemble of electrophoretically driven colloidal particles that are forced to assemble around a single topological defect in a nematic liquid crystal by an alternating current electric field. Our generic model combines phoretic propulsion with electrostatic interactions and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while nematic elasticity plays a subdominant role. Simulations based on this model fully capture the collective organization process observed in the experiments and other striking effects as the emergence of conformal ordering and a nearly frequency-independent repulsive interaction above 10Hz. Our results demonstrate the importance of hydrodynamic interactions on the assembly of driven microscale matter in anisotropic media. Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevResearch.1.022008 VL - 1 SP - 022008 ER - TY - GEN A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Building Large Compressed PDBs for the Sliding Tile Puzzle N2 - The performance of heuristic search algorithms depends crucially on the effectiveness of the heuristic. A pattern database (PDB) is a powerful heuristic in the form of a pre-computed lookup table. Larger PDBs provide better bounds and thus allow more cut-offs in the search process. Today, the largest PDB for the 24-puzzle is a 6-6-6-6 PDB with a size of 486 MB. We created 8-8-8, 9-8-7 and 9-9-6 PDBs that are three orders of magnitude larger (up to 1.4 TB) than the 6-6-6-6 PDB. We show how to compute such large PDBs and we present statistical and empirical data on their efficiency. The largest single PDB gives on average an 8-fold improvement over the 6-6-6-6 PDB. Combining several large PDBs gives on average an 12-fold improvement. T3 - ZIB-Report - 13-21 KW - heuristic search KW - pattern databases Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-18095 SN - 1438-0064 ER - TY - JOUR A1 - Golas, Ulrike A1 - Hoffmann, Kathrin A1 - Ehrig, Hartmut A1 - Rein, A. A1 - Padberg, J. T1 - Functorial Analysis of Algebraic Higher-Order Net Systems with Applications to Mobile Ad-Hoc Networks JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/631 VL - 40 SP - 1 EP - 20 ER - TY - CHAP A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Balasko, Akos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Fels, Gregor A1 - Herres-Pawlis, Sonja A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Wewior, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Kohlbacher, Oliver T1 - Granular Security for a Science Gateway in Structural Bioinformatics T2 - Proc. IWSG-Life 2011 Y1 - 2011 ER - TY - CHAP A1 - Chabarek, F. A1 - Golas, Ulrike ED - Heiß, H.-U. ED - Pepper, P. ED - Schlingloff, H. ED - Schneider, Jörg T1 - Interaktive Vervollständigung der Szenariobasierten Spezifikation eines Parkassistenzsystems T2 - Proceedings of GI-ASE 2011 Y1 - 2011 ER - TY - CHAP A1 - Plantikow, Stefan A1 - Jorra, Maik ED - Xu, Jianliang ED - Yu, Ge ED - Zhou, Shuigeng ED - Unland, Rainer T1 - Latency-Optimal Walks in Replicated and Partitioned Graphs T2 - Database Systems for Adanced Applications Y1 - 2011 UR - http://dx.doi.org/10.1007/978-3-642-20244-5{\_}3 U6 - https://doi.org/10.1007/978-3-642-20244-5_3 VL - 6637 SP - 14 EP - 27 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Proc. of Grid Workflow Workshop 2011, Cologne, Germany Y1 - 2011 UR - http://CEUR-WS.org/Vol-826/paper02.pdf VL - 826 PB - CEUR Workshop Proceedings ER - TY - CHAP A1 - Peter, Kathrin T1 - Reliability Study of Coding Schemes for Wide-Area Distributed Storage Systems T2 - PDP 2011: The 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing Y1 - 2011 U6 - https://doi.org/10.1109/PDP.2011.70 PB - Euromicro ER - TY - JOUR A1 - Dickmann, Frank A1 - Falkner, Jürgen A1 - Gunia, Wilfried A1 - Hampe, Jochen A1 - Hausmann, Michael A1 - Herrmann, Alexander A1 - Kepper, Nick A1 - Knoch, Tobias A1 - Lauterbach, Svenja A1 - Lippert, Jörg A1 - Peter, Kathrin A1 - Schmitt, Eberhard A1 - Schwardmann, Ulrich A1 - Solodenko, Juri A1 - Sommerfeld, Dietmar A1 - Steinke, Thomas A1 - Weisbecker, Anette A1 - Sax, Ulrich T1 - Solutions for biomedical grid computing – Case studies from the D-Grid project Services@MediGRID JF - Journal of Computational Science Y1 - 2011 UR - http://www.sciencedirect.com/science/article/pii/S1877750311000603 U6 - https://doi.org/10.1016/j.jocs.2011.06.006 VL - - IS - 0 ER - TY - JOUR A1 - Kruber, Nico A1 - Högqvist, Mikael A1 - Schütt, Thorsten T1 - The Benefits of Estimated Global Information in DHT Load Balancing JF - Cluster Computing and the Grid, IEEE International Symposium on Y1 - 2011 U6 - https://doi.org/10.1109/CCGrid.2011.11 VL - 0 SP - 382 EP - 391 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Stender, Jan A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Hupfeld, Felix T1 - BabuDB: Fast and Efficient File System Metadata Storage T2 - Storage Network Architecture and Parallel I/Os, IEEE International Workshop on Y1 - 2010 U6 - https://doi.org/10.1109/SNAPI.2010.14 SP - 51 EP - 58 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - CHAP A1 - Böse, Joos-Hendrik A1 - Andrzejak, Artur A1 - Högqvist, Mikael T1 - Beyond online aggregation: Parallel and incremental data mining with online Map-Reduce T2 - Proceedings of the 2010 Workshop on Massive Data Analytics on the Cloud Y1 - 2010 U6 - https://doi.org/10.1145/1779599.1779602 SP - 3:1 EP - 3:6 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Kindermann, S. A1 - Schintke, Florian A1 - Fritzsch, B. T1 - A Collaborative Data Management Infrastructure for Climate Data Analysis T2 - Geophysical Research Abstracts Y1 - 2012 UR - http://meetingorganizer.copernicus.org/EGU2012/EGU2012-10569.pdf U6 - https://doi.org/10013/epic.39635.d001 VL - 14, EGU2012-10569 ER - TY - CHAP A1 - Soboll, T. A1 - Golas, Ulrike ED - Filipe, J. ED - Fred, A. T1 - A Local-Global Model for Multiagent Systems - Sheaves on the Category MAS T2 - Proceedings of ICAART 2012 Y1 - 2012 VL - 2 SP - 331 EP - 334 PB - SciTePress ER - TY - JOUR A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Orejas, Fernando T1 - Attributed Graph Transformation with Inheritance JF - Theoretical Computer Science Y1 - 2012 U6 - https://doi.org/10.1016/j.tcs.2012.01.032 VL - 424 SP - 46 EP - 68 ER - TY - CHAP A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, Andre A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - The MoSGrid Community – From National to International Scale T2 - EGI Community Forum 2012 Y1 - 2012 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science JF - Journal of Cheminformatics 2011 Y1 - 2011 UR - http://www.jcheminf.com/content/3/S1/P14 U6 - https://doi.org/10.1186/1758-2946-3-S1-P14 VL - 3 IS - Suppl 1 ER - TY - CHAP A1 - Gesing, Sandra A1 - Kacsuk, Peter A1 - Kozlovszky, Miklos A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Krüger, Jens A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Szikszay Fabri, Anna A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin A1 - Kohlbacher, Oliver T1 - A Science Gateway for Molecular Simulations T2 - EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts Y1 - 2011 SP - 94 EP - 95 ER - TY - JOUR A1 - Golas, Ulrike A1 - Biermann, E. A1 - Ehrig, Hartmut A1 - Ermel, Claudia T1 - A Visual Interpreter Semantics for Statecharts Based on Amalgamated Graph Transformation JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/645 VL - 39 SP - 1 EP - 24 ER - TY - JOUR A1 - Enke, Harry A1 - Steinmetz, Matthias A1 - Adorf, Hans-Martin A1 - Beck-Ratzka, Alexander A1 - Breitling, Frank A1 - Brüsemeister, Thomas A1 - Carlson, Arthur A1 - Ensslin, Torsten A1 - Högqvist, Mikael A1 - Nickelt, Iliya A1 - Radke, Thomas A1 - Reinefeld, Alexander A1 - Reiser, Angelika A1 - Scholl, Tobias A1 - Spurzem, Rainer A1 - Steinacker, Jürgen A1 - Voges, Wolfgang A1 - Wambsganß, Joachim A1 - White, Steve T1 - AstroGrid-D: Grid technology for astronomical science JF - New Astronomy Y1 - 2011 UR - http://www.sciencedirect.com/science/article/pii/S1384107610000837 U6 - https://doi.org/10.1016/j.newast.2010.07.005 VL - 16 IS - 2 SP - 79 EP - 93 ER - TY - JOUR A1 - Kolbeck, Björn A1 - Högqvist, Mikael A1 - Stender, Jan A1 - Hupfeld, Felix T1 - Flease - Lease Coordination Without a Lock Server JF - Parallel and Distributed Processing Symposium, International Y1 - 2011 U6 - https://doi.org/10.1109/IPDPS.2011.94 VL - 0 SP - 978 EP - 988 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Golas, Ulrike A1 - Ehrig, Hartmut A1 - Hermann, Frank T1 - Formal Specification of Model Transformations by Triple Graph Grammars with Application Conditions JF - ECEASST Y1 - 2011 UR - http://journal.ub.tu-berlin.de/eceasst/article/view/646 VL - 39 SP - 1 EP - 26 ER - TY - CHAP A1 - Enke, Harry A1 - Fiedler, Norman A1 - Fischer, Thomas A1 - Gnadt, Timo A1 - Ketzan, Erik A1 - Ludwig, Jens A1 - Rathmann, Torsten A1 - Stöckle, Gabriel A1 - Schintke, Florian ED - Enke, Harry ED - Ludwig, Jens T1 - Leitfaden zum Forschungsdaten-Management T2 - Leitfaden zum Forschungsdaten-Management Y1 - 2013 PB - Verlag Werner Hülsbusch, Glückstadt ER - TY - THES A1 - Högqvist, Mikael T1 - Consistent Key-Based Routing in Decentralized and Reconfigurable Data Services Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:11-100206145 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=39763 ER - TY - THES A1 - Kolbeck, Björn T1 - A fault-tolerant and scalable protocol for replication in distributed file systems Y1 - 2012 ER - TY - CHAP A1 - Flik, T. A1 - Reinefeld, Alexander ED - Czichos, Horst ED - Hennecke, Manfred T1 - Rechnerorganisation T2 - Hütte – Das Ingenieurwissen Y1 - 2012 SP - J6 EP - J124 PB - Springer-Verlag Berlin ET - 34 ER - TY - CHAP A1 - Peter, Kathrin A1 - Reinefeld, Alexander T1 - Consistency and fault tolerance for erasure-coded distributed storage systems T2 - Proceedings of the fifth international workshop on Data-Intensive Distributed Computing Date Y1 - 2012 UR - http://doi.acm.org/10.1145/2286996.2287002 U6 - https://doi.org/10.1145/2286996.2287002 SP - 23 EP - 32 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering T2 - Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/SAAHPC.2012.12 SP - 74 EP - 83 ER - TY - CHAP A1 - Peter, Kathrin A1 - Sobe, Peter T1 - Application of Regenerating Codes for Fault Tolerance in Distributed Storage Systems T2 - Network Computing and Applications (NCA), 2012 11th IEEE International Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/NCA.2012.35 SP - 67 EP - 70 ER - TY - JOUR A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - A Science Gateway Getting Ready for Serving the International Molecular Simulation Community JF - Proceedings of Science Y1 - 2012 UR - http://pos.sissa.it/archive/conferences/162/050/EGICF12-EMITC2_050.pdf VL - PoS(EGICF12-EMITC2)050 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment JF - Journal of Cheminformatics Y1 - 2012 UR - http://www.jcheminf.com/content/4/S1/P21 U6 - https://doi.org/10.1186/1758-2946-4-S1-P21 VL - 4 IS - Suppl 1 SP - 21 ER - TY - JOUR A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Wewior, Martin A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Herres-Pawlis, Sonja A1 - Breuers, Sebastian A1 - Balasko, Akos A1 - Kozlovszky, Miklos A1 - Szikszay Fabri, Anna A1 - Packschies, Lars A1 - Kacsuk, Peter A1 - Blunk, Dirk A1 - Steinke, Thomas A1 - Brinkmann, André A1 - Fels, Gregor A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Kohlbacher, Oliver T1 - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics JF - Journal of Grid Computing Y1 - 2012 ER - TY - CHAP A1 - Grunzke, Richard A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Kruse, Martin A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Steinke, Thomas A1 - Zink, Andreas T1 - A Data Driven Science Gateway for Computational Workflows T2 - Proceedings of the UNICORE Summit Y1 - 2012 CY - Dresden, Germany ER - TY - JOUR A1 - Enke, Harry A1 - Partl, Adrian A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Handling Big Data in Astronomy and Astrophysics JF - Datenbank-Spektrum Y1 - 2012 UR - http://dx.doi.org/10.1007/s13222-012-0099-1 U6 - https://doi.org/10.1007/s13222-012-0099-1 VL - 12 IS - 3 SP - 173 EP - 181 PB - Springer-Verlag ER - TY - CHAP A1 - Golas, Ulrike ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - A General Attribution Concept for Models in M-Adhesive Transformation Systems T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_13 VL - 7562 SP - 187 EP - 202 PB - Springer ER - TY - CHAP A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Giese, H. ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Towards Bridging the Gap between Formal Foundations and Current Practice for Triple Graph Grammars - Flexible Relations between Source and Target Elements T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_10 VL - 7562 SP - 141 EP - 155 PB - Springer ER - TY - CHAP A1 - Heckel, R. A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Hermann, Frank ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Parallelism and Concurrency of Stochastic Graph Transformations T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_7 VL - 7562 SP - 96 EP - 110 PB - Springer ER - TY - CHAP A1 - Döbbelin, Robert A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - An Analysis of SMP Memory Allocators T2 - Proceedings of the 41st International Conference on Parallel Processing Workshops (Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2)) Y1 - 2012 U6 - https://doi.org/10.1109/ICPPW.2012.10 SP - 48 EP - 54 PB - IEEE Computer Society ER - TY - JOUR A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - Energy consumption of CUDA kernels with varying thread topology JF - Computer Science - Research and Development Y1 - 2012 UR - http://dx.doi.org/10.1007/s00450-012-0230-4 U6 - https://doi.org/10.1007/s00450-012-0230-4 SP - 1 EP - 9 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 2 JF - Fundamenta Informaticae Y1 - 2012 U6 - https://doi.org/10.3233/FI-2012-705 VL - 118 IS - 1-2 SP - 35 EP - 63 ER - TY - GEN ED - Golas, Ulrike ED - Soboll, T. T1 - Proceedings of ACCAT 2012 T2 - Electronic Proceedings in Theoretical Computer Science 93 Y1 - 2012 U6 - https://doi.org/10.4204/EPTCS.93 ER - TY - CHAP A1 - Schäfer, Patrick A1 - Högqvist, Mikael T1 - SFA : a symbolic fourier approximation and index for similarity search in high dimensional datasets T2 - Proceedings of the 15th International Conference on Extending Database Technology Y1 - 2012 UR - http://doi.acm.org/10.1145/2247596.2247656 U6 - https://doi.org/10.1145/2247596.2247656 SP - 516 EP - 527 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Ries, F. A1 - Ditze, M. A1 - Piater, A. A1 - Singer, E. A1 - Fäßler, V. A1 - Dreßler, Sebastian A1 - Soddemann, T. T1 - Tool-Supported Integration of Hardware Acceleration in Automotive CFD-Simulations T2 - NAFEMS 2013 Proceedings Y1 - 2013 ER - TY - GEN A1 - Dreßler, Sebastian A1 - Steinke, Thomas T1 - Automated Analysis of Complex Data Objects T2 - 28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013 Y1 - 2013 N1 - Posterbeitrag ER - TY - CHAP A1 - Schütt, Thorsten A1 - Döbbelin, Robert A1 - Reinefeld, Alexander T1 - Forward Perimeter Search with Controlled Use of Memory T2 - International Joint Conference on Artificial Intelligence, IJCAI-13, Beijing Y1 - 2013 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Döbbelin, Robert T1 - MR-search: massively parallel heuristic search JF - Concurrency and Computation: Practice and Experience Y1 - 2011 U6 - https://doi.org/10.1002/cpe.1833 VL - 25 IS - 1 SP - 40 EP - 54 ER - TY - CHAP A1 - Stender, Jan A1 - Berlin, Michael A1 - Reinefeld, Alexander ED - Kyriazis, D. ED - Voulodimos, A. ED - Gogouvitis, S. ED - Varvarigou, Theodora A. T1 - XtreemFS – a File System for the Cloud T2 - Data Intensive Storage Services for Cloud Environments Y1 - 2013 UR - http://dx.doi.org/10.4018/978-1-4666-3934-8 U6 - https://doi.org/10.4018/978-1-4666-3934-8 PB - IGI Global ER - TY - THES A1 - Sobe, Kathrin T1 - Consistency and Fault Tolerance of Distributed Storage Systems Y1 - 2013 UR - http://www.epubli.de/shop/buch/Consistency-and-Fault-Tolerance-of-Distributed-Storage-Systems-Kathrin-Sobe-9783844258899/27831 ER - TY - THES A1 - Stender, Jan T1 - Snapshots in Large-Scale Distributed File Systems Y1 - 2013 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=39839 ER - TY - JOUR A1 - Schintke, Florian T1 - XtreemFS & Scalaris JF - Science & Technology Y1 - 2013 IS - 6 SP - 54 EP - 55 PB - Pan European Networks ER - TY - CHAP A1 - Orejas, Fernando A1 - Boronat, Artur A1 - Golas, Ulrike A1 - Mylonakis, Nikos ED - Pfenning, Frank T1 - Checking Bisimilarity for Attributed Graph Transformation T2 - Foundations of Software Science and Computation Structures. Proceedings of FOSSACS 2013 Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-37075-5_8 VL - 7794 SP - 113 EP - 128 PB - Springer ER - TY - JOUR A1 - Berlin, Michael T1 - Consistent and Partition-Tolerant File Replication in the Cloud File System Xtreem FS JF - Praxis der Informationsverarbeitung und Kommunikation Y1 - 2013 UR - http://dx.doi.org/10.1515/pik-2012-0144 U6 - https://doi.org/10.1515/pik-2012-0144 VL - 36 IS - 1 SP - 39 ER - TY - CHAP A1 - Schäfer, Patrick A1 - Dreßler, Sebastian T1 - Shooting Audio Recordings of Insects with SFA T2 - AmiBio Workshop, Bonn, Germany Y1 - 2013 ER - TY - THES A1 - Reinbacher, Uwe T1 - Implementierung und Evaluierung eines FPGA-basierten statischen Paketfilters Y1 - 2013 ER - TY - THES A1 - Borgers, Philipp T1 - Erweiterung eines verteilten Key-Value-Stores (Riak) um einen räumlichen Index Y1 - 2012 ER - TY - JOUR A1 - Kreisbeck, Christoph A1 - Kramer, Tobias A1 - Molina, Rafael T1 - Time-dependent wave packet simulations of transport through Aharanov–Bohm rings with an embedded quantum dot JF - Journal of Physics: Condensed Matter N2 - We have performed time-dependent wave packet simulations of realistic Aharonov-Bohm (AB) devices with a quantum dot embedded in one of the arms of the interferometer. The AB ring can function as a measurement device for the intrinsic transmission phase through the quantum dot, however, care has to be taken in analyzing the influence of scattering processes in the junctions of the interferometer arms. We consider a harmonic quantum dot and show how the Darwin–Fock spectrum emerges as a unique pattern in the interference fringes of the AB oscillations. Y1 - 2017 U6 - https://doi.org/10.1088/1361-648X/aa605d VL - 29 IS - 15 SP - 155301 ER - TY - CHAP A1 - Ritter, Zully A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo tibial compressive stiffness variations after HR-pQCT measurements of 60 days immobility during the Berlin bed rest study II using μfinite element analysis T2 - 6th World Congress of Biomechanics (WCB 2010), August 1-6, 2010 Singapore: In Conjunction with 14th International Conference on Biomedical Engineering (ICBME) and 5th Asia Pacific Conference on Biomechanics (APBiomech) KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-14515-5_209 VL - 31 SP - 823 EP - 826 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodriguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems JF - Journal of Physical Chemistry B N2 - Time-resolved spectroscopy provides the main tool for analyzing the dynamics of excitonic energy transfer in light-harvesting complexes. To infer time-scales and effective coupling parameters from experimental data requires to develop numerical exact theoretical models. The finite duration of the laser-molecule interactions and the reorganization process during the exciton migration affect the location and strength of spectroscopic signals. We show that the non-perturbative hierarchical equations of motion (HEOM) method captures these processes in a model exciton system, including the charge transfer state. Y1 - 2017 U6 - https://doi.org/10.1021/acs.jpcb.6b09858 VL - 121 SP - 463 EP - 470 ER - TY - GEN A1 - Noack, Matthias A1 - Wende, Florian A1 - Zitzlsberger, Georg A1 - Klemm, Michael A1 - Steinke, Thomas T1 - KART – A Runtime Compilation Library for Improving HPC Application Performance N2 - The effectiveness of ahead-of-time compiler optimization heavily depends on the amount of available information at compile time. Input-specific information that is only available at runtime cannot be used, although it often determines loop counts, branching predicates and paths, as well as memory-access patterns. It can also be crucial for generating efficient SIMD-vectorized code. This is especially relevant for the many-core architectures paving the way to exascale computing, which are more sensitive to code-optimization. We explore the design-space for using input-specific information at compile-time and present KART, a C++ library solution that allows developers to compile, link, and execute code (e.g., C, C++ , Fortran) at application runtime. Besides mere runtime compilation of performance-critical code, KART can be used to instantiate the same code multiple times using different inputs, compilers, and options. Other techniques like auto-tuning and code-generation can be integrated into a KART-enabled application instead of being scripted around it. We evaluate runtimes and compilation costs for different synthetic kernels, and show the effectiveness for two real-world applications, HEOM and a WSM6 proxy. T3 - ZIB-Report - 16-48 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60730 SN - 1438-0064 ER -