@misc{Kruber2009, type = {Master Thesis}, author = {Kruber, Nico}, title = {DHT Load Balancing with Estimated Global Information}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11514}, school = {Zuse Institute Berlin (ZIB)}, year = {2009}, abstract = {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\%.}, language = {en} } @misc{MoserHaridiShafaatetal.2009, author = {Moser, Monika and Haridi, Seif and Shafaat, Tallat and Sch{\"u}tt, Thorsten and H{\"o}gqvist, Mikael and Reinefeld, Alexander}, title = {Transactional DHT Algorithms}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11532}, number = {09-34}, year = {2009}, abstract = {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.}, language = {en} } @misc{Mauter2009, type = {Master Thesis}, author = {Mauter, Daniel}, title = {Ein eingebettetes Hauptspeicher-Datenbanksystem mit Snapshot-Reads}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11552}, school = {Zuse Institute Berlin (ZIB)}, year = {2009}, abstract = {Entwurf und Entwicklung eines eingebetteten Hauptspeicher-Datenbanksystems mit Snapshot-Reads.}, language = {de} } @misc{SchintkeReinefeldHaridietal.2009, author = {Schintke, Florian and Reinefeld, Alexander and Haridi, Seif and Sch{\"u}tt, Thorsten}, title = {Enhanced Paxos Commit for Transactions on DHTs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11448}, number = {09-28}, year = {2009}, abstract = {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.}, language = {en} } @misc{Tuschl2009, type = {Master Thesis}, author = {Tuschl, Roland}, title = {Ein Userspace-Dateisystem zur Verwaltung von Grid-Daten}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11483}, school = {Zuse Institute Berlin (ZIB)}, year = {2009}, abstract = {Das Ziel dieser Arbeit ist die Schaffung einer Zugriffs-Komponente f{\"u}r 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 {\"A}nderungen am ZIB-DMS.}, language = {de} } @misc{Prollius2009, type = {Master Thesis}, author = {Prollius, Christian von}, title = {Ein Peer-to-Peer System mit Bereichsabfragen in PlanetLab}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11492}, school = {Zuse Institute Berlin (ZIB)}, year = {2009}, abstract = {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 f{\"u}r 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 gew{\"u}nschten Daten hat. Client-Server Architekturen, wie zum Beispiel Napster, haben sich als ung{\"u}nstig herausgestellt. Wenige Server, die eine große Anzahl an Clients bedienen m{\"u}ssen, sind einerseits sehr anf{\"a}llig gegen{\"u}ber Angriffen und Ausf{\"a}llen (Single Point of Failure)und kommen auch nicht mit der st{\"a}ndig wachsenden Anzahl an Nutzern zurecht. Verteilte Hashtabellen (DHT) bieten hier einen guten L{\"o}sungsansatz, der mit einer großen Anzahl an Nutzern skaliert und ausfallsicher ist. Andere dezentrale L{\"o}sungen, wie zum Beispiel das P2P Netzwerk Gnutella haben zwar das Problem des Single Point of Failure gel{\"o}st, 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 erkl{\"a}rt, dass eine Suchanfrage bei Standardeinstellungen in der Clientsoftware einen Netzwerkverkehr von 17MB erzeugt. Deswegen wird zus{\"a}tzlich eine L{\"o}sung ben{\"o}tigt, die Keys und Values geordnet verteilt, damit sie gezielt gesucht werden k{\"o}nnen. Aus diesem Grund besch{\"a}ftigt sich die folgende Arbeit mit einer v{\"o}llig dezentralen Architektur, die außerdem eine sinnvolle Platzierung der Keys vornimmt. Die dezentrale Architektur hat den Vorteil, dass die Endger{\"a}te den Hauptteil des Dienstes selbst erbringen und damit jeder zus{\"a}tzliche Teilnehmer seine eigenen Ressourcen beisteuert. Diese Arbeit pr{\"a}sentiert Chord\#, eine dezentrale, skalierbare und selbstorganisierende verteilte Hashtabelle. Chord\# wurde ausgew{\"a}hlt, da in dieser Arbeit auch Wert auf Bereichsabfragen gelegt wurde. Diese sind zum Beispiel bei dem Chord Algorithmus nicht m{\"o}glich, da dieser eine Hashfunktion f{\"u}r die Keys verwendet und somit die Daten zwar gleichm{\"a}ßig 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 k{\"o}nnen durch den Verzicht auf die Hashfunktion Bereichsabfragen erm{\"o}glicht werden. Daf{\"u}r wird der Chord\# Algorithmus in Java implementiert (ca. 1500 Zeilen Code) und in dem Forschungsnetz PlanetLab ausf{\"u}hrlich auf Laufzeiten, Instandhaltungskosten und Skalierung getestet.}, language = {de} } @misc{AllalenBrehmStueben2008, author = {Allalen, Mohammed and Brehm, Matthias and St{\"u}ben, Hinnerk}, title = {Performance of Quantum Chromodynamics (QCD) Simulations on the SGI Altix}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11086}, number = {08-54}, year = {2008}, abstract = {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.}, language = {en} } @misc{StreuerStueben2008, author = {Streuer, Thomas and St{\"u}ben, Hinnerk}, title = {Simulations of QCD in the Era of Sustained Tflop/s Computing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10623}, number = {07-48}, year = {2008}, abstract = {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.}, language = {en} } @phdthesis{Roeblitz2009, author = {R{\"o}blitz, Thomas}, title = {Co-Reservation of Resources in the Grid}, isbn = {978-3-86853-137-4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11626}, year = {2009}, abstract = {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.}, language = {en} } @misc{KolbeckHoegqvistStenderetal.2010, author = {Kolbeck, Bj{\"o}rn and H{\"o}gqvist, Mikael and Stender, Jan and Hupfeld, Felix}, title = {Fault-Tolerant and Decentralized Lease Coordination in Distributed Systems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11658}, number = {10-02}, year = {2010}, abstract = {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.}, language = {en} } @misc{Plantikow2007, type = {Master Thesis}, author = {Plantikow, Stefan}, title = {Transaktionen f{\"u}r verteilte Wikis auf strukturierten Overlay Netzwerken}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10176}, school = {Zuse Institute Berlin (ZIB)}, year = {2007}, abstract = {Die Diplomarbeit pr{\"a}sentiert ein Transaktionsverfahren f{\"u}r strukturierte Overlay-Netzwerke, das an die Erfordernisse verteilter Informationssysteme mit relationalem Datenmodell angepasst ist. Insbesondere wird der Einsatz von Transaktionen f{\"u}r verteilte Wikis betrachtet, die moderne Funktionalit{\"a}ten, wie Metadaten und zus{\"a}tzliche Indexe f{\"u}r die Navigation, unterst{\"u}tzen. Konsistenz und Dauerhaftigkeit der gespeicherten Daten erfordert die Behandlung von Knotenausf{\"a}llen. Die Arbeit schl{\"a}gt daf{\"u}r das Zellenmodell vor: Das Overlay wird aus replizierten Zustandsmaschinen gebildet, um Verf{\"u}gbarkeit zu gew{\"a}hrleisten. 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 Nebenl{\"a}ufigkeitskontrollverfahren geboten, die die Minimierung von Latenzeffekten und die schnelle Ausf{\"u}hrung von Nur-Lese-Transaktionen erm{\"o}glichen. F{\"u}r die Beispielanwendung Wiki wird der erforderliche Pseudocode angegeben und die verschiedenen Nebenl{\"a}ufigkeitskontrollverfahren hinsichtlich ihrer Nachrichtenkomplexit{\"a}t verglichen.}, language = {de} } @misc{MayBauerKoeberleetal.2006, author = {May, Patrick and Bauer, Markus and K{\"o}berle, Christian and Klau, Gunnar}, title = {A computational approach to microRNA detection}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9383}, number = {06-44}, year = {2006}, abstract = {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.}, language = {en} } @misc{MaySteinke2006, author = {May, Patrick and Steinke, Thomas}, title = {THESEUS - Protein Structure Prediction at ZIB}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9184}, number = {06-24}, year = {2006}, abstract = {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.}, language = {en} } @misc{Golas2012, author = {Golas, Ulrike}, title = {A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version}, issn = {1438-0064}, doi = {10.1007/978-3-642-33654-6_13}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-15547}, year = {2012}, abstract = {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.}, language = {en} } @misc{DresslerSteinke2012, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {A Novel Hybrid Approach to Automatically Determine Kernel Interface Data Volumes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-15569}, year = {2012}, abstract = {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.}, language = {en} } @misc{Wende2010, type = {Master Thesis}, author = {Wende, Florian}, title = {Simulation of Spin Models on Nvidia Graphics Cards using CUDA}, school = {Humboldt-Universit{\"a}t zu Berlin}, pages = {149}, year = {2010}, abstract = {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.}, language = {en} } @masterthesis{Wende2013, type = {Bachelor Thesis}, author = {Wende, Florian}, title = {Dynamic Load Balancing on Massively Parallel Computer Architectures}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42166}, school = {Zuse Institute Berlin (ZIB)}, pages = {100}, year = {2013}, abstract = {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.}, language = {en} } @misc{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, year = {2013}, abstract = {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.}, language = {en} } @misc{DresslerSteinke2013, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects}, issn = {1438-0064}, doi = {10.1007/978-3-642-54420-0_25}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42224}, year = {2013}, abstract = {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.}, language = {en} } @misc{Maier2011, type = {Master Thesis}, author = {Maier, Robert}, title = {Massiv-parallele Suche und effiziente Heuristiken}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42448}, school = {Humboldt-Universit{\"a}t zu Berlin}, pages = {81}, year = {2011}, abstract = {Pattern Datenbanken (PDBs) werden in der heuristischen Suche eingesetzt, um irrelevante Pfade in der Suche auszuschließen. Da die Leistung einer PDB mit ihrer Gr{\"o}ße steigt und f{\"u}r die effektive heuristische Suche in großen Zustandsr{\"a}umen große PDBs n{\"o}tig sind, ist ein paralleler Ansatz notwendig, um sehr große PDBs zu erzeugen. Diese Arbeit erweitert einen, auf MapReduce basierenden, Algorithmus von Reinefeld und Sch{\"u}tt (2009) zur massiv-parallelen Breitensuche so, dass damit sehr große PDBs erzeugt werden k{\"o}nnen. So entsteht die erste vollst{\"a}ndige 8+8+8 PDB f{\"u}r das 24er-Puzzle. Reinefeld und Sch{\"u}tt implementieren ebenfalls das heuristische Suchverfahren BFIDA* f{\"u}r MapReduce. In dieser Arbeit wird dieser Implementation ein Speedup von 857 bei 2039 Kernen nachgewiesen. Weiterhin f{\"u}hrt diese Arbeit ein Schema ein, mit dem PDBs bei der Suche direkt von der Festplatte gelesen werden k{\"o}nnen. 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 Gr{\"o}ße 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 Verf{\"u}gung stehende Hauptspeicher ausreicht, eine Gruppe zusammen mit einigen kleineren PDBs zu bilden.}, language = {de} } @misc{Mueller2013, type = {Master Thesis}, author = {M{\"u}ller, Magnus}, title = {Flexible Routing Tables in a Distributed Key-Value Store}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42742}, school = {Zuse Institute Berlin (ZIB)}, pages = {118}, year = {2013}, abstract = {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.}, language = {en} } @masterthesis{Dillmann2013, type = {Bachelor Thesis}, author = {Dillmann, Johannes}, title = {Konsistentes Hinzuf{\"u}gen und Entfernen von Replikaten in XtreemFS}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43109}, school = {Zuse Institute Berlin (ZIB)}, pages = {42}, year = {2013}, abstract = {In replizierten Systemen muss es m{\"o}glich sein ausgefallene Server zu ersetzen und Replikate dynamisch hinzuzuf{\"u}gen oder zu entfernen. Ver{\"a}nderungen an der Menge der eingesetzten Replikate k{\"o}nnen zu inkonsistenten Daten f{\"u}hren. In dieser Arbeit wird ein Algorithmus f{\"u}r das konsistente Hinzuf{\"u}gen und Entfernen von Replikaten f{\"u}r das verteilte Dateisystem XtreemFS vorgestellt. Der Algorithmus nutzt einen fehlertoleranten Service, der die Replikatliste speichert sowie Ver{\"a}nderungen koordiniert und diese aus globaler Sicht atomar ausf{\"u}hrt.}, language = {de} } @masterthesis{Kairies2013, type = {Bachelor Thesis}, author = {Kairies, Lukas}, title = {Leistungsanalyse von XtreemFS als Ersatz f{\"u}r HDFS in Hadoop}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43130}, school = {Zuse Institute Berlin (ZIB)}, pages = {46}, year = {2013}, abstract = {In dieser Arbeit wird die Leistungsf{\"a}higkeit des MapReduce-Framework Hadoop mit XtreemFS als verteiltes und POSIX-konformes Dateisystem bestimmt. Damit wird XtreemFS das f{\"u}r die Nutzung mit Hadoop entwickelte Dateisystem HDFS ersetzen. HDFS und XtreemFS werden verglichen und XtreemFS f{\"u}r 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.}, language = {de} } @misc{Pyszkalski2013, author = {Pyszkalski, Wolfgang}, title = {{\"U}bersicht {\"u}ber die Datenhaltung im ZIB und die M{\"o}glichkeiten einer Nutzung durch Projekte}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42060}, year = {2013}, abstract = {Dieser Bericht beschreibt in allgemein verst{\"a}ndlicher Form die Struktur der Datenhaltung im Zuse-Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer st{\"a}rker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten {\"u}ber im Grunde unbegrenzte Zeit.}, language = {de} } @inproceedings{DoebbelinSchuettReinefeld2013, author = {D{\"o}bbelin, Robert and Sch{\"u}tt, Thorsten and Reinefeld, Alexander}, title = {Building Large Compressed PDBs for the Sliding Tile Puzzle}, booktitle = {Workshop on Computer Games}, year = {2013}, language = {en} } @article{KramerLaeuter2019, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {Outgassing induced acceleration of comet 67P/Churyumov-Gerasimenko}, volume = {630}, journal = {Astronomy \& Astrophysics}, arxiv = {http://arxiv.org/abs/1902.02701}, doi = {10.1051/0004-6361/201935229}, pages = {A4}, year = {2019}, abstract = {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.}, language = {en} } @article{DelleSiteKrekelerWhittakeretal.2019, author = {Delle Site, Luigi and Krekeler, Christian and Whittaker, John and Agarwal, Animesh and Klein, Rupert and H{\"o}fling, Felix}, title = {Molecular Dynamics of Open Systems: Construction of a Mean-Field Particle Reservoir}, volume = {2}, journal = {Advanced Theory and Simulations}, arxiv = {http://arxiv.org/abs/1902.07067}, doi = {10.1002/adts.201900014}, pages = {1900014}, year = {2019}, abstract = {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.}, language = {en} } @article{WendeMarsmanKimetal.2018, author = {Wende, Florian and Marsman, Martijn and Kim, Jeongnim and Vasilev, Fedor and Zhao, Zhengji and Steinke, Thomas}, title = {OpenMP in VASP: Threading and SIMD}, journal = {International Journal of Quantum Chemistry}, number = {Emerging Architectures in Computational Chemistry}, publisher = {Wiley Online Library}, doi = {10.1002/qua.25851}, pages = {e25851}, year = {2018}, abstract = {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.}, language = {en} } @article{SalemSchintkeSchuettetal.2018, author = {Salem, Farouk and Schintke, Florian and Sch{\"u}tt, Thorsten and Reinefeld, Alexander}, title = {Data-flow scheduling for a scalable FLESnet}, journal = {CBM Progress Report 2017}, isbn = {978-3-9815227-5-4}, doi = {10.15120/GSI-2018-00485}, pages = {130 -- 131}, year = {2018}, language = {en} } @article{RodriguezKramer2019, author = {Rodr{\´i}guez, Mirta and Kramer, Tobias}, title = {Machine Learning of Two-Dimensional Spectroscopic Data}, volume = {520}, journal = {Chemical Physics}, arxiv = {http://arxiv.org/abs/1810.01124}, doi = {10.1016/j.chemphys.2019.01.002}, pages = {52 -- 60}, year = {2019}, abstract = {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.}, language = {en} } @article{KramerLaeuterHviidetal.2019, author = {Kramer, Tobias and L{\"a}uter, Matthias and Hviid, Stubbe and Jorda, Laurent and Keller, Horst Uwe and K{\"u}hrt, Ekkehard}, title = {Comet 67P/Churyumov-Gerasimenko rotation changes derived from sublimation induced torques}, volume = {630}, journal = {Astronomy \& Astrophysics}, arxiv = {http://arxiv.org/abs/1812.01490}, doi = {10.1051/0004-6361/201834349}, pages = {A3}, year = {2019}, abstract = {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.}, language = {en} } @misc{SchneckWeiserWende2019, author = {Schneck, Jakob and Weiser, Martin and Wende, Florian}, title = {Impact of mixed precision and storage layout on additive Schwarz smoothers}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71305}, year = {2019}, abstract = {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.}, language = {en} } @misc{Deppisch2019, type = {Master Thesis}, author = {Deppisch, Daniel}, title = {Advancing the Heterogeneous Active Messages Approach}, year = {2019}, language = {en} } @inproceedings{GholamiSchintkeSchuett2018, author = {Gholami, Masoud and Schintke, Florian and Sch{\"u}tt, Thorsten}, title = {Checkpoint Scheduling for Shared Usage of Burst-Buffers in Supercomputers}, booktitle = {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}, doi = {10.1145/3229710.3229755}, pages = {44:1 -- 44:10}, year = {2018}, abstract = {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.}, language = {en} } @misc{GholamiSchintkeSchuettetal.2018, author = {Gholami, Masoud and Schintke, Florian and Sch{\"u}tt, Thorsten and Reinefeld, Alexander}, title = {Modeling Checkpoint Schedules for Concurrent HPC Applications}, journal = {CoSaS 2018 International Symposium on Computational Science at Scale}, year = {2018}, language = {en} } @inproceedings{SchmidtkeSchintkeSchuett2018, author = {Schmidtke, Robert and Schintke, Florian and Sch{\"u}tt, Thorsten}, title = {From Application to Disk: Tracing I/O Through the Big Data Stack}, booktitle = {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)}, doi = {10.1007/978-3-030-02465-9_6}, pages = {89 -- 102}, year = {2018}, abstract = {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.}, language = {en} } @misc{Steininger2018, type = {Master Thesis}, author = {Steininger, Lennart}, title = {Atomarer Datenzugriff auf verteilten persistenten Arbeitsspeicher}, year = {2018}, abstract = {Nicht fl{\"u}chtiger Arbeitsspeicher bzw. Non-volatile Random Access Memory oder auch Persistent Memory befindet sich im fr{\"u}hen Markteintritt. Diese Art von Speicher nimmt eine Stellung zwischen bisherigem fl{\"u}chtigen 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 m{\"o}glichst passivem Zugriff auf entfernten Speicher performante verteilte Systeme implementieren lassen. Es werden Anforderungen und Voraussetzungen eines solchen Systems bestimmt und daraufhin L{\"o}sungsm{\"o}glichkeiten aufgezeigt, wie sich diese Anforderungen mit Nutzung nicht fl{\"u}chtigen Arbeitsspeichers umsetzen lassen. Die notwendigen Eigenschaften der Hard- und Software sowie der eingesetzten Netzwerkprotokolle werden beschrieben.}, language = {de} } @article{LaeuterKramerRubinetal.2019, author = {L{\"a}uter, Matthias and Kramer, Tobias and Rubin, Martin and Altwegg, Kathrin}, title = {Surface localization of gas sources on comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data}, volume = {483}, journal = {Monthly Notices of the Royal Astronomical Society}, publisher = {Monthly Notices of the Royal Astronomical Society}, arxiv = {http://arxiv.org/abs/1804.06696}, doi = {10.1093/mnras/sty3103}, pages = {852 -- 861}, year = {2019}, abstract = {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.}, language = {en} } @article{StoopStraubeJohansenetal.2020, author = {Stoop, Ralph L. and Straube, Arthur and Johansen, Tom H. and Tierno, Pietro}, title = {Collective directional locking of colloidal monolayers on a periodic substrate}, volume = {124}, journal = {Phys. Rev. Lett.}, doi = {10.1103/PhysRevLett.124.058002}, pages = {058002}, year = {2020}, abstract = {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.}, language = {en} } @inproceedings{WeinholdLackorzynskiBierbaumetal.2019, author = {Weinhold, Carsten and Lackorzynski, Adam and Bierbaum, Jan and K{\"u}ttler, Martin and Planeta, Maksym and Weisbach, Hannes and Hille, Matthias and H{\"a}rtig, Hermann and Margolin, Alexander and Sharf, Dror and Levy, Ely and Gak, Pavel and Barak, Amnon and Gholami, Masoud and Schintke, Florian and Sch{\"u}tt, Thorsten and Reinefeld, Alexander and Lieber, Matthias and Nagel, Wolfgang}, title = {FFMK: A Fast and Fault-Tolerant Microkernel-Based System for Exascale Computing}, booktitle = {Software for Exascale Computing - SPPEXA 2016-2019}, publisher = {Springer}, doi = {10.1007/978-3-030-47956-5_16}, pages = {483 -- 516}, year = {2019}, language = {en} } @article{AbbottStraubeAartsetal.2019, author = {Abbott, Joshua L. and Straube, Arthur and Aarts, Dirk G. A. L. and Dullens, Roel P. A.}, title = {Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape}, volume = {21}, journal = {New J. Phys.}, doi = {10.1088/1367-2630/ab3765}, pages = {083027}, year = {2019}, abstract = {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.}, language = {en} } @article{StraubePagesTiernoetal.2019, author = {Straube, Arthur and Pag{\`e}s, Josep M. and Tierno, Pietro and Ign{\´e}s-Mullol, Jordi and Sagu{\´e}s, Francesc}, title = {Collective dynamics and conformal ordering in electrophoretically driven nematic colloids}, volume = {1}, journal = {Phys. Rev. Research}, doi = {10.1103/PhysRevResearch.1.022008}, pages = {022008}, year = {2019}, abstract = {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.}, language = {en} } @misc{DoebbelinSchuettReinefeld2013, author = {D{\"o}bbelin, Robert and Sch{\"u}tt, Thorsten and Reinefeld, Alexander}, title = {Building Large Compressed PDBs for the Sliding Tile Puzzle}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-18095}, year = {2013}, abstract = {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.}, language = {en} } @article{GolasHoffmannEhrigetal.2011, author = {Golas, Ulrike and Hoffmann, Kathrin and Ehrig, Hartmut and Rein, A. and Padberg, J.}, title = {Functorial Analysis of Algebraic Higher-Order Net Systems with Applications to Mobile Ad-Hoc Networks}, volume = {40}, journal = {ECEASST}, pages = {1 -- 20}, year = {2011}, language = {en} } @inproceedings{GesingGrunzkeBalaskoetal.2011, author = {Gesing, Sandra and Grunzke, Richard and Balasko, Akos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Herres-Pawlis, Sonja and Kacsuk, Peter and Kozlovszky, Miklos and Kr{\"u}ger, Jens and Packschies, Lars and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Steinke, Thomas and Szikszay Fabri, Anna and Wewior, Martin and M{\"u}ller-Pfefferkorn, Ralph and Kohlbacher, Oliver}, title = {Granular Security for a Science Gateway in Structural Bioinformatics}, booktitle = {Proc. IWSG-Life 2011}, year = {2011}, language = {en} } @inproceedings{ChabarekGolas2011, author = {Chabarek, F. and Golas, Ulrike}, title = {Interaktive Vervollst{\"a}ndigung der Szenariobasierten Spezifikation eines Parkassistenzsystems}, booktitle = {Proceedings of GI-ASE 2011}, editor = {Heiß, H.-U. and Pepper, P. and Schlingloff, H. and Schneider, J{\"o}rg}, year = {2011}, language = {en} } @incollection{PlantikowJorra2011, author = {Plantikow, Stefan and Jorra, Maik}, title = {Latency-Optimal Walks in Replicated and Partitioned Graphs}, volume = {6637}, booktitle = {Database Systems for Adanced Applications}, editor = {Xu, Jianliang and Yu, Ge and Zhou, Shuigeng and Unland, Rainer}, publisher = {Springer Berlin / Heidelberg}, doi = {10.1007/978-3-642-20244-5_3}, pages = {14 -- 27}, year = {2011}, language = {en} } @inproceedings{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuster, Johannes and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: Progress of Workflow driven Chemical Simulations}, volume = {826}, booktitle = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, publisher = {CEUR Workshop Proceedings}, year = {2011}, language = {en} } @inproceedings{Peter2011, author = {Peter, Kathrin}, title = {Reliability Study of Coding Schemes for Wide-Area Distributed Storage Systems}, booktitle = {PDP 2011: The 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing}, publisher = {Euromicro}, doi = {10.1109/PDP.2011.70}, year = {2011}, language = {en} } @article{DickmannFalknerGuniaetal.2011, author = {Dickmann, Frank and Falkner, J{\"u}rgen and Gunia, Wilfried and Hampe, Jochen and Hausmann, Michael and Herrmann, Alexander and Kepper, Nick and Knoch, Tobias and Lauterbach, Svenja and Lippert, J{\"o}rg and Peter, Kathrin and Schmitt, Eberhard and Schwardmann, Ulrich and Solodenko, Juri and Sommerfeld, Dietmar and Steinke, Thomas and Weisbecker, Anette and Sax, Ulrich}, title = {Solutions for biomedical grid computing - Case studies from the D-Grid project Services@MediGRID}, volume = {-}, journal = {Journal of Computational Science}, number = {0}, doi = {10.1016/j.jocs.2011.06.006}, year = {2011}, language = {en} } @article{KruberHoegqvistSchuett2011, author = {Kruber, Nico and H{\"o}gqvist, Mikael and Sch{\"u}tt, Thorsten}, title = {The Benefits of Estimated Global Information in DHT Load Balancing}, volume = {0}, journal = {Cluster Computing and the Grid, IEEE International Symposium on}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, doi = {10.1109/CCGrid.2011.11}, pages = {382 -- 391}, year = {2011}, language = {en} } @inproceedings{StenderKolbeckHoegqvistetal.2010, author = {Stender, Jan and Kolbeck, Bj{\"o}rn and H{\"o}gqvist, Mikael and Hupfeld, Felix}, title = {BabuDB: Fast and Efficient File System Metadata Storage}, booktitle = {Storage Network Architecture and Parallel I/Os, IEEE International Workshop on}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, doi = {10.1109/SNAPI.2010.14}, pages = {51 -- 58}, year = {2010}, language = {en} } @inproceedings{BoeseAndrzejakHoegqvist2010, author = {B{\"o}se, Joos-Hendrik and Andrzejak, Artur and H{\"o}gqvist, Mikael}, title = {Beyond online aggregation: Parallel and incremental data mining with online Map-Reduce}, booktitle = {Proceedings of the 2010 Workshop on Massive Data Analytics on the Cloud}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/1779599.1779602}, pages = {3:1 -- 3:6}, year = {2010}, language = {en} } @inproceedings{KindermannSchintkeFritzsch2012, author = {Kindermann, S. and Schintke, Florian and Fritzsch, B.}, title = {A Collaborative Data Management Infrastructure for Climate Data Analysis}, volume = {14, EGU2012-10569}, booktitle = {Geophysical Research Abstracts}, doi = {10013/epic.39635.d001}, year = {2012}, language = {en} } @inproceedings{SobollGolas2012, author = {Soboll, T. and Golas, Ulrike}, title = {A Local-Global Model for Multiagent Systems - Sheaves on the Category MAS}, volume = {2}, booktitle = {Proceedings of ICAART 2012}, editor = {Filipe, J. and Fred, A.}, publisher = {SciTePress}, pages = {331 -- 334}, year = {2012}, language = {en} } @article{GolasLambersEhrigetal.2012, author = {Golas, Ulrike and Lambers, L. and Ehrig, Hartmut and Orejas, Fernando}, title = {Attributed Graph Transformation with Inheritance}, volume = {424}, journal = {Theoretical Computer Science}, doi = {10.1016/j.tcs.2012.01.032}, pages = {46 -- 68}, year = {2012}, language = {en} } @inproceedings{GesingHerresPawlisBirkenheueretal.2012, author = {Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, Andre and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Kr{\"u}ger, Jens and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas}, title = {The MoSGrid Community - From National to International Scale}, booktitle = {EGI Community Forum 2012}, year = {2012}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science}, volume = {3}, journal = {Journal of Cheminformatics 2011}, number = {Suppl 1}, doi = {10.1186/1758-2946-3-S1-P14}, year = {2011}, language = {en} } @inproceedings{GesingKacsukKozlovszkyetal.2011, author = {Gesing, Sandra and Kacsuk, Peter and Kozlovszky, Miklos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Grunzke, Richard and Herres-Pawlis, Sonja and Kr{\"u}ger, Jens and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Szikszay Fabri, Anna and Warzecha, Klaus Dieter and Wewior, Martin and Kohlbacher, Oliver}, title = {A Science Gateway for Molecular Simulations}, booktitle = {EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts}, pages = {94 -- 95}, year = {2011}, language = {en} } @article{GolasBiermannEhrigetal.2011, author = {Golas, Ulrike and Biermann, E. and Ehrig, Hartmut and Ermel, Claudia}, title = {A Visual Interpreter Semantics for Statecharts Based on Amalgamated Graph Transformation}, volume = {39}, journal = {ECEASST}, pages = {1 -- 24}, year = {2011}, language = {en} } @article{EnkeSteinmetzAdorfetal.2011, author = {Enke, Harry and Steinmetz, Matthias and Adorf, Hans-Martin and Beck-Ratzka, Alexander and Breitling, Frank and Br{\"u}semeister, Thomas and Carlson, Arthur and Ensslin, Torsten and H{\"o}gqvist, Mikael and Nickelt, Iliya and Radke, Thomas and Reinefeld, Alexander and Reiser, Angelika and Scholl, Tobias and Spurzem, Rainer and Steinacker, J{\"u}rgen and Voges, Wolfgang and Wambsganß, Joachim and White, Steve}, title = {AstroGrid-D: Grid technology for astronomical science}, volume = {16}, journal = {New Astronomy}, number = {2}, doi = {10.1016/j.newast.2010.07.005}, pages = {79 -- 93}, year = {2011}, language = {en} } @article{KolbeckHoegqvistStenderetal.2011, author = {Kolbeck, Bj{\"o}rn and H{\"o}gqvist, Mikael and Stender, Jan and Hupfeld, Felix}, title = {Flease - Lease Coordination Without a Lock Server}, volume = {0}, journal = {Parallel and Distributed Processing Symposium, International}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, doi = {10.1109/IPDPS.2011.94}, pages = {978 -- 988}, year = {2011}, language = {en} } @article{GolasEhrigHermann2011, author = {Golas, Ulrike and Ehrig, Hartmut and Hermann, Frank}, title = {Formal Specification of Model Transformations by Triple Graph Grammars with Application Conditions}, volume = {39}, journal = {ECEASST}, pages = {1 -- 26}, year = {2011}, language = {en} } @incollection{EnkeFiedlerFischeretal.2013, author = {Enke, Harry and Fiedler, Norman and Fischer, Thomas and Gnadt, Timo and Ketzan, Erik and Ludwig, Jens and Rathmann, Torsten and St{\"o}ckle, Gabriel and Schintke, Florian}, title = {Leitfaden zum Forschungsdaten-Management}, booktitle = {Leitfaden zum Forschungsdaten-Management}, editor = {Enke, Harry and Ludwig, Jens}, publisher = {Verlag Werner H{\"u}lsbusch, Gl{\"u}ckstadt}, year = {2013}, language = {en} } @phdthesis{Hoegqvist2012, author = {H{\"o}gqvist, Mikael}, title = {Consistent Key-Based Routing in Decentralized and Reconfigurable Data Services}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:11-100206145}, year = {2012}, language = {en} } @phdthesis{Kolbeck2012, author = {Kolbeck, Bj{\"o}rn}, title = {A fault-tolerant and scalable protocol for replication in distributed file systems}, year = {2012}, language = {en} } @incollection{FlikReinefeld2012, author = {Flik, T. and Reinefeld, Alexander}, title = {Rechnerorganisation}, booktitle = {H{\"u}tte - Das Ingenieurwissen}, editor = {Czichos, Horst and Hennecke, Manfred}, edition = {34}, publisher = {Springer-Verlag Berlin}, pages = {J6 -- J124}, year = {2012}, language = {en} } @inproceedings{PeterReinefeld2012, author = {Peter, Kathrin and Reinefeld, Alexander}, title = {Consistency and fault tolerance for erasure-coded distributed storage systems}, booktitle = {Proceedings of the fifth international workshop on Data-Intensive Distributed Computing Date}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/2286996.2287002}, pages = {23 -- 32}, year = {2012}, language = {en} } @inproceedings{WendeCordesSteinke2012, author = {Wende, Florian and Cordes, Frank and Steinke, Thomas}, title = {On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering}, booktitle = {Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on}, doi = {10.1109/SAAHPC.2012.12}, pages = {74 -- 83}, year = {2012}, language = {en} } @inproceedings{PeterSobe2012, author = {Peter, Kathrin and Sobe, Peter}, title = {Application of Regenerating Codes for Fault Tolerance in Distributed Storage Systems}, booktitle = {Network Computing and Applications (NCA), 2012 11th IEEE International Symposium on}, doi = {10.1109/NCA.2012.35}, pages = {67 -- 70}, year = {2012}, language = {en} } @article{GesingHerresPawlisBirkenheueretal.2012, author = {Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, Andr{\´e} and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Kr{\"u}ger, Jens and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas}, title = {A Science Gateway Getting Ready for Serving the International Molecular Simulation Community}, volume = {PoS(EGICF12-EMITC2)050}, journal = {Proceedings of Science}, year = {2012}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2012, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment}, volume = {4}, journal = {Journal of Cheminformatics}, number = {Suppl 1}, doi = {10.1186/1758-2946-4-S1-P21}, pages = {21}, year = {2012}, language = {en} } @article{GesingGrunzkeKruegeretal.2012, author = {Gesing, Sandra and Grunzke, Richard and Kr{\"u}ger, Jens and Birkenheuer, Georg and Wewior, Martin and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Herres-Pawlis, Sonja and Breuers, Sebastian and Balasko, Akos and Kozlovszky, Miklos and Szikszay Fabri, Anna and Packschies, Lars and Kacsuk, Peter and Blunk, Dirk and Steinke, Thomas and Brinkmann, Andr{\´e} and Fels, Gregor and M{\"u}ller-Pfefferkorn, Ralph and J{\"a}kel, Ren{\´e} and Kohlbacher, Oliver}, title = {A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics}, journal = {Journal of Grid Computing}, year = {2012}, language = {en} } @inproceedings{GrunzkeBirkenheuerBlunketal.2012, author = {Grunzke, Richard and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Gesing, Sandra and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Kruse, Martin and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuller, Bernd and Steinke, Thomas and Zink, Andreas}, title = {A Data Driven Science Gateway for Computational Workflows}, booktitle = {Proceedings of the UNICORE Summit}, address = {Dresden, Germany}, year = {2012}, language = {en} } @article{EnkePartlReinefeldetal.2012, author = {Enke, Harry and Partl, Adrian and Reinefeld, Alexander and Schintke, Florian}, title = {Handling Big Data in Astronomy and Astrophysics}, volume = {12}, journal = {Datenbank-Spektrum}, number = {3}, publisher = {Springer-Verlag}, doi = {10.1007/s13222-012-0099-1}, pages = {173 -- 181}, year = {2012}, language = {en} } @inproceedings{Golas2012, author = {Golas, Ulrike}, title = {A General Attribution Concept for Models in M-Adhesive Transformation Systems}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_13}, pages = {187 -- 202}, year = {2012}, language = {en} } @inproceedings{GolasLambersEhrigetal.2012, author = {Golas, Ulrike and Lambers, L. and Ehrig, Hartmut and Giese, H.}, title = {Towards Bridging the Gap between Formal Foundations and Current Practice for Triple Graph Grammars - Flexible Relations between Source and Target Elements}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_10}, pages = {141 -- 155}, year = {2012}, language = {en} } @inproceedings{HeckelEhrigGolasetal.2012, author = {Heckel, R. and Ehrig, Hartmut and Golas, Ulrike and Hermann, Frank}, title = {Parallelism and Concurrency of Stochastic Graph Transformations}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_7}, pages = {96 -- 110}, year = {2012}, language = {en} } @inproceedings{DoebbelinSchuettReinefeld2012, author = {D{\"o}bbelin, Robert and Sch{\"u}tt, Thorsten and Reinefeld, Alexander}, title = {An Analysis of SMP Memory Allocators}, booktitle = {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))}, publisher = {IEEE Computer Society}, doi = {10.1109/ICPPW.2012.10}, pages = {48 -- 54}, year = {2012}, language = {en} } @article{DresslerSteinke2012, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {Energy consumption of CUDA kernels with varying thread topology}, journal = {Computer Science - Research and Development}, publisher = {Springer Berlin / Heidelberg}, doi = {10.1007/s00450-012-0230-4}, pages = {1 -- 9}, year = {2012}, language = {en} } @article{EhrigGolasHabeletal.2012, author = {Ehrig, Hartmut and Golas, Ulrike and Habel, A. and Lambers, L. and Orejas, Fernando}, title = {M-Adhesive Transformation Systems with Nested Application Conditions. Part 2}, volume = {118}, journal = {Fundamenta Informaticae}, number = {1-2}, doi = {10.3233/FI-2012-705}, pages = {35 -- 63}, year = {2012}, language = {en} } @misc{OPUS4-3402, title = {Proceedings of ACCAT 2012}, journal = {Electronic Proceedings in Theoretical Computer Science 93}, editor = {Golas, Ulrike and Soboll, T.}, doi = {10.4204/EPTCS.93}, year = {2012}, language = {en} } @inproceedings{SchaeferHoegqvist2012, author = {Sch{\"a}fer, Patrick and H{\"o}gqvist, Mikael}, title = {SFA : a symbolic fourier approximation and index for similarity search in high dimensional datasets}, booktitle = {Proceedings of the 15th International Conference on Extending Database Technology}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/2247596.2247656}, pages = {516 -- 527}, year = {2012}, language = {en} } @inproceedings{RiesDitzePiateretal.2013, author = {Ries, F. and Ditze, M. and Piater, A. and Singer, E. and F{\"a}ßler, V. and Dreßler, Sebastian and Soddemann, T.}, title = {Tool-Supported Integration of Hardware Acceleration in Automotive CFD-Simulations}, booktitle = {NAFEMS 2013 Proceedings}, year = {2013}, language = {en} } @misc{DresslerSteinke2013, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {Automated Analysis of Complex Data Objects}, journal = {28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013}, year = {2013}, language = {en} } @inproceedings{SchuettDoebbelinReinefeld2013, author = {Sch{\"u}tt, Thorsten and D{\"o}bbelin, Robert and Reinefeld, Alexander}, title = {Forward Perimeter Search with Controlled Use of Memory}, booktitle = {International Joint Conference on Artificial Intelligence, IJCAI-13, Beijing}, year = {2013}, language = {en} } @article{SchuettReinefeldDoebbelin2011, author = {Sch{\"u}tt, Thorsten and Reinefeld, Alexander and D{\"o}bbelin, Robert}, title = {MR-search: massively parallel heuristic search}, volume = {25}, journal = {Concurrency and Computation: Practice and Experience}, number = {1}, doi = {10.1002/cpe.1833}, pages = {40 -- 54}, year = {2011}, language = {en} } @incollection{StenderBerlinReinefeld2013, author = {Stender, Jan and Berlin, Michael and Reinefeld, Alexander}, title = {XtreemFS - a File System for the Cloud}, booktitle = {Data Intensive Storage Services for Cloud Environments}, editor = {Kyriazis, D. and Voulodimos, A. and Gogouvitis, S. and Varvarigou, Theodora A.}, publisher = {IGI Global}, doi = {10.4018/978-1-4666-3934-8}, year = {2013}, language = {en} } @phdthesis{Sobe2013, author = {Sobe, Kathrin}, title = {Consistency and Fault Tolerance of Distributed Storage Systems}, year = {2013}, language = {en} } @phdthesis{Stender2013, author = {Stender, Jan}, title = {Snapshots in Large-Scale Distributed File Systems}, year = {2013}, language = {en} } @article{Schintke2013, author = {Schintke, Florian}, title = {XtreemFS \& Scalaris}, journal = {Science \& Technology}, number = {6}, publisher = {Pan European Networks}, pages = {54 -- 55}, year = {2013}, language = {en} } @inproceedings{OrejasBoronatGolasetal.2013, author = {Orejas, Fernando and Boronat, Artur and Golas, Ulrike and Mylonakis, Nikos}, title = {Checking Bisimilarity for Attributed Graph Transformation}, volume = {7794}, booktitle = {Foundations of Software Science and Computation Structures. Proceedings of FOSSACS 2013}, editor = {Pfenning, Frank}, publisher = {Springer}, doi = {10.1007/978-3-642-37075-5_8}, pages = {113 -- 128}, year = {2013}, language = {en} } @article{Berlin2013, author = {Berlin, Michael}, title = {Consistent and Partition-Tolerant File Replication in the Cloud File System Xtreem FS}, volume = {36}, journal = {Praxis der Informationsverarbeitung und Kommunikation}, number = {1}, doi = {10.1515/pik-2012-0144}, pages = {39}, year = {2013}, language = {en} } @inproceedings{SchaeferDressler2013, author = {Sch{\"a}fer, Patrick and Dreßler, Sebastian}, title = {Shooting Audio Recordings of Insects with SFA}, booktitle = {AmiBio Workshop, Bonn, Germany}, year = {2013}, language = {en} } @misc{Reinbacher2013, type = {Master Thesis}, author = {Reinbacher, Uwe}, title = {Implementierung und Evaluierung eines FPGA-basierten statischen Paketfilters}, year = {2013}, language = {de} } @masterthesis{Borgers2012, type = {Bachelor Thesis}, author = {Borgers, Philipp}, title = {Erweiterung eines verteilten Key-Value-Stores (Riak) um einen r{\"a}umlichen Index}, year = {2012}, language = {de} } @article{KreisbeckKramerMolina2017, author = {Kreisbeck, Christoph and Kramer, Tobias and Molina, Rafael}, title = {Time-dependent wave packet simulations of transport through Aharanov-Bohm rings with an embedded quantum dot}, volume = {29}, journal = {Journal of Physics: Condensed Matter}, number = {15}, doi = {10.1088/1361-648X/aa605d}, pages = {155301}, year = {2017}, abstract = {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.}, language = {en} } @inproceedings{RitterBaumannFelsenberg2010, author = {Ritter, Zully and Baumann, Wolfgang and Felsenberg, Dieter}, title = {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}, volume = {31}, booktitle = {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)}, doi = {10.1007/978-3-642-14515-5_209}, pages = {823 -- 826}, year = {2010}, language = {en} } @article{KramerRodriguezZelinskyi2017, author = {Kramer, Tobias and Rodriguez, Mirta and Zelinskyi, Yaroslav}, title = {Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems}, volume = {121}, journal = {Journal of Physical Chemistry B}, arxiv = {http://arxiv.org/abs/1811.10683}, doi = {10.1021/acs.jpcb.6b09858}, pages = {463 -- 470}, year = {2017}, abstract = {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.}, language = {en} } @misc{NoackWendeZitzlsbergeretal.2016, author = {Noack, Matthias and Wende, Florian and Zitzlsberger, Georg and Klemm, Michael and Steinke, Thomas}, title = {KART - A Runtime Compilation Library for Improving HPC Application Performance}, issn = {1438-0064}, doi = {10.1007/978-3-319-67630-2_29}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60730}, year = {2016}, abstract = {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.}, language = {en} }