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The work done in this thesis enhances the MMD algorithm in multi-core environments. The MMD algorithm, a transformation based algorithm for reversible logic synthesis, is based on the works introduced by Maslov, Miller and Dueck and their original, sequential implementation. It synthesises a formal function specification, provided by a truth table, into a reversible network and is able to perform several optimization steps after the synthesis. This work concentrates on one of these optimization steps, the template matching. This approach is used to reduce the size of the reversible circuit by replacing a number of gates that match a template which implements the same function and uses less gates. Smaller circuits have several benefits since they need less area and are not as costly. The template matching approach introduced in the original works is computationally expensive since it tries to match a library of templates against the given circuit. For each template at each position in the circuit, a number of different combinations have to be calculated during runtime resulting in high execution times, especially for large circuits. In order to make the template matching approach more efficient and usable, it has been reimplemented in order to take advantage of modern multi-core architectures such as the Cell Broadband Engine or a Graphics Processing Unit. For this work, two algorithmically different approaches that try to consider each multi-core architecture’s strengths, have been analyzed and improved. For the analysis these approaches have been cross-implemented on the two target hardware architectures and compared to the original parallel versions. Important metrics for this analysis are the execution time of the algorithm and the result of the minimization with the template matching approach. It could be shown that the algorithmically different approaches produce the same minimization results, independent of the used hardware architecture. However, both cross-implementations also show a significantly higher execution time which makes them practically irrelevant. The results of the first analysis and comparison lead to the decision to enhance only the original parallel approaches. Using the same metrics for successful enhancements as mentioned above, it could be shown that improving the algorithmic concepts and exploiting the capabilities of the hardware lead to better results for the execution time and the minimization results compared to their original implementations.
This thesis presents an approach to automatically adjust the parameters of a Java application run on the IBM J9 Virtual Machine in order to improve its performance. It works by analyzing the logfile the VM generates and searching for specific behavioral patterns. These patterns are matched against a list of known patterns for which rules exist that specify how to adapt the VM to the given application. Adapting the application is done by adding parameters and changing existing ones, for example to achieve a better heap usage. The process is fully automated and carried out by a toolkit developed for this thesis. The toolkit iteratively cycles through multiple possible parameter sets, benchmarks them and proposes the best alternative to the user. The user can, without any prior knowledge about the Java application or the VM improve the performance of the deployed application.
The Java Virtual Machine (JVM) executes the compiled bytecode version of a Java program and acts as a layer between the program and the operating system. The JVM provides additional features such as Process, Thread, and Memory Management to manage the execution of these programs. The Garbage Collection (GC) is part of the memory management and has an impact on the overall runtime performance because it is responsible for removing dead objects from the heap. Currently, the execution of a program needs to be halted during every GC run. The problem of this stop-the-world approach is that all threads in the JVM need to be suspended. It would be desirable to have a thread-local GC that only blocks the current thread and does not affect any other threads. In particular, this would improve the execution of multi-threaded Java programs. An object that is accessible by more than one thread is called escaped. It is not possible to thread-locally determine if escaped objects are still alive so that they cannot be handled in a thread-local GC. To gain significant performance improvements with a thread-local GC, it is therefore necessary to determine if it is possible to reliably predict if a given object will escape. Experimental results show that the escaping of objects can be predicted with high accuracy based on the line of code the object was allocated from. A thread-local GC was developed to minimize the number of stop-the-world GCs. The prototype implementation delivers a proof-of-concept that shows that this goal can be achieved in certain scenarios.
An analysis of sharing string objects with the Java Virtual Machine was conducted; they are the most used objects in Java programs and they are immutable - thus they are read-only and easily identified. While the results are promising, it is clear that sharing more objects would result in better performance. Automatic object selection for sharing is non-trivial, because in the current state only read-only objects can be shared. This attribute can not be easily determined during runtime by an algorithm; the developer on the other hand can. This thesis presents the development of an Application Programmer Interface (API) that allows programmers to use the Java Virtual Machine (JVM) internal sharing functionality. Furthermore, we present the usage of the sharing API. Open-source software was used as real-world test cases. Afterwards the evaluation shows that the ratio between memory savings and start-up time overhead is reasonable.
RNA is one of the most important molecules in living organisms. One of its main functions is to regulate gene expression. This involves binding to and forming a joint structure with a messenger RNA. An RNAs functions is determined by its sequence and the structure it folds into. Accordingly, the prediction of individual as well as joint structures is an important area of research. In this thesis a method for the prediction of RNA-RNA joint structure using their minimum free energy (mfe) structures was developed. It is able to extensively explore the joint structural landscape of two interacting RNAs by taking advantage of the locality of changes in the RNAs structures as well as natural and energetic constraints. The method predicts the mfe joint structure as well as alternative stable joint structures while also computing non-optimal folding pathways from the unbound individual mfe structures to the predicted joint structures. It is shown how an enumeration approach is used which is able to deal with the enormous search space as well as to avoid any cyclic behaviour. The method is evaluated using two standard datasets of known interacting RNAs and shows good results.
„Sind Sie Gärtner oder Maschinist?“ (Zechlin 2010) – wer diese Frage einem Hochschulmanager stellt, der transportiert damit gleich dreierlei: zum einen die Frage, was für ein Typ man ist. Im Fokus steht der Hochschulmanager, der gießt, pflegt, vielleicht einmal die Äste stutzt, oder, im Gegenteil, den Hebel umlegt und erwartet, dass die Produktion läuft. Zum anderen stellt sich die Frage, um welches Gebilde es sich da eigentlich handelt, dem der Gärtner zum Wachstum und der Maschinist zur Produktivität verhilft. Zum Dritten offenbart sich die Frage nach dem Oder, also nach den vielfältigen denkbaren Konstellationen der beiden Pole Gärtner oder Maschinist sowie Gebilden, die weder Garten noch Maschine sind und ganz anderer Steuerungsimpulse bedürfen. Um Hochschulleitungen und Hochschulen zu beschreiben, gibt es, darauf deutet die Metapher hin, zahlreiche Modelle und Typologien. Die Praxis des Steuerungshandelns offenbart jedoch im Detail zahllose individuelle Ausprägungen und situationsbedingte Spezifika. Immer wieder heißt es, mit Blick auf die vielen Unterschiede müsse die Haltbarkeit von Annahmen und Modellen über Hochschulsteuerung am konkreten Einzelfall geprüft werden. In der Führungspraxis an einer Hochschule, hier am Beispiel der Hochschule Bonn-Rhein-Sieg, wird ein solcher Einzelfall beschrieben. Die per Gesetz gestärkte Hochschulleitung nutzte ihren Gestaltungsspielraum, um Hochschulentwicklungsplanungsprozesse nach eigener Aussage partizipativ vorzunehmen. Die partizipativen Prozesse sollten es ermöglichen, die Leitungsaufgaben im Hinblick auf Profilbildung, Richtungsweisung, Zukunftsgestaltung und Ressourcenzuweisung adäquat erfüllen zu können.
Hochschulbibliotheken haben heutzutage neben der traditionellen Aufgabe der Literaturversorgung und Informationsversorgung auch die Aufgabe, über ihre Website im Internet präsent zu sein und sich dort als zentraler Informationsanbieter zu positionieren. Die Webauftritte haben dabei die Funktionen als Zugangspunkt und Vermittlungsstelle für Informationen sowie als Werbemittel bzw. Instrument der Öffentlichkeitsarbeit. Im Hinblick auf die immer stärkere Benutzerorientierung der Bibliotheken werden die Webangebote von fünf Universitätsbibliotheken und einer Fachhochschulbibliothek nach diversen Kriterien analysiert: es wird herausgearbeitet, welche Inhalte auf den Websites zu finden sind, die Struktur wird näher betrachtet, ebenso wie die Navigationsmöglichkeiten, die Sprache und Textgestaltung und das Design.