Scalable, Data- intensive Network Computation

To enable groups of collaborating researchers at different locations to effectively share large datasets and investigate their spontaneous hypotheses on the fly, we are interested in de- veloping a distributed system that can be easily leveraged by a variety of data intensive applications. The system is composed of (i) a number of best effort logistical depots to en- able large-scale data sharing and in-network data processing, (ii) a set of end-to-end tools to effectively aggregate, manage and schedule a large number of network computations with attendant data movements, and (iii) a Distributed Hash Table (DHT) on top of the generic depot services for scalable data management. The logistical depot is extended by following the end-to-end principles and is modeled with a closed queuing network model. Its performance characteristics are studied by solving the steady state distributions of the model using local balance equations. The modeling results confirm that the wide area network is the performance bottleneck and running concurrent jobs can increase resource utilization and system throughput. As a novel contribution, techniques to effectively support resource demanding data- intensive applications using the ¯ne-grained depot services are developed. These techniques include instruction level scheduling of operations, dynamic co-scheduling of computation and replication, and adaptive workload control. Experiments in volume visualization have proved the effectiveness of these techniques. Due to the unique characteristic of data- intensive applications and our co-scheduling algorithm, a DHT is implemented on top of the basic storage and computation services. It demonstrates the potential of the Logistical Networking infrastructure to serve as a service creation platform

Aggregating the Bandwidth of Multiple Network Interfaces to Increase the Performance of Networked Applications

Devices capable of connecting to two or more different networks simultaneously, known as host multihoming, are becoming increasingly common. For example, most laptops are equipped with a least a Local Area Network (LAN) and a Wireless LAN (WLAN) interface, and smartphones can connect to both WLANs and 3G-networks (High-Speed Downlink Packet Access, HSDPA). Being connected to multiple networks simultaneously allows for desirable features like bandwidth aggregation and redundancy. Enabling and making efficient use of multiple network interfaces or links (network interface and link will be used interchangeably throughout this thesis) requires solving several challenges related to deployment, link heterogeneity and dynamic behavior. Even though multihoming has existed for a long time, for example routers must support connecting to different networks, most existing operating systems, network protocols and applications do not take host multihoming into consideration. The default behavior is still to use a single interface for all traffic. Using a single interface is, for example, often insufficient to meet the requirements of popular, bandwidth intensive services like video streaming. In this thesis, we have focused on bandwidth aggregation on host multihomed devices. Even though bandwidth aggregation has been a research field for several years, the related works have failed to consider the challenges present in real world networks properly, or does not apply to scenarios where a device is connected to different heterogeneous networks. In order to solve the deployment challenges and enable the use of multiple links in away that works in a real-world network environment, we have created a platform-independent framework, called MULTI. MULTI was used as the foundation for designing transparent (to the applications) and application-specific bandwidth aggregation techniques. MULTI works in the presence of Network Address Translation (NAT), automatically detects and configures the device based on changes in link state, and notifies the application(s) of any changes. The application-specific bandwidth aggregation technique presented in this thesis was optimised for and evaluated with quailty-adaptive video streaming. The technique was evaluated with different types of streaming in both a controlled network environment and real-world networks. Adding a second link gave a significant increase in both video and playback quality. However, the technique is not limited to video streaming and can be used to improve the performance of several, common application types. In many cases, it is not possible to extend applications directly with multilink support. Working on the network-layer allows for the creation of bandwidth aggregation techniques that are transparent to applications. Transparent, network-layer bandwidth aggregation techniques must support the behavior of the different transport protocol in order to achieve efficient bandwidth aggregation. The transparent bandwidth aggregation techniques introduced in this thesis are targeted at Universal Datagram Protocol (UDP) and Transmission Control Protocol (TCP), the two most common transport protocols in the Internet today

Optimizing IETF multimedia signaling protocols and architectures in 3GPP networks : an evolutionary approach

Signaling in Next Generation IP-based networks heavily relies in the family of multimedia signaling protocols defined by IETF. Two of these signaling protocols are RTSP and SIP, which are text-based, client-server, request-response signaling protocols aimed at enabling multimedia sessions over IP networks. RTSP was conceived to set up streaming sessions from a Content / Streaming Server to a Streaming Client, while SIP was conceived to set up media (e.g.: voice, video, chat, file sharing, …) sessions among users. However, their scope has evolved and expanded over time to cover virtually any type of content and media session. As mobile networks progressively evolved towards an IP-only (All-IP) concept, particularly in 4G and 5G networks, 3GPP had to select IP-based signaling protocols for core mobile services, as opposed to traditional SS7-based protocols used in the circuit-switched domain in use in 2G and 3G networks. In that context, rather than reinventing the wheel, 3GPP decided to leverage Internet protocols and the work carried on by the IETF. Hence, it was not surprise that when 3GPP defined the so-called Packet-switched Streaming Service (PSS) for real-time continuous media delivery, it selected RTSP as its signaling protocol and, more importantly, SIP was eventually selected as the core signaling protocol for all multimedia core services in the mobile (All-)IP domain. This 3GPP decision to use off-the-shelf IETF-standardized signaling protocols has been a key cornerstone for the future of All-IP fixed / mobile networks convergence and Next Generation Networks (NGN) in general. In this context, the main goal of our work has been analyzing how such general purpose IP multimedia signaling protocols are deployed and behave over 3GPP mobile networks. Effectively, usage of IP protocols is key to enable cross-vendor interoperability. On the other hand, due to the specific nature of the mobile domain, there are scenarios where it might be possible to leverage some additional “context” to enhance the performance of such protocols in the particular case of mobile networks. With this idea in mind, the bulk of this thesis work has consisted on analyzing and optimizing the performance of SIP and RTSP multimedia signaling protocols and defining optimized deployment architectures, with particular focus on the 3GPP PSS and the 3GPP Mission Critical Push-to-Talk (MCPTT) service. This work was preceded by a detailed analysis work of the performance of underlying IP, UDP and TCP protocol performance over 3GPP networks, which provided the best baseline for the future work around IP multimedia signaling protocols. Our contributions include the proposal of new optimizations to enhance multimedia streaming session setup procedures, detailed analysis and optimizations of a SIP-based Presence service and, finally, the definition of new use cases and optimized deployment architectures for the 3GPP MCPTT service. All this work has been published in the form of one book, three papers published in JCR cited International Journals, 5 articles published in International Conferences, one paper published in a National Conference and one awarded patent. This thesis work provides a detailed description of all contributions plus a comprehensive overview of their context, the guiding principles beneath all contributions, their applicability to different network deployment technologies (from 2.5G to 5G), a detailed overview of the related OMA and 3GPP architectures, services and design principles. Last but not least, the potential evolution of this research work into the 5G domain is also outlined as well.Els mecanismes de Senyalització en xarxes de nova generació es fonamenten en protocols de senyalització definits per IETF. En particular, SIP i RTSP són dos protocols extensibles basats en missatges de text i paradigma petició-resposta. RTSP va ser concebut per a establir sessions de streaming de continguts, mentre SIP va ser creat inicialment per a facilitar l’establiment de sessions multimèdia (veu, vídeo, xat, compartició) entre usuaris. Tot i així, el seu àmbit d’aplicació s’ha anat expandint i evolucionant fins a cobrir virtualment qualsevol tipus de contingut i sessió multimèdia. A mesura que les xarxes mòbils han anat evolucionant cap a un paradigma “All-IP”, particularment en xarxes 4G i 5G, 3GPP va seleccionar els protocols i arquitectures destinats a gestionar la senyalització dels serveis mòbils presents i futurs. En un moment determinat 3GPP decideix que, a diferència dels sistemes 2G i 3G que fan servir protocols basats en SS7, els sistemes de nova generació farien servir protocols estandarditzats per IETF. Quan 3GPP va començar a estandarditzar el servei de Streaming sobre xarxes mòbils PSS (Packet-switched Streaming Service) va escollir el protocol RTSP com a mecanisme de senyalització. Encara més significatiu, el protocol SIP va ser escollit com a mecanisme de senyalització per a IMS (IP Multimedia Subsystem), l’arquitectura de nova generació que substituirà la xarxa telefònica tradicional i permetrà el desplegament de nous serveis multimèdia. La decisió per part de 3GPP de seleccionar protocols estàndards definits per IETF ha representat una fita cabdal per a la convergència del sistemes All-IP fixes i mòbils, i per al desenvolupament de xarxes NGN (Next Generation Networks) en general. En aquest context, el nostre objectiu inicial ha estat analitzar com aquests protocols de senyalització multimèdia, dissenyats per a xarxes IP genèriques, es comporten sobre xarxes mòbils 3GPP. Efectivament, l’ús de protocols IP és fonamental de cara a facilitar la interoperabilitat de solucions diferents. Per altra banda, hi ha escenaris a on és possible aprofitar informació de “context” addicional per a millorar el comportament d’aquests protocols en al cas particular de xarxes mòbils. El cos principal del treball de la tesi ha consistit en l’anàlisi i optimització del rendiment dels protocols de senyalització multimèdia SIP i RTSP, i la definició d’arquitectures de desplegament, amb èmfasi en els serveis 3GPP PSS i 3GPP Mission Critical Push-to-Talk (MCPTT). Aquest treball ha estat precedit per una feina d’anàlisi detallada del comportament dels protocols IP, TCP i UDP sobre xarxes 3GPP, que va proporcionar els fonaments adequats per a la posterior tasca d’anàlisi de protocols de senyalització sobre xarxes mòbils. Les contribucions inclouen la proposta de noves optimitzacions per a millorar els procediments d’establiment de sessions de streaming multimèdia, l’anàlisi detallat i optimització del servei de Presència basat en SIP i la definició de nous casos d’ús i exemples de desplegament d’arquitectures optimitzades per al servei 3GPP MCPTT. Aquestes contribucions ha quedat reflectides en un llibre, tres articles publicats en Revistes Internacionals amb índex JCR, 5 articles publicats en Conferències Internacionals, un article publicat en Congrés Nacional i l’adjudicació d’una patent. La tesi proporciona una descripció detallada de totes les contribucions, així com un exhaustiu repàs del seu context, dels principis fonamentals subjacents a totes les contribucions, la seva aplicabilitat a diferents tipus de desplegaments de xarxa (des de 2.5G a 5G), així una presentació detallada de les arquitectures associades definides per organismes com OMA o 3GPP. Finalment també es presenta l’evolució potencial de la tasca de recerca cap a sistemes 5G.Postprint (published version

Methods and design issues for next generation network-aware applications

Networks are becoming an essential component of modern cyberinfrastructure and this work describes methods of designing distributed applications for high-speed networks to improve application scalability, performance and capabilities. As the amount of data generated by scientific applications continues to grow, to be able to handle and process it, applications should be designed to use parallel, distributed resources and high-speed networks. For scalable application design developers should move away from the current component-based approach and implement instead an integrated, non-layered architecture where applications can use specialized low-level interfaces. The main focus of this research is on interactive, collaborative visualization of large datasets. This work describes how a visualization application can be improved through using distributed resources and high-speed network links to interactively visualize tens of gigabytes of data and handle terabyte datasets while maintaining high quality. The application supports interactive frame rates, high resolution, collaborative visualization and sustains remote I/O bandwidths of several Gbps (up to 30 times faster than local I/O). Motivated by the distributed visualization application, this work also researches remote data access systems. Because wide-area networks may have a high latency, the remote I/O system uses an architecture that effectively hides latency. Five remote data access architectures are analyzed and the results show that an architecture that combines bulk and pipeline processing is the best solution for high-throughput remote data access. The resulting system, also supporting high-speed transport protocols and configurable remote operations, is up to 400 times faster than a comparable existing remote data access system. Transport protocols are compared to understand which protocol can best utilize high-speed network connections, concluding that a rate-based protocol is the best solution, being 8 times faster than standard TCP. An HD-based remote teaching application experiment is conducted, illustrating the potential of network-aware applications in a production environment. Future research areas are presented, with emphasis on network-aware optimization, execution and deployment scenarios

FPGA acceleration of sequence analysis tools in bioinformatics

Thesis (Ph.D.)--Boston UniversityWith advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of thousands of lines of code and a large number of heuristics. Our idea is to emulate the main phases of its algorithm on FPGA. Utilizing our FPGA engine, we quickly reduce the size of the database to a small fraction, and then use the original code to process the query. Using a standard FPGA-based system, we achieved 12x speedup over a highly optimized multithread reference code. Multiple Sequence Alignment (MSA)--the extension of pairwise Sequence Alignment to multiple Sequences--is critical to solve many biological problems. Previous attempts to accelerate Clustal-W, the most commonly used MSA code, have directly mapped a portion of the code to the FPGA. We use a new approach: we apply prefiltering of the kind commonly used in BLAST to perform the initial all-pairs alignments. This results in a speedup of from 8Ox to 190x over the CPU code (8 cores). The quality is comparable to the original according to a commonly used benchmark suite evaluated with respect to multiple distance metrics. The challenge in FPGA-based acceleration is finding a suitable application mapping. Unfortunately many software heuristics do not fall into this category and so other methods must be applied. One is restructuring: an entirely new algorithm is applied. Another is to analyze application utilization and develop accuracy/performance tradeoffs. Using our prefiltering approach and novel FPGA programming models we have achieved significant speedup over reference programs. We have applied approximation, seeding, and filtering to this end. The bulk of this study is to introduce the pros and cons of these acceleration models for biosequence analysis tools

Adaptive Media Streaming to Mobile Devices: Challenges, Enhancements, and Recommendations

Video streaming is predicted to become the dominating traffic in mobile broadband networks. At the same time, adaptive HTTP streaming is developing into the preferred way of streaming media over the Internet. In this paper, we evaluate how different components of a streaming system can be optimized when serving content to mobile devices in particular. We first analyze the media traffic from a Norwegian network and media provider. Based on our findings, we outline benefits and challenges for HTTP streaming, on the sender and the receiver side, and we investigate how HTTP-based streaming affects server performance. Furthermore, we discuss various aspects of efficient coding of the video segments from both performance and user perception point of view. The final part of the paper studies efficient adaptation and delivery to mobile devices over wireless networks. We experimentally evaluate and improve adaptation strategies, multilink solutions, and bandwidth prediction techniques. Based on the results from our evaluations, we make recommendations for how an adaptive streaming system should handle mobile devices. Small changes, or simple awareness of how users perceive quality, can often have large effects