Methods to Improve Applicability and Efficiency of Distributed Data-Centric Compute Frameworks

The success of modern applications depends on the insights they collect from their data repositories. Data repositories for such applications currently exceed exabytes and are rapidly increasing in size, as they collect data from varied sources - web applications, mobile phones, sensors and other connected devices. Distributed storage and data-centric compute frameworks have been invented to store and analyze these large datasets. This dissertation focuses on extending the applicability and improving the efficiency of distributed data-centric compute frameworks

2013 Doctoral Workshop on Distributed Systems

The Doctoral Workshop on Distributed Systems was held at Les Plans-sur-Bex, Switzerland, from June 26-28, 2013. Ph.D. students from the Universities of Neuchâtel and Bern as well as the University of Applied Sciences of Fribourg presented their current research work and discussed recent research results. This technical report includes the extended abstracts of the talks given during the workshop

Understanding the characteristics of Internet traffic and designing an efficient RaptorQ-based data transport protocol for modern data centres

This thesis is the amalgamation of research on efficient data transport protocols for data centres and a comprehensive and systematic study of Internet traffic, which came as a result of the need to understand traffic patterns and workloads in modern computer networks. The first part of the thesis is on the development of efficient data transport pro- tocols for data centres. We study modern data transport protocols for data centres through large scale simulations using the OMNeT++ simulator. We developed and experimented with an OMNeT++ model of NDP. This has led to the identification of limitations of the state of the art and the formulation of research questions with respect to data transport protocols for modern data centres. The developed model includes an implementation of a Fat-tree topology and per-packet ECMP load bal- ancing. We discuss how we integrated the model with the INET Framework and validated it by running various experiments that test different model parameters and components. This work revealed limitations of NDP with respect to efficient one-to-many and many-to-one communication in data centres, which led to the de- velopment of SCDP, a novel and general-purpose data transport protocol for data centres that, in contrast to all other protocols proposed to date, natively supports one-to-many and many-to-one data communication, which is extremely common in modern data centres. SCDP does so without compromising on efficiency for short and long unicast flows. SCDP achieves this by integrating RaptorQ codes with receiver-driven data transport, in-network packet trimming and Multi-Level Feed- back Queuing (MLFQ); (1) RaptorQ codes enable efficient one-to-many and many- to-one data transport; (2) on top of RaptorQ codes, receiver- driven flow control, in combination with in-network packet trimming, enable efficient usage of network re- sources as well as multi-path transport and packet spraying for all transport modes. Incast and Outcast are eliminated; (3) the systematic nature of RaptorQ codes, in combination with MLFQ, enable fast, decoding-free completion of short flows. We extensively evaluated SCDP in a wide range of simulated scenarios with realistic data centre workloads. For one-to-many and many-to-one transport sessions, SCDP performs significantly better than NDP. For short and long unicast flows, SCDP performs equally well or better compared to NDP. In the second part of the thesis, we extensively study Internet traffic. Getting good statistical models of traffic on network links is a well-known, often-studied problem. A lot of attention has been given to correlation patterns and flow duration. The distribution of the amount of traffic per unit time is an equally important but less studied problem. We study a large number of traffic traces from many different networks including academic, commercial and residential networks using state-of-the-art statistical techniques. We show that the log-normal distribution is a better fit than the Gaussian distribution. We also investigate a second, heavy- tailed distribution and show that its performance is better than Gaussian but worse than log-normal. We examine anomalous traces which are a poor fit for all tested distributions and show that this is often due to traffic outages or links that hit maximum capacity. Stationarity tests showed that the traffic is stationary at some range of aggregation times. We demonstrate the utility of the log-normal distribution in two contexts: predicting the proportion of time traffic will exceed a given level (for link capacity estimation) and predicting 95th percentile pricing. We also show the log-normal distribution is a better predictor than Gaussian orWeibull distributions

Matching distributed file systems with application workloads

Modern storage systems have a large number of configurable parameters, distributed over many layers of abstraction. The number of combinations of these parameters, that can be altered to create an instance of such a system, is enormous. In practise, many of these parameters are never altered; instead default values, intended to support generic workloads and access patterns, are used. As systems become larger and evolve to support different workloads, the appropriateness of using default parameters in this way comes into question. This thesis examines the implications of changing some of these parameters and explores the effects these changes have on performance. As part of that work multiple contributions have been made, including the creation of a structured method to create and evaluate different storage configurations, choosing appropriate access sizes for the evaluation, picking representative cloud workloads and capturing storage traces for further analysis, extraction of the workload storage characteristics, creating logical partitions of the distributed file system used for the optimization, the creation of heterogeneous storage pools within the homogeneous system and the mapping and evaluation of the chosen workloads to the examined configurations

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward