Reducing main memory access latency through SDRAM address mapping techniques and access reordering mechanisms

As the performance gap between microprocessors and memory continues to increase, main memory accesses result in long latencies which become a factor limiting system performance. Previous studies show that main memory access streams contain significant localities and SDRAM devices provide parallelism through multiple banks and channels. These locality and parallelism have not been exploited thoroughly by conventional memory controllers. In this thesis, SDRAM address mapping techniques and memory access reordering mechanisms are studied and applied to memory controller design with the goal of reducing observed main memory access latency. The proposed bit-reversal address mapping attempts to distribute main memory accesses evenly in the SDRAM address space to enable bank parallelism. As memory accesses to unique banks are interleaved, the access latencies are partially hidden and therefore reduced. With the consideration of cache conflict misses, bit-reversal address mapping is able to direct potential row conflicts to different banks, further improving the performance. The proposed burst scheduling is a novel access reordering mechanism, which creates bursts by clustering accesses directed to the same rows of the same banks. Subjected to a threshold, reads are allowed to preempt writes and qualified writes are piggybacked at the end of the bursts. A sophisticated access scheduler selects accesses based on priorities and interleaves accesses to maximize the SDRAM data bus utilization. Consequentially burst scheduling reduces row conflict rate, increasing and exploiting the available row locality. Using a revised SimpleScalar and M5 simulator, both techniques are evaluated and compared with existing academic and industrial solutions. With SPEC CPU2000 benchmarks, bit-reversal reduces the execution time by 14% on average over traditional page interleaving address mapping. Burst scheduling also achieves a 15% reduction in execution time over conventional bank in order scheduling. Working constructively together, bit-reversal and burst scheduling successfully achieve a 19% speedup across simulated benchmarks

Algorithmic and Statistical Perspectives on Large-Scale Data Analysis

In recent years, ideas from statistics and scientific computing have begun to interact in increasingly sophisticated and fruitful ways with ideas from computer science and the theory of algorithms to aid in the development of improved worst-case algorithms that are useful for large-scale scientific and Internet data analysis problems. In this chapter, I will describe two recent examples---one having to do with selecting good columns or features from a (DNA Single Nucleotide Polymorphism) data matrix, and the other having to do with selecting good clusters or communities from a data graph (representing a social or information network)---that drew on ideas from both areas and that may serve as a model for exploiting complementary algorithmic and statistical perspectives in order to solve applied large-scale data analysis problems.Comment: 33 pages. To appear in Uwe Naumann and Olaf Schenk, editors, "Combinatorial Scientific Computing," Chapman and Hall/CRC Press, 201

Some common errors of experimental design, interpretation and inference in agreement studies

We signal and discuss common methodological errors in agreement studies and the use of kappa indices, as found in publications in the medical and behavioural sciences. Our analysis is based on a proposed statistical model that is in line with the typical models employed in metrology and measurement theory. A first cluster of errors is related to nonrandom sampling, which results in a potentially substantial bias in the estimated agreement. Second, when class prevalences are strongly nonuniform, the use of the kappa index becomes precarious, as its large partial derivatives result in typically large standard errors of the estimates. In addition, the index reflects rather one-sidedly in such cases the consistency of the most prevalent class, or the class prevalences themselves. A final cluster of errors concerns interpretation pitfalls, which may lead to incorrect conclusions based on agreement studies. These interpretation issues are clarified on the basis of the proposed statistical modelling. The signalled errors are illustrated from actual studies published in prestigious journals. The analysis results in a number of guidelines and recommendations for agreement studies, including the recommendation to use alternatives to the kappa index in certain situations

Disentangling the effects of selection and loss bias on gene dynamics

We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes

Lottery and stride scheduling : flexible proportional-share resource management

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1995.Includes bibliographical references (p. 145-151).by Carl A. Waldspurger.Ph.D

Quantifying coincidence in non-uniform time series with mutual graph approximation : speech and ECG examples

Compressive sensing and arbitrary sampling are techniques of data volume reduction challenging the Shannon sampling theorem and expected to provide efficient storage while preserving original information. Irregularity of sampling is either a result of intentional optimization of a sampling grid or stems from sporadic occurrence or intermittent observability of a phenomenon. Quantitative comparison of irregular patterns similarity is usually preceded by a projection to a regular sampling space. In this paper, we study methods for direct comparison of time series in their original non-uniform grids. We also propose a linear graph to be a representation of the non-uniform signal and apply the Mutual Graph Approximation (MGA) method as a metric to infer the degree of similarity of the considered patterns. The MGA was implemented together with four state-of-the-art methods and tested with example speech signals and electrocardiograms projected to bandwidth-related and random sampling grids. Our results show that the performance of the proposed MGA method is comparable to most accurate (correlation of 0.964 vs. Frechet: 0.962 and Kleinberg: 0.934 for speech signals) and to less computationally expensive state-of-the-art distance metrics (both MGA and Hausdorf: O(L$_{1}$ + L$_{2}$)). Moreover, direct comparison of non-uniform signals can be equivalent to cross-correlation of resampled signals (correlation of 0.964 vs. resampled: 0.960 for speech signals, and 0.956 vs. 0.966 for electrocardiograms) in applications as signal classification in both accuracy and computational complexity. Finally, the bandwidth-based resampling model plays a substantial role; usage of random grid is the primary cause of inaccuracy (correlation of 0.960 vs. for random sampling grid: 0.900 for speech signals, and 0.966 vs. 0.878, respectively, for electrocardiograms). These figures indicate that the proposed MGA method can be used as a simple yet effective tool for scoring similarity of signals directly in non-uniform sampling grids