694204
Compiler Techniques for Concurrent Multithreading with Hardware Speculation Support
Recently proposed concurrent multithreading architectures employ sophisticated hardware to support speculation on control and data dependences as well as run-time data dependence check, which enables parallelization of program regions such as while-loops which previously were ignored. The new architectures demand compilers to put more emphasis on the formation and selection of parallel threads. Compilers also play an important role in reducing the cost of run-time data dependence check. This paper discusses these new issues.
31492830
On Reducing Data Synchronization in Multiprocessed Loops
In this correspondence we present and prove the correctness of an algorithm for reducing the number of synchronized memory references to shared data elements in multiprocessed loops. Optimizing compilers for shared memory multiprocessors can use this algorithm to reduce synchronization overhead. The algorithm has been implemented as a new module in the multiprocessors version of Parafrase, the restructuring system of the University of Illinois. We present a brief discussion of experiments we performed to asses the effectiveness of this algorithm in reducing the synchronization overhead for the 61 subroutines of EISPACK, a package for computing matrix eigenvectors and eigenvalues.
20563509
A theoretical foundation for program transformations to reduce cache thrashing due to true data sharing
Cache thrashing due to true data sharing can degrade the performance of parallel programs significantly. Our previous work showed that parallel task alignment via program transformations can be quite effective for the reduction of such cache thrashing. In this paper, we present a theoretical foundation for such program transformations. Based on linear algebra and the theory of numbers, our work analyzes the data dependences among the tasks created by a fork-join parallel program and determines at compile time how these tasks should be assigned to processors in order to reduce cache thrashing due to true data sharing. Our analysis and program transformations can be easily performed by compilers for parallel computers.
5807481
Compiler algorithms for event variable synchronization
Event variable synchronization is a well known mecha nism for enforcing data dependences in a program that runs in parallel on a shared memory multiprocessor This paper presents compiler algorithms to automati cally generate event variable synchronization code Pre viously published algorithms dealt with single parallel loops in which dependence distances are constant and known by the compiler However loops in real appli cation programs are often arbitrarily nested Moreover compilers are often unable to determine dependence dis tances In contrast our algorithms generate synchro nization code based directly on array subscripts and do not require constant distances in data dependences The algorithms are designed for arbitrarily nested loops in cluding triangular or trapezoidal loops
15170626
New tiling techniques to improve cache temporal locality
Tiling is a well-known loop transformation to improve temporal locality of nested loops. Current compiler algorithms for tiling are limited to loops which are perfectly nested or can be transformed, in trivial ways, into a perfect nest. This paper presents a number of program transformations to enable tiling for a class of nontrivial imperfectly-nested loops such that cache locality is improved. We define a program model for such loops and develop compiler algorithms for their tiling. We propose to adopt odd-even variable duplication to break anti- and output dependences without unduly increasing the working-set size, and to adopt speculative execution to enable tiling of loops which may terminate prematurely due to, e.g. convergence tests in iterative algorithms. We have implemented these techniques in a research compiler, Panorama. Initial experiments with several benchmark programs are performed on SGI workstations based on MIPS R5K and R10K processors. Overall, the transformed programs run faster by 9% to 164%.
833146
Experience in the Automatic Parallelization of Four Perfect-Benchmark Programs
This paper discusses the techniques used to hand-parallelize, for the Alliant FX/80, four Fortran programs from the Perfect-Benchmark suite. The paper also includes the execution times of the programs before and after the transformations. The four programs considered here were not effectively parallelized by the automatic translators available to the authors. However, most of the techniques used for hand parallelization, and perhaps all of them, have wide applicability and can be incorporated into existing translators.
5391500
A High-Throughput Overlay Multicast Infrastructure with Network Coding
Network coding has been recently proposed in information theory as a new dimension of the information multicast problem that helps achieve optimal transmission rate or cost. End hosts in overlay networks are natural candidates to perform network coding, due to its available computational capabilities. In this paper, we seek to bring theoretical advances in network coding to the practice of high-throughput multicast in overlay networks. We have completed the first real implementation of network coding in end hosts, as well as decentralized algorithms to construct the routing strategies and to perform random code assignment. Our experiences suggest that approaching maximum throughput with network coding is not only theoretically sound, but also practically promising. We also present a number of unique challenges in designing and realizing coded data dissemination, and corresponding solution techniques to address them.
10936659
Haplotype reconstruction from SNP fragments by minimum error correction
MOTIVATION
Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA.


RESULTS
In the first part of this paper, an exact algorithm for the MEC model is presented. Owing to the NP-hardness of the MEC model, we also design a genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown using experimental results on real data and simulation data. In the second part of this paper, to improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive datasets show that the new model has much higher accuracy in haplotype reconstruction than the pure MEC model.
14010825
C-Miner: Mining Block Correlations in Storage Systems
Block correlations are common semantic patterns in storage systems. These correlations can be exploited for improving the effectiveness of storage caching, prefetching, data layout and disk scheduling. Unfortunately, information about block correlations is not available at the storage system level. Previous approaches for discovering file correlations in file systems do not scale well enough to be used for discovering block correlations in storage systems. 
 
In this paper, we propose C-Miner, an algorithm which uses a data mining technique called frequent sequence mining to discover block correlations in storage systems. C-Miner runs reasonably fast with feasible space requirement, indicating that it is a practical tool for dynamically inferring correlations in a storage system. Moreover, we have also evaluated the benefits of block correlation-directed prefetching and data layout through experiments. Our results using real system workloads show that correlation-directed prefetching and data layout can reduce average I/O response time by 12-25% compared to the base case, and 7-20% compared to the commonly used sequential prefetching scheme.
566308
Reducing Energy Consumption of Disk Storage Using Power-Aware Cache Management
Reducing energy consumption is an important issue for data centers. Among the various components of a data center, storage is one of the biggest consumers of energy. Previous studies have shown that the average idle period for a server disk in a data center is very small compared to the time taken to spin down and spin up. This significantly limits the effectiveness of disk power management schemes. This paper proposes several power-aware storage cache management algorithms that provide more opportunities for the underlying disk power management schemes to save energy. More specifically, we present an off-line power-aware greedy algorithm that is more energy-efficient than Belady’s off-line algorithm (which minimizes cache misses only). We also propose an online power-aware cache replacement algorithm. Our trace-driven simulations show that, compared to LRU, our algorithm saves 16% more disk energy and provides 50% better average response time for OLTP I/O workloads. We have also investigated the effects of four storage cache write policies on disk energy consumption.
13022636
A Neural Model of Contour Integration in the Primary Visual Cortex
Experimental observations suggest that contour integration may take place in V1. However, there has yet to be a model of contour integration that uses only known V1 elements, operations, and connection patterns.This article introduces such a model, using orient ation selective cells, local cortical circuits, and horizontal intracortical connections. The model is composed of recurrently connected excitatory neurons and inhibitory interneurons, receiving visual input via oriented receptive fields resembling those found in primary visual cortex. Intracortical interactions modify initial activity patterns from input, selectively amplifying the activities of edges that form smooth contours in the image. The neural activities produced by such interactions are oscillatory and edge segments within a contour oscillate in synchrony. It is shown analytically and empirically that the extent of contour enhancement and neural synchrony increases with the smoothness, length, and closure of contours, as observed in experiments on some of these phenomena. In addition, the model incorporates a feedback mechanism that allows higher visual centers selectively to enhance or suppress sensitivities to given contours, effectively segmenting one from another. The model makes the testable prediction that the horizontal cortical connections are more likely to target excitatory (or inhibitory) cells when the two linked cells have their preferred orientation aligned with (or orthogonal to) their relative receptive field center displacements.