Charles E. Leiserson

Bio: Charles E. Leiserson is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Cilk & Scheduling (computing). The author has an hindex of 65, co-authored 185 publications receiving 49312 citations. Previous affiliations of Charles E. Leiserson include Vassar College & Carnegie Mellon University.

Memory-mapping support for reducer hyperobjects

Abstract: Reducer hyperobjects (reducers) provide a linguistic abstraction for dynamic multithreading that allows different branches of a parallel program to maintain coordinated local views of the same nonlocal variable. In this paper, we investigate how thread-local memory mapping (TLMM) can be used to improve the performance of reducers. Existing concurrency platforms that support reducer hyperobjects, such as Intel Cilk Plus and Cilk++, take a hypermap approach in which a hash table is used to map reducer objects to their local views. The overhead of the hash table is costly --- roughly 12x overhead compared to a normal L1-cache memory access on an AMD Opteron 8354. We replaced the Intel Cilk Plus runtime system with our own Cilk-M runtime system which uses TLMM to implement a reducer mechanism that supports a reducer lookup using only two memory accesses and a predictable branch, which is roughly a 3x overhead compared to an ordinary L1-cache memory access. An empirical evaluation shows that the Cilk-M memory-mapping approach is close to 4x faster than the Cilk Plus hypermap approach. Furthermore, the memory-mapping approach admits better locality than the hypermap approach during parallel execution, which allows an application using reducers to scale better.

VLSI theory and parallel supercomputing

Abstract: : Since its inception, VLSI theory has expanded in many fruitful and interesting directions. One major branch is layout theory which studies the efficiency with which graphs can be embedded in the plane according to VLSI design rules. In this survey paper, I review some of the major accomplishments of VLSI layout theory and discuss how layout theory engendered the notion of area and volume-universal networks, such as fat-trees. These scalable networks offer a flexible alternative to the more common hypercube-based networks for inter-connecting the processors of large parallel supercomputers. Keywords: Integrated circuits; Interconnection networks; Parallel computing; Super-computing; Universality; Thompson's model; Tree of meshes.

Parallel computer system including arrangement for quickly draining messages from message router

Abstract: A computer including a processor array and a routing network. Processors in the processor array generate messages for transfer to over the routing network, each message including a path identifier portion identifying a path from a source, message processor to a destination processor. The routing network comprises a plurality of interconnected router nodes, at least some of said router nodes being connected to the processors to receive messages therefrom and transmit messages thereto. Each router node operates in a plurality of modes. In a first mode, the router nodes couple received messages to a router node connected thereto in accordance with the path identifier portion to thereby transfer each respective message along the path identified in its path identifier portion. In a second mode, the router node couple received messages to predetermined ones of the router nodes or processors connected thereto, the predetermined ones of said router nodes or processors being selected to facilitate transfer of a message to a nearby processor to facilitate the rapid emptying of the routing network of messages. A control element controls the router nodes to enable them to operate in the first mode or second mode generally contemporaneously.

The monge array: an abstraction and its applications

Abstract: This thesis develops a body of versatile algorithmic techniques. We demonstrate the power and generality of these techniques by applying them to a wide variety of problems. These problems are drawn from such diverse areas of study as computational geometry, VLSI theory, operations research, and molecular biology. The algorithmic techniques described in this thesis are centered around a family of highlystructured arrays known as Monge arrays. An m x n array A = {a[i,j]} is called Monge if a[i,j] + a[k, < a[i, + a[k,j] for all i, j, k, and I such that 1 < i < k < m and 1 < j < e < n. We will show that Monge arrays capture the essential structure of many practical problems, in the sense that algorithms for searching in the abstract world of Monge arrays can be used to obtain efficient algorithms for these practical problems. The first part of this thesis describes the basic Monge-array abstraction. We begin by defining several different types of Monge and Monge-like arrays. These definitions include a generalization of the notion of two-dimensional Monge arrays to higher-dimensional arrays. We also present several important properties of Monge and Monge-like arrays and introduce a computational framework for manipulating such arrays. We then develop a variety of algorithms for searching in Monge arrays. In particular, we give efficient sequential and parallel (PRAM) algorithms for computing minimal entries in Monge arrays and efficient sequential algorithms for selection and sorting in Monge arrays. Highlights include an O(dn lgd2 n)-time sequential algorithm for computing the minimum entry in an n x n x . -x n d-dimensional Monge array, an O(n3/2lg 2 n)-time sequential algorithm for computing the median entry in each row of an n x n two-dimensional Monge array, and an optimal O(lg n)-time, (n2 / lg n)-processor CREWPRAM algorithm for computing the minimum entry in each 1 x n x 1 subarray of an n x n x n three-dimensional Monge array. The second part of this thesis investigates the diverse applications of the Monge-array abstraction. We first consider a number of geometric problem relating to convex polygons in the plane. Specifically, we use Monge-array techniques to develop efficient algorithms for several proximity problems involving the vertices of a convex polygon, as well as the maximumperimeter-inscribed-k-gon problem and the minimum-area-circumscribing-k-gon problem. We

Handbook of Applied Cryptography

Abstract: From the Publisher: A valuable reference for the novice as well as for the expert who needs a wider scope of coverage within the area of cryptography, this book provides easy and rapid access of information and includes more than 200 algorithms and protocols; more than 200 tables and figures; more than 1,000 numbered definitions, facts, examples, notes, and remarks; and over 1,250 significant references, including brief comments on each paper.

ROUGE: A Package for Automatic Evaluation of Summaries

Abstract: ROUGE stands for Recall-Oriented Understudy for Gisting Evaluation. It includes measures to automatically determine the quality of a summary by comparing it to other (ideal) summaries created by humans. The measures count the number of overlapping units such as n-gram, word sequences, and word pairs between the computer-generated summary to be evaluated and the ideal summaries created by humans. This paper introduces four different ROUGE measures: ROUGE-N, ROUGE-L, ROUGE-W, and ROUGE-S included in the ROUGE summarization evaluation package and their evaluations. Three of them have been used in the Document Understanding Conference (DUC) 2004, a large-scale summarization evaluation sponsored by NIST.

RADAR: an in-building RF-based user location and tracking system

Abstract: The proliferation of mobile computing devices and local-area wireless networks has fostered a growing interest in location-aware systems and services. In this paper we present RADAR, a radio-frequency (RF)-based system for locating and tracking users inside buildings. RADAR operates by recording and processing signal strength information at multiple base stations positioned to provide overlapping coverage in the area of interest. It combines empirical measurements with signal propagation modeling to determine user location and thereby enable location-aware services and applications. We present experimental results that demonstrate the ability of RADAR to estimate user location with a high degree of accuracy.

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Abstract: We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w1118; iso-2; iso-3 strain and the reference y1; cn1 bw1 sp1 strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in...