The last 20 years have seen enormous progress in the design of algorithms, but very little of it has been put into practice, even within academia; indeed, the gap between theory and practice has continuously widened over these years. Moreover, many of the recently developed algorithms are very hard to characterize theoretically and, as initially described, suffer from large running-time coefficients. Thus the algorithms and data structures community needs to return to implementation as the standard of value; we call such an approach Experimental Algorithmics. Experimental Algorithmics studies algorithms and data structures by joining experimental studies with the more traditional theoretical analyses. Experimentation with algorithms and data structures is proving indispensable in the assessment of heuristics for hard problems, in the design of test cases, in the characterization of asymptotic behavior of complex algorithms, in the comparison of competing designs for tractabl...

Our study in this paper focuses on implementing parallel spanning tree algorithms on SMPs. Spanning tree is an important problem in the sense that it is the building block for many other parallel graph algorithms and also because it is representative of a large class of irregular combinatorial problems that have simple and efficient sequential implementations and fast PRAM algorithms, but often have no known efficient parallel implementations. In this paper we present a new randomized algorithm and implementation with superior performance that for the first-time achieves parallel speedup on arbitrary graphs (both regular and irregular topologies) when compared with the best sequential implementation for finding a spanning tree. This new algorithm uses several techniques to give an expected running time that scales linearly with the number p of processors for suitably large inputs (n> p 2). As the spanning tree problem is notoriously hard for any parallel implementation to achieve reasonable speedup, our study may shed new light on implementing PRAM algorithms for shared-memory parallel computers. The main results of this paper are 1. A new and practical spanning tree algorithm for symmetric multiprocessors that exhibits parallel speedups on graphs with regular and irregular topologies; and 2. An experimental study of parallel spanning tree algorithms that reveals the superior performance of our new approach compared with the previous algorithms. The source code for these algorithms is freely-available from our web site hpc.ece.unm.edu.

A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool in biological, pharmaceutical, and medical research. Phylogeny reconstruction from molecular data is very difficult: almost all optimization models give rise to NP-hard (and thus computationally intractable) problems. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms, as well as help designers produce better algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a speedup in running time by over eight orders of magnitude over the original implementation on a variety of real and simulated datasets. We show how these algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.

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We study parallel algorithms for computing the minimum spanning tree of a weighted undirected graph G with n vertices and m edges. We consider an input graph G with m=n p, where p is the number of processors. For this case, we show that simple algorithms with dataindependent communication patterns are efficient, both in theory and in practice. The algorithms are evaluated theoretically using Valiant's BSP model of parallel computation and empirically through implementation results.

Abstract We develop an external memory algorithm for computing minimum spanning trees. The algorithm is considerably simpler than previously known external memory algorithms for this problem and needs a factor of at least four less I/Os for realistic inputs. Our implementation indicates that this algorithm processes graphs only limited by the disk capacity of most current machines in time no more than a factor 2–5 of a good internal algorithm with sufficient memory space.

this paper, we focus on one such: the integer sorting algorithm least signicant bit (LSB) radix sort. LSB radix sort sorts w-bit integer keys with an r-bit radix in O(dw=re(n+2

We evaluate the practical eciency of a new shortest path algorithm for undirected graphs which was developed by the rst two authors. This algorithm works on the fundamental comparison-addition model.

We study the eects of caches on basic graph and hashing algorithms and show how cache eects inuence the best solutions to these problems. We study the performance of basic data structures for storing lists of values and use these results to design and evaluate algorithms for hashing, Breadth-First-Search (BFS) and Depth-First-Search (DFS).

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