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Simple linear work suffix array construction
, 2003
"... Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more exp ..."
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Cited by 214 (6 self)
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Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more explicit structure. We narrow this gap between theory and practice with a simple lineartime construction algorithm for suffix arrays. The simplicity is demonstrated with a C++ implementation of 50 effective lines of code. The algorithm is called DC3, which stems from the central underlying concept of difference cover. This view leads to a generalized algorithm, DC, that allows a spaceefficient implementation and, moreover, supports the choice of a space–time tradeoff. For any v ∈ [1, √ n], it runs in O(vn) time using O(n / √ v) space in addition to the input string and the suffix array. We also present variants of the algorithm for several parallel and hierarchical memory models of computation. The algorithms for BSP and EREWPRAM models are asymptotically faster than all previous suffix tree or array construction algorithms.
CGMgraph/CGMlib: Implementing and Testing CGM Graph Algorithms on PC Clusters
 International Journal of High Performance Computing Applications
, 2003
"... In this paper, we present CGMgraph, the first integrated library of parallel graph methods for PCclu8(T9 based on CGM algo rithms. CGMgraph implements parallel methods for variou graph prob lems. Ou implementations of deterministic list ranking, Eu er tou con nected components, spanning forest, and ..."
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Cited by 25 (2 self)
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In this paper, we present CGMgraph, the first integrated library of parallel graph methods for PCclu8(T9 based on CGM algo rithms. CGMgraph implements parallel methods for variou graph prob lems. Ou implementations of deterministic list ranking, Eu er tou con nected components, spanning forest, and bipartite graph detection are, to ou r knowledge, the first e#cient implementations for PC clu sters.Ou library also inclu des CGMlib, a library of basic CGM tools su ch as sort ing, prefix su m, one to all broadcast, all to one gather, h Relation, all to all broadcast, array balancing, and CGM partitioning. Both libraries are available for download at http://cgm.dehne.net. 1
Solving Large FPT Problems On Coarse Grained Parallel Machines
"... Fixedparameter tractability(FPT) techniques have recently been successful in solving NPcomplete problem instances of practical importance which were too large to be solved with previous methods. In this paper we show how to enhance this approach through the addition of parallelism, thereby allowin ..."
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Cited by 22 (1 self)
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Fixedparameter tractability(FPT) techniques have recently been successful in solving NPcomplete problem instances of practical importance which were too large to be solved with previous methods. In this paper we show how to enhance this approach through the addition of parallelism, thereby allowing even larger problem instances to be solved in practice. More precisely, we demonstrate the potential of parallelism when applied to the bounded tree search phase of FPT algorithms. We apply our methodology to the kVertex Cover problem which has important applications, e.g., in multiple sequence alignments for computational biochemistry. We have implemented our parallel FPT method and application specific "plugin" code for the kVertex Cover problem using C and the MPI communication library, and tested it on a network of 10 Sun SPARC workstations. This is the first experimental examination of parallel FPT techniques. In our experiments, we obtain excellent speedup results. Not only do we achieve a speedup of p in most cases, many cases even exhibit a super linear speedup. The latter result implies that our parallel methods, when simulated on a single processor, also yield a significant improvement over existing sequential methods.
A CoarseGrained Multicomputer Algorithm for the Longest Repeated Suffix Ending at Each Point in a Word
 11TH EUROMICRO CONFERENCE ON PARALLEL DISTRIBUTED AND NETWORK BASED PROCESSING (PDP'03)
, 2003
"... The paper presents a CoarseGrained Multicomputer algorithm that solves the problem of finding the longest repeated su#x ending at each point in a word. This algorithm can be implemented in the CGM with P processors in O( )intimeandO(P ) communication steps. It is the first CGM algorithm fo ..."
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Cited by 8 (1 self)
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The paper presents a CoarseGrained Multicomputer algorithm that solves the problem of finding the longest repeated su#x ending at each point in a word. This algorithm can be implemented in the CGM with P processors in O( )intimeandO(P ) communication steps. It is the first CGM algorithm for this problem. We present also experimental results showing that the CGM algorithm is very e#cient.
CoarseGrained Parallel Geometric Search
 Journal of Parallel and Distributed Computing
, 1999
"... This paper improves on op. cit. in several ways: (1) It studies the more general next element search problem which also solves, e.g., planar point location. (2) The algorithms require only O((n#p) log n) local computation instead of O(log p*(n#p) log n). (3) The algorithms require only O((n#p) l ..."
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Cited by 4 (1 self)
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This paper improves on op. cit. in several ways: (1) It studies the more general next element search problem which also solves, e.g., planar point location. (2) The algorithms require only O((n#p) log n) local computation instead of O(log p*(n#p) log n). (3) The algorithms require only O((n#p) log p) local memory instead of O((n#p) log n)
Parallel suffix array construction by accelerated sampling
"... Abstract. A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique that we call accelerated sampling. It runs in optimal O(n p) local computation and communication, and requires a near optimal O(log log p) supersteps. The algorithm provides ..."
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Cited by 1 (0 self)
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Abstract. A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique that we call accelerated sampling. It runs in optimal O(n p) local computation and communication, and requires a near optimal O(log log p) supersteps. The algorithm provides an improvement over the synchronisation costs of existing algorithms, and reinforces the importance of the sampling technique.
Efficient parallel Text Retrieval techniques on Bulk Synchronous Parallel (BSP)/Coarse Grained
, 2008
"... Abstract In this paper, we present efficient, scalable, and portable parallel algorithms for the offline clustering, the online retrieval and the update phases of the Text Retrieval (TR) problem based on the vector space model and using clustering to organize and handle a dynamic document collect ..."
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Abstract In this paper, we present efficient, scalable, and portable parallel algorithms for the offline clustering, the online retrieval and the update phases of the Text Retrieval (TR) problem based on the vector space model and using clustering to organize and handle a dynamic document collection. The algorithms are running on the CoarseGrained Multicomputer (CGM) and/or the Bulk Synchronous Parallel (BSP) model which are two models that capture within a few parameters the characteristics of the parallel machine. To the best of our knowledge, our parallel retrieval algorithms are the first ones analyzed under these specific parallel models. For all the phases of the proposed algorithms, we analytically determine the relevant communication and computation cost thereby formally proving the efficiency of the proposed solutions. In addition, we prove that our technique for the online retrieval phase performs very well in comparison to other possible alternatives in the typical case of a multiuser information retrieval (IR) system where a number of user queries are concurrently submitted to an IR system. Finally, we discuss external memory issues and
Dynamic Creation of BSP/CGM Clusters on Cloud Computing Platforms
"... Abstract—Cloud computing platforms have the potential to benefit scientific projects on all fields of knowledge. Its virtualized resources and large storage capacity enable any scientist to have access to high performance computing platforms at low costs. In this paper, we present the MyCloud projec ..."
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Abstract—Cloud computing platforms have the potential to benefit scientific projects on all fields of knowledge. Its virtualized resources and large storage capacity enable any scientist to have access to high performance computing platforms at low costs. In this paper, we present the MyCloud project, a cloud computing infrastructure for the Technological University of Paraná campuses, in southern Brazil. We show how to build and instantiate virtual machines templates for BSP/CGM applications that can be used on private cloud computing platforms. Keywords—Bulk Synchronous Parallel; Coarse Grained Multicomputer; Virtual Machines; Cloud Computing.
ALGORITHMS ON PC CLUSTERS AND SHARED MEMORY MACHINES
"... In this paper, we present CGMgraph, the first integrated library of parallel graph methods for PC clusters based on Coarse Grained Multicomputer (CGM) algorithms. CGMgraph implements parallel methods for various graph problems. Our implementations of deterministic list ranking, Euler tour, connected ..."
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In this paper, we present CGMgraph, the first integrated library of parallel graph methods for PC clusters based on Coarse Grained Multicomputer (CGM) algorithms. CGMgraph implements parallel methods for various graph problems. Our implementations of deterministic list ranking, Euler tour, connected components, spanning forest, and bipartite graph detection are, to our knowledge, the first efficient implementations for PC clusters. Our library also includes CGMlib, a library of basic CGM tools such as sorting, prefix sum, onetoall broadcast, alltoone gather, hRelation, alltoall broadcast, array balancing, and CGM partitioning. Both libraries are available for download at