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Engineering a cacheoblivious sorting algorithm
 In Proc. 6th Workshop on Algorithm Engineering and Experiments
, 2004
"... The cacheoblivious model of computation is a twolevel memory model with the assumption that the parameters of the model are unknown to the algorithms. A consequence of this assumption is that an algorithm efficient in the cache oblivious model is automatically efficient in a multilevel memory mod ..."
Abstract

Cited by 23 (1 self)
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The cacheoblivious model of computation is a twolevel memory model with the assumption that the parameters of the model are unknown to the algorithms. A consequence of this assumption is that an algorithm efficient in the cache oblivious model is automatically efficient in a multilevel memory model. Since the introduction of the cacheoblivious model by Frigo et al. in 1999, a number of algorithms and data structures in the model has been proposed and analyzed. However, less attention has been given to whether the nice theoretical proporities of cacheoblivious algorithms carry over into practice. This paper is an algorithmic engineering study of cacheoblivious sorting. We investigate a number of implementation issues and parameters choices for the cacheoblivious sorting algorithm Lazy Funnelsort by empirical methods, and compare the final algorithm with Quicksort, the established standard for comparison based sorting, as well as with recent cacheaware proposals. The main result is a carefully implemented cacheoblivious sorting algorithm, which we compare to the best implementation of Quicksort we can find, and find that it competes very well for input residing in RAM, and outperforms Quicksort for input on disk. 1
Cacheoblivious algorithms and data structures
 IN SWAT
, 2004
"... Frigo, Leiserson, Prokop and Ramachandran in 1999 introduced the idealcache model as a formal model of computation for developing algorithms in environments with multiple levels of caching, and coined the terminology of cacheoblivious algorithms. Cacheoblivious algorithms are described as stand ..."
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Cited by 8 (1 self)
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Frigo, Leiserson, Prokop and Ramachandran in 1999 introduced the idealcache model as a formal model of computation for developing algorithms in environments with multiple levels of caching, and coined the terminology of cacheoblivious algorithms. Cacheoblivious algorithms are described as standard RAM algorithms with only one memory level, i.e. without any knowledge about memory hierarchies, but are analyzed in the twolevel I/O model of Aggarwal and Vitter for an arbitrary memory and block size and an optimal offline cache replacement strategy. The result are algorithms that automatically apply to multilevel memory hierarchies. This paper gives an overview of the results achieved on cacheoblivious algorithms and data structures since the seminal paper by Frigo et al.
A Novel InPlace Sorting Algorithm with O(n log z) Comparisons and O(n log z) Moves
, 2006
"... Abstract—Inplace sorting algorithms play an important role in many fields such as very large database systems, data warehouses, data mining, etc. Such algorithms maximize the size of data that can be processed in main memory without input/output operations. In this paper, a novel inplace sorting a ..."
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Abstract—Inplace sorting algorithms play an important role in many fields such as very large database systems, data warehouses, data mining, etc. Such algorithms maximize the size of data that can be processed in main memory without input/output operations. In this paper, a novel inplace sorting algorithm is presented. The algorithm comprises two phases; rearranging the input unsorted array in place, resulting segments that are ordered relative to each other but whose elements are yet to be sorted. The first phase requires linear time, while, in the second phase, elements of each segment are sorted inplace in the order of z log (z), where z is the size of the segment, and O(1) auxiliary storage. The algorithm performs, in the worst case, for an array of size n, an O(n log z) element comparisons and O(n log z) element moves. Further, no auxiliary arithmetic operations with indices are required. Besides these theoretical achievements of this algorithm, it is of practical interest, because of its simplicity. Experimental results also show that it outperforms other inplace sorting algorithms. Finally, the analysis of time and space complexity, and required number of moves are presented, along with the auxiliary storage requirements of the proposed algorithm. Keywords—Auxiliary storage sorting, inplace sorting, sorting. I.
Masking Patterns in Sequences: A New Class of Motif Discovery with Don’t Cares
, 2009
"... In this paper, we introduce a new notion of motifs, called masks, that succinctly represent the repeated patterns for an input sequence T of n symbols drawn from an alphabet Σ. We show how to build the set of all maximal masks of length L and quorum q, in O(2 L n) time and space in the worst case. W ..."
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In this paper, we introduce a new notion of motifs, called masks, that succinctly represent the repeated patterns for an input sequence T of n symbols drawn from an alphabet Σ. We show how to build the set of all maximal masks of length L and quorum q, in O(2 L n) time and space in the worst case. We analytically show that our algorithms perform better than constanttime enumerating and checking all the potential (Σ  + 1) L candidate patterns in T after a polynomialtime preprocessing of T. Our algorithms are also cachefriendly, attaining O(2 L sort(n)) block transfers, where sort(n) is the cache oblivious complexity of sorting n items. Key words: Motif inference, motifs with don’t care, motif partial order, motifs with masks. 1.