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» Patterns for programming in parallel, pedagogically
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IPPS
2009
IEEE
14 years 2 months ago
Dynamic parallelization for RNA structure comparison
In this paper we describe the parallelization of a dynamic programming algorithm used to find common RNA secondary structures including pseudoknots and similar structures. The se...
Eric Snow, Eric Aubanel, Patricia Evans
HIPC
2000
Springer
13 years 11 months ago
Meta-data Management System for High-Performance Large-Scale Scientific Data Access
Many scientific applications manipulate large amount of data and, therefore, are parallelized on high-performance computing systems to take advantage of their computational power a...
Wei-keng Liao, Xiaohui Shen, Alok N. Choudhary
SC
2003
ACM
14 years 20 days ago
Fast Parallel Non-Contiguous File Access
Many applications of parallel I/O perform non-contiguous file accesses: instead of accessing a single (large) block of data in a file, a number of (smaller) blocks of data scatt...
Joachim Worringen, Jesper Larsson Träff, Hube...
CGO
2004
IEEE
13 years 11 months ago
Custom Data Layout for Memory Parallelism
In this paper, we describe a generalized approach to deriving a custom data layout in multiple memory banks for array-based computations, to facilitate high-bandwidth parallel mem...
Byoungro So, Mary W. Hall, Heidi E. Ziegler
ALGORITHMICA
2005
195views more  ALGORITHMICA 2005»
13 years 7 months ago
Bit-Parallel Witnesses and Their Applications to Approximate String Matching
We present a new bit-parallel technique for approximate string matching. We build on two previous techniques. The first one, BPM [Myers, J. of the ACM, 1999], searches for a patte...
Heikki Hyyrö, Gonzalo Navarro