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» Reducing Parallel Overheads Through Dynamic Serialization
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BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
13 years 11 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
ISCA
1997
IEEE
90views Hardware» more  ISCA 1997»
13 years 9 months ago
The Interaction of Software Prefetching with ILP Processors in Shared-Memory Systems
Current microprocessors aggressively exploit instructionlevel parallelism (ILP) through techniques such as multiple issue, dynamic scheduling, and non-blocking reads. Recent work ...
Parthasarathy Ranganathan, Vijay S. Pai, Hazim Abd...
CF
2005
ACM
13 years 6 months ago
A case for a working-set-based memory hierarchy
Modern microprocessor designs continue to obtain impressive performance gains through increasing clock rates and advances in the parallelism obtained via micro-architecture design...
Steve Carr, Soner Önder
SCFBM
2008
92views more  SCFBM 2008»
13 years 4 months ago
CRANKITE: A fast polypeptide backbone conformation sampler
Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sample...
Alexei A. Podtelezhnikov, David L. Wild