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» A Parallel Programming Style and Its Algebra of Programs
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IPPS
2003
IEEE
15 years 3 months ago
Sequence Alignment on the Cray MTA-2
The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigatio...
Shahid H. Bokhari, Jon R. Sauer
ASPLOS
2010
ACM
15 years 4 months ago
COMPASS: a programmable data prefetcher using idle GPU shaders
A traditional fixed-function graphics accelerator has evolved into a programmable general-purpose graphics processing unit over the last few years. These powerful computing cores...
Dong Hyuk Woo, Hsien-Hsin S. Lee
PVM
1998
Springer
15 years 2 months ago
SKaMPI: A Detailed, Accurate MPI Benchmark
Abstract. SKaMPI is a benchmark for MPI implementations. Its purpose is the detailed analysis of the runtime of individual MPI operations and comparison of these for di erent imple...
Ralf Reussner, Peter Sanders, Lutz Prechelt, Matth...
IPPS
2010
IEEE
14 years 7 months ago
Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs
The Coarse-Grained Monte Carlo (CGMC) method is a multi-scale stochastic mathematical and simulation framework for spatially distributed systems. CGMC simulations are important too...
Lifan Xu, Michela Taufer, Stuart Collins, Dionisio...
ICPP
2006
IEEE
15 years 3 months ago
A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction
RNA pseudoknot prediction is an algorithm for RNA sequence search and alignment. An important building block towards pseudoknot prediction is RNA secondary structure prediction. T...
Wenduo Zhou, David K. Lowenthal