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IPPS
2009
IEEE
10 years 1 months ago
Using hardware transactional memory for data race detection
Abstract—Widespread emergence of multicore processors will spur development of parallel applications, exposing programmers to degrees of hardware concurrency hitherto unavailable...
Shantanu Gupta, Florin Sultan, Srihari Cadambi, Fr...
IPPS
2009
IEEE
10 years 1 months ago
Minimizing startup costs for performance-critical threading
—Using the well-known ATLAS and LAPACK dense linear algebra libraries, we demonstrate that the parallel management overhead (PMO) can grow with problem size on even statically sc...
Anthony M. Castaldo, R. Clint Whaley
IPPS
2009
IEEE
10 years 1 months ago
Annotation-based empirical performance tuning using Orio
In many scientific applications, significant time is spent tuning codes for a particular highperformance architecture. Tuning approaches range from the relatively nonintrusive (...
Albert Hartono, Boyana Norris, Ponnuswamy Sadayapp...
IPPS
2009
IEEE
10 years 1 months ago
Uniform scattering of autonomous mobile robots in a grid
Lali Barrière, Paola Flocchini, Eduardo Mes...
IPPS
2009
IEEE
10 years 1 months ago
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA
Computing large multiple protein sequence alignments using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. ClustalW uses a th...
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
IPPS
2009
IEEE
10 years 1 months ago
Multi-dimensional characterization of temporal data mining on graphics processors
Through the algorthmic design patterns of data parallelism and task parallelism, the graphics processing unit (GPU) offers the potential to vastly accelerate discovery and innovat...
Jeremy S. Archuleta, Yong Cao, Thomas Scogland, Wu...
IPPS
2009
IEEE
10 years 1 months ago
Accelerating HMMer on FPGAs using systolic array based architecture
HMMer is a widely-used bioinformatics software package that uses profile HMMs (Hidden Markov Models) to model the primary structure consensus of a family of protein or nucleic aci...
Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan ...
IPPS
2009
IEEE
10 years 1 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
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