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PPOPP
2006
ACM
15 years 3 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
BIBE
2005
IEEE
126views Bioinformatics» more  BIBE 2005»
15 years 3 months ago
Highly Scalable and Accurate Seeds for Subsequence Alignment
We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic ...
Abhijit Pol, Tamer Kahveci
EMSOFT
2005
Springer
15 years 3 months ago
Optimizing inter-processor data locality on embedded chip multiprocessors
Recent research in embedded computing indicates that packing multiple processor cores on the same die is an effective way of utilizing the ever-increasing number of transistors. T...
Guilin Chen, Mahmut T. Kandemir
IWMM
2010
Springer
118views Hardware» more  IWMM 2010»
15 years 2 months ago
Speculative parallelization using state separation and multiple value prediction
With the availability of chip multiprocessor (CMP) and simultaneous multithreading (SMT) machines, extracting thread level parallelism from a sequential program has become crucial...
Chen Tian, Min Feng, Rajiv Gupta
IPPS
2010
IEEE
14 years 7 months ago
Optimization of linked list prefix computations on multithreaded GPUs using CUDA
We present a number of optimization techniques to compute prefix sums on linked lists and implement them on multithreaded GPUs using CUDA. Prefix computations on linked structures ...
Zheng Wei, Joseph JáJá