Gpu Parallelization Of Algebraic Dynamic Programming
PPAM'09: Proceedings of the 8th international conference on Parallel processing and applied mathematics: Part II（2010）
摘要
Algebraic Dynamic Programming (ADP) is a framework to encode a broad range of optimization problems, including common bioinformatics problems like RNA folding or pairwise sequence alignment The ADP complier translates such ADP programs into C As all the ADP problems have similar data dependencies in the dynamic programming tables a genetic parallelization is possible We updated the compiler to include a parallel backend launching a large number of independent threads Depending on the application, we report speedups ranging from 6.1 x to 25.8 x on a Nvidia GTX 280 through the CUDA libraries
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关键词
ADP compiler,ADP problem,ADP program,Algebraic Dynamic Programming,CUDA library,Nvidia GTX,RNA folding,broad range,common bioinformatics problem,dynamic programming table,GPU parallelization,algebraic dynamic programming
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