Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

ABSTRACT:

Background

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at

SUBMITTER: Palkowski M 

PROVIDER: S-EPMC5769393 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature