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GPUs devices are becoming critical building blocks of High-Performance platforms for performance and energy efficiency reasons. As a consequence, parallel programming environment such as OpenMP were extended to support offloading code to such devices. OpenMP compilers are faced with offering an efficient implementation of device-targeting constructs.One main issue in implementing OpenMP on a GPU is...
RNA folding is a compute-intensive task that lies at the core of search applications in bioinformatics such as RNAfold and UNAFold. In this work, we analyze the Zuker RNA folding algorithm, which is challenging to accelerate because it is resource intensive and has a large number of variable-length dependencies. We use a technique of Lyngso to rewrite the recurrence in a form that makes polyhedral...
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