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We propose a multilevel method to speed highly optimized parallel codes whose runtime increases faster than their workload. This method requires the ability to solve large in- stances by decomposing them into smaller instances. Using a simple parallel computing model, we derive a mathematical model that predicts whether or not our method can im- prove…

We consider the problem of aligning two very long biological sequences. The score for the best alignment may be found using the Smith-Waterman scoring algorithm while the best alignment itself may be determined using Myers and Miller’s alignment algorithm. Neither of these algorithms takes advantage of computer caches to obtain high efficiency. We propose cache-efficient…