PZLAST: an ultra-fast sequence similarity search tool implemented on a MIMD processor

Abstract

We have developed an ultra-fast sequence similarity search tool named PZLAST on a MIMD processor PEZY-SC2. In this paper, we show the merit of MIMD features in reducing the load imbalance among the threads. They are also effective in the implementation of the alignment for long sequences. Additionally, we point out two problems related to the implementation on an ultra-parallel computation accelerator as follows: (1) Deciding the optimal amount of inputs prior to the run is extremely difficult and usually even impossible, and (2) Keeping up the parallelism efficiently throughout the whole computation is not always possible. A feedback strategy and an accumulation strategy are proposed to overcome these problems and their results are shown to be valuable in reducing the accidental memory overflow in runtime and speeding up the processing time.