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

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. Additional...

Full description

Saved in:
Bibliographic Details
Published inInternational Journal of Networking and Computing Vol. 12; no. 2; pp. 446 - 466
Main Authors Ishikawa, Hitoshi, Mori, Hiroshi, Higashi, Koichi, Kato, Yoshiaki, Sakai, Tomofumi, Ebisuzaki, Toshikazu, Kurokawa, Ken
Format Journal Article
LanguageEnglish
Published IJNC Editorial Committee 2022
Subjects
BLAST
CLAST
MIMD Processor
PEZY-SC
PEZY-SC2
PZLAST
Sequence Similarity Search Tool
Online AccessGet full text

Cover

More Information
Summary: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.
ISSN:2185-2839
2185-2847
DOI:10.15803/ijnc.12.2_446