PZLAST: an ultra-fast sequence similarity search tool implemented on a MIMD processor
- Resource Type
- Conference
- Authors
- Ishikawa, H.; Mori, H.; Higashi, K.; Kato, Y.; Sakai, T.; Ebisuzaki, T.; Kurokawa, K.
- Source
- 2021 Ninth International Symposium on Computing and Networking (CANDAR) CANDAR Computing and Networking (CANDAR),2021 Ninth International Symposium on. :102-107 Nov, 2021
- Subject
- Computing and Processing
Runtime
Instruction sets
Parallel processing
Computational efficiency
Sequence Similarity Search Tool
MIMD Processor
PEZY-SC
PEZY-SC2
BLAST
CLAST
PZLAST
- Language
- ISSN
- 2379-1896
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. 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.