Search results for "SW26010"
showing 3 items of 3 documents
Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer
2020
Molecular dynamics (MD) simulations are playing an increasingly important role in many research areas. Pair-wise potentials are widely used in MD simulations of bio-molecules, polymers, and nano-scale materials. Due to a low compute-to-memory-access ratio, their calculation is often bounded by memory transfer speeds. Sunway TaihuLight is one of the fastest supercomputers featuring a custom SW26010 many-core processor. Since the SW26010 has some critical limitations regarding main memory bandwidth and scratchpad memory size, it is considered as a good platform to investigate the optimization of pair-wise potentials especially in terms of data reusage. MD algorithms often use a neighbor-list …
S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light
2017
The availability and amount of sequenced genomes have been rapidly growing in recent years because of the adoption of next-generation sequencing (NGS) technologies that enable high-throughput short-read generation at highly competitive cost. Since this trend is expected to continue in the foreseeable future, the design and implementation of efficient and scalable NGS bioinformatics algorithms are important to research and industrial applications. In this paper, we introduce S-Aligner–a highly scalable read mapper designed for the Sunway Taihu Light supercomputer and its fourth-generationShenWei many-core architecture (SW26010). S-Aligner employs a combination of optimization techniques to o…
FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight
2022
Abstract One of the most important application in bioinformatics is read mapping. With the rapidly increasing number of reads produced by next-generation sequencing (NGS) technology, there is a need for fast and efficient high-throughput read mappers. In this paper, we present FMapper – a highly scalable read mapper on the TaihuLight supercomputer optimized for its fourth-generation ShenWei many-core architecture (SW26010). In order to fully exploit the computational power of the SW26010, we employ dynamic scheduling of tasks, asynchronous I/O and data transfers and implement a vectorized version of the banded Myers algorithm tailored to the 256 bit vector registers of the SW26010. Our perf…