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First Steps towards Efficient Genome Assembly on ARM-Based HPC

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Publicado en:Electronics vol. 13, no. 1 (2024), p. 39
Autor principal: Poje, Kristijan
Otros Autores: Brcic, Mario, Knezovic, Josip, Kovac, Mario
Publicado:
MDPI AG
Materias:
Europe
Assembly
Central processing units > CPUs
Performance evaluation
Bioinformatics
Bandwidths
Pipelining (computers)
Optimization techniques
Energy efficiency
Vector processing (computers)
Genomes
Algorithms
Genomics
Energy consumption
High performance computing
Acceso en línea:Citation/Abstract
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Resumen:Exponential advances in computational power have fueled advances in many disciplines, and biology is no exception. High-Performance Computing (HPC) is gaining traction as one of the essential tools in scientific research. Further advances to exascale capabilities will necessitate more energy-efficient hardware. In this article, we present our efforts to improve the efficiency of genome assembly on ARM-based HPC systems. We use vectorization to optimize the popular genome assembly pipeline of minimap2, miniasm, and Racon. We compare different implementations using the Scalable Vector Extension (SVE) instruction set architecture and evaluate their performance in different aspects. Additionally, we compare the performance of autovectorization to hand-tuned code with intrinsics. Lastly, we present the design of a CPU dispatcher included in the Racon consensus module that enables the automatic selection of the fastest instruction set supported by the utilized CPU. Our findings provide a promising direction for further optimization of genome assembly on ARM-based HPC systems.
ISSN:2079-9292
DOI:10.3390/electronics13010039
Fuente:Advanced Technologies & Aerospace Database