First Steps towards Efficient Genome Assembly on ARM-Based HPC
Guardado en:
| Publicado en: | Electronics vol. 13, no. 1 (2024), p. 39 |
|---|---|
| Autor principal: | |
| Otros Autores: | , , |
| Publicado: |
MDPI AG
|
| Materias: | |
| Acceso en línea: | Citation/Abstract Full Text + Graphics Full Text - PDF |
| Etiquetas: |
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
MARC
| LEADER | 00000nab a2200000uu 4500 | ||
|---|---|---|---|
| 001 | 2912642981 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 2079-9292 | ||
| 024 | 7 | |a 10.3390/electronics13010039 |2 doi | |
| 035 | |a 2912642981 | ||
| 045 | 2 | |b d20240101 |b d20241231 | |
| 084 | |a 231458 |2 nlm | ||
| 100 | 1 | |a Poje, Kristijan | |
| 245 | 1 | |a First Steps towards Efficient Genome Assembly on ARM-Based HPC | |
| 260 | |b MDPI AG |c 2024 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a 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. | |
| 651 | 4 | |a Europe | |
| 653 | |a Assembly | ||
| 653 | |a Central processing units--CPUs | ||
| 653 | |a Performance evaluation | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Bandwidths | ||
| 653 | |a Pipelining (computers) | ||
| 653 | |a Optimization techniques | ||
| 653 | |a Energy efficiency | ||
| 653 | |a Vector processing (computers) | ||
| 653 | |a Genomes | ||
| 653 | |a Algorithms | ||
| 653 | |a Genomics | ||
| 653 | |a Energy consumption | ||
| 653 | |a High performance computing | ||
| 700 | 1 | |a Brcic, Mario | |
| 700 | 1 | |a Knezovic, Josip | |
| 700 | 1 | |a Kovac, Mario | |
| 773 | 0 | |t Electronics |g vol. 13, no. 1 (2024), p. 39 | |
| 786 | 0 | |d ProQuest |t Advanced Technologies & Aerospace Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/2912642981/abstract/embedded/H09TXR3UUZB2ISDL?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text + Graphics |u https://www.proquest.com/docview/2912642981/fulltextwithgraphics/embedded/H09TXR3UUZB2ISDL?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/2912642981/fulltextPDF/embedded/H09TXR3UUZB2ISDL?source=fedsrch |