gcn.MOPS: Accelerating cn.MOPS with GPU

12 pages•Published: March 18, 2019

Abstract

cn.MOPS is a frequently cited model-based algorithm used to quantitatively detect copy-number variations in next-generation, DNA-sequencing data. Previous work has implemented the algorithm as an R package and has achieved considerable yet limited performance improvement by employing multi-CPU parallelism (maximum achievable speedup was experimentally determined to be 9.24). In this paper, we propose an alternative mechanism of process acceleration. Using one CPU core and a GPU device in the proposed solution, gcn.MOPS, we achieve a speedup factor of 159 and reduce memory usage by more than half compared to cn.MOPS running on one CPU core.

Keyphrases: branch divergence, coalesced memory access, copy number variation, host/device concurrency, parallel processing

In: Oliver Eulenstein, Hisham Al-Mubaid and Qin Ding (editors). Proceedings of 11th International Conference on Bioinformatics and Computational Biology, vol 60, pages 15-26.

Links:	https://easychair.org/publications/paper/t6bD
	https://doi.org/10.29007/hb5r

BibTeX entry

@inproceedings{BiCOB2019:gcn.MOPS_Accelerating_cn.MOPS_with,
  author    = {Mohammad Alkhamis and Amirali Baniasadi},
  title     = {gcn.MOPS: Accelerating cn.MOPS with GPU},
  booktitle = {Proceedings of 11th International Conference on Bioinformatics and Computational Biology},
  editor    = {Oliver Eulenstein and Hisham Al-Mubaid and Qin Ding},
  series    = {EPiC Series in Computing},
  volume    = {60},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/t6bD},
  doi       = {10.29007/hb5r},
  pages     = {15-26},
  year      = {2019}}

Download PDF Open PDF in browser