FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters

Journal of computational biology: A journal of computational molecular cell biology

HéctorMartínez^1,2¹  SergioBarrachina^2²  MaribelCastillo^2³ 

[1] Address correspondence to:Héctor Martínez, PhD studentDepartment of Computer Science and EngineeringJaume I UniversityCastellón 12006Spain^1;Department of Computer Science and Engineering, Jaume I University, Castellón, Spain^2;Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain^3

关键词: clusters of computers;    epistasis;    FaST-LMM;    genome-wide association studies (GWAS);    GPUs;    multicore processors;   

DOI  :  10.1089/cmb.2018.0087

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear on 12–16 nodes of two recent platforms, with respect to improved implementation of FaST-LMM presented in an earlier work. This efficiency is attained through several enhancements on the original single-node version of FaST-LMM, together with the development of a message passing interface (MPI)-based version that ensures a balanced distribution of the workload as well as a multigraphics processing unit (GPU) module that can exploit the presence of multiple GPUs per node.

【 授权许可】

Unknown