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

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Héctor MartínezArcadi Navarro

Abstract

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.

References

Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Sep 8, 2010·American Journal of Human Genetics·Xiang WanWeichuan Yu
Sep 6, 2011·Nature Methods·Christoph LippertDavid Heckerman
Jan 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Or ZukEric S Lander
Feb 28, 2014·Nature·Gibran HemaniJoseph E Powell
Apr 30, 2015·European Journal of Human Genetics : EJHG·Ciara ColemanRoss McManus
Jun 27, 2015·Nature Genetics·Ilkka LappalainenPaul Flicek

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Citations

Jan 29, 2020·Ecology and Evolution·Ting ShiZhihong Gao
Aug 8, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Miguel A Vega-Rodríguez, José M Granado-Criado

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Software Mentioned

Piz
MPI
Open MPI
CUDA
MPI Slurm
LMM
Python
Scikit
Intel MKL Update
FaST

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