Grid, Public and GPU Computing for the Tree of Life

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The University of Maryland College Park is awarded a grant to create tools that expand the computing power freely available to all ATOL (Assembling the Tree of Life), and other phylogenetic researchers. The central idea is to combine Grid and GPU (graphics processing unit) computing to take better advantage of a diversity of computing resources, particularly existing desktop processing capacity available through public-computing. The main product will be a Grid system, customized for phylogenetic tree search and accessed through a user-friendly web interface, that links thousands of individual computers world-wide. The likelihood-based tree search program GARLI (Genetic Algorithm for Rapid Likelihood Inference), will serve as the initial model application during development. The new system is intended to allow analyses that far transcend what one can do on a single desktop computer or moderate-sized cluster. For example, it should become possible to carry out extensive bootstrap analyses in little more time than is now required for a single tree search. The project will also exploit a second under-utilized resource inside desktop computers, namely the graphics processing unit (GPU), which can do many scientific calculations faster than the central processing unit (CPU). A free, open-source library (C/C++) for maximum likelihood calculations using parallel CPU/GPU processing will be developed. GARLI versions will be developed that take advantage of major GPU platforms. Subsequent development will extend to other likelihood-intensive methods (e.g., Bayesian analysis). Five participating ATOL projects will help test the new tools, and publish a collaborative evaluation of the performance of the new system across the diverse phylogenetic problems they represent. The project will be a joint effort with Bowie State University, Coppin State College, and the University of Kansas Center for Research, Inc.