Large-scale linear regression: Development of high-performance routines

In statistics, series of ordinary least squares problems (OLS) are used to study the linear correlation among sets of variables of interest; in many studies, the number of such variables is at least in the millions, and the corresponding datasets occupy terabytes of disk space. As the availability of large-scale datasets increases regularly, so does the challenge in dealing with them. Indeed, traditional solvers—which rely on the use of “black-box” routines optimized for one single OLS—are highly inefficient and fail to provide a viable solution for big-data analyses. As a case study, in this paper we consider a linear regression consisting of two-dimensional grids of related OLS problems that arise in the context of genome-wide association analyses, and give a careful walkthrough for the development of ols-grid, a high-performance routine for shared-memory architectures; analogous steps are relevant for tailoring OLS solvers to other applications. In particular, we first illustrate the design of efficient algorithms that exploit the structure of the OLS problems and eliminate redundant computations; then, we show how to effectively deal with datasets that do not fit in main memory; finally, we discuss how to cast the computation in terms of efficient kernels and how to achieve scalability. Importantly, each design decision along the way is justified by simple performance models. ols-grid enables the solution of 1011 correlated OLS problems operating on terabytes of data in a matter of hours.