@phdthesis{Koanantakool:EECS-2017-221,
Author = {Koanantakool, Penporn},
Title = {Communication Avoidance for Algorithms with Sparse All-to-all Interactions},
School = {EECS Department, University of California, Berkeley},
Year = {2017},
Month = {Dec},
URL = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-221.html},
Number = {UCB/EECS-2017-221},
Abstract = {In parallel computing environments from multicore systems to cloud computers and supercomputers, data movement is the dominant cost in both running time and energy usage. Even worse, hardware trends suggest that the gap between computing and data movement, both in memory systems and interconnect networks, will continue to grow. Minimizing communication is therefore necessary in devising scalable parallel algorithms. This work discusses parallelizing kernels in applications ranging from chemistry and cosmology to machine learning.
We have developed new communication-avoiding algorithms for problems with all-to-all interactions such as many-body and matrix computations, taking into account their sparsity patterns, either from cutoff distance, symmetry, or data sparsity. Our algorithms are communication-efficient (some are provably optimal) and scalable to tens of thousands of processors, exhibiting orders of magnitude speedup over more commonly used algorithms.
These all-to-all computational patterns arise in scientific simulations and machine learning. The last part of the thesis will present a case study of communication-avoiding sparse-dense matrix multiplication as used in graphical model structure learning. The resulting high-performance sparse inverse covariance matrix estimation algorithm enables processing high-dimensional data with arbitrary underlying structures at a scale that was previously intractable, e.g., 1.28 million dimensions (over 800 billion parameters) in under 21 minutes on 24,576 cores of a Cray XC30. Our method is used to automatically estimate the underlying functional connectivity of the human brain from resting-state fMRI data. The results show good agreement with a state-of-the-art clustering, which used manual intervention, from the neuroscience literature.}
}