Active data structures on GPGPUs

Active data structures support operations that may affect a large number of elements of an aggregate data structure. They are well suited for extremely fine grain parallel systems, including circuit parallelism. General purpose GPUs were designed to support regular graphics algorithms, but their intermediate level of granularity makes them potentially viable also for active data structures. We consider the characteristics of active data structures and discuss the feasibility of implementing them on GPGPUs. We describe the GPU implementations of two such data structures (ESF arrays and index intervals), assess their performance, and discuss the potential of active data structures as an unconventional programming model that can exploit the capabilities of emerging fine grain architectures such as GPUs

Fast kk-NNG construction with GPU-based quick multi-select

In this paper we describe a new brute force algorithm for building the $k$-Nearest Neighbor Graph ($k$-NNG). The $k$-NNG algorithm has many applications in areas such as machine learning, bio-informatics, and clustering analysis. While there are very efficient algorithms for data of low dimensions, for high dimensional data the brute force search is the best algorithm. There are two main parts to the algorithm: the first part is finding the distances between the input vectors which may be formulated as a matrix multiplication problem. The second is the selection of the $k$-NNs for each of the query vectors. For the second part, we describe a novel graphics processing unit (GPU) -based multi-select algorithm based on quick sort. Our optimization makes clever use of warp voting functions available on the latest GPUs along with use-controlled cache. Benchmarks show significant improvement over state-of-the-art implementations of the $k$-NN search on GPUs