A Memory Bandwidth-Efficient Hybrid Radix Sort on GPUs

Sorting is at the core of many database operations, such as index creation, sort-merge joins, and user-requested output sorting. As GPUs are emerging as a promising platform to accelerate various operations, sorting on GPUs becomes a viable endeavour. Over the past few years, several improvements have been proposed for sorting on GPUs, leading to the first radix sort implementations that achieve a sorting rate of over one billion 32-bit keys per second. Yet, state-of-the-art approaches are heavily memory bandwidth-bound, as they require substantially more memory transfers than their CPU-based counterparts. Our work proposes a novel approach that almost halves the amount of memory transfers and, therefore, considerably lifts the memory bandwidth limitation. Being able to sort two gigabytes of eight-byte records in as little as 50 milliseconds, our approach achieves a 2.32-fold improvement over the state-of-the-art GPU-based radix sort for uniform distributions, sustaining a minimum speed-up of no less than a factor of 1.66 for skewed distributions. To address inputs that either do not reside on the GPU or exceed the available device memory, we build on our efficient GPU sorting approach with a pipelined heterogeneous sorting algorithm that mitigates the overhead associated with PCIe data transfers. Comparing the end-to-end sorting performance to the state-of-the-art CPU-based radix sort running 16 threads, our heterogeneous approach achieves a 2.06-fold and a 1.53-fold improvement for sorting 64 GB key-value pairs with a skewed and a uniform distribution, respectively.Comment: 16 pages, accepted at SIGMOD 201

Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo