@inproceedings{b76d2f90d74f4e3cb3b2761985dcd32b,
title = "Mercator: A GPGPU framework for irregular streaming applications",
abstract = "GPUs have a natural affinity for streaming applications exhibiting consistent, predictable dataflow. However, many high-impact irregular streaming applications, including sequence pattern matching, decision-tree and decision-cascade evaluation, and large-scale graph processing, exhibit unpredictable dataflow due to data-dependent filtering or expansion of the data stream. Existing GPU frameworks do not support arbitrary irregular streaming dataflow tasks, and developing application-specific optimized implementations for such tasks requires expert GPU knowledge. We introduce MERCATOR, a lightweight framework supporting modular CUDA streaming application development for irregular applications. A developer can use MERCATOR to decompose an irregular application for the GPU without explicitly remapping work to threads at runtime. MERCATOR applications are efficiently parallelized on the GPU through a combination of replication across blocks and queueing between nodes to accommodate irregularity. We quantify the performance impact of MERCATOR's support for irregularity and illustrate its utility by implementing a biological sequence comparison pipeline similar to the well-known NCBI BLASTN algorithm. MERCATOR code is available by request to the first author.",
keywords = "GPU, Irregular computation, Parallel computing, SIMD, Streaming dataflow",
author = "Cole, {Stephen V.} and Jeremy Buhler",
note = "Funding Information: Work supported by NSF CNS-1500173 and by Exegy, Inc. Publisher Copyright: {\textcopyright} 2017 IEEE.; 15th International Conference on High Performance Computing and Simulation, HPCS 2017 ; Conference date: 17-07-2017 Through 21-07-2017",
year = "2017",
month = sep,
day = "12",
doi = "10.1109/HPCS.2017.111",
language = "English",
series = "Proceedings - 2017 International Conference on High Performance Computing and Simulation, HPCS 2017",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "727--736",
editor = "Smari, {Waleed W.}",
booktitle = "Proceedings - 2017 International Conference on High Performance Computing and Simulation, HPCS 2017",
}