SC is the International Conference for
 High Performnance Computing, Networking, Storage and Analysis

SCHEDULE: NOV 13-19, 2010

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

SESSION: GPGPU Performance


TIME: 2:00PM - 2:30PM

SESSION CHAIR: Gerhard Wellein

AUTHOR(S):Abdullah Gharaibeh, Matei Ripeanu


GPUs offer drastically different performance characteristics compared to traditional multicore architectures. To explore the tradeoffs exposed by this difference, we refactor MUMmer, a widely-used, highly engineered bioinformatics application which has both CPU- and GPU-based implementations. We synthesize our experience as three high-level guidelines to design efficient GPU-based applications. First, minimizing the communication overheads is as important as optimizing the computation. Second, trading-off higher computational complexity for a more compact in-memory representation is a valuable technique to increase overall performance (by enabling higher parallelism levels and reducing transfer overheads). Finally, ensuring that the chosen solution entails low pre- and post-processing overheads is essential to maximize the overall performance gains. Based on these insights, MUMmerGPU++, our GPU-based design of the MUMmer sequence alignment tool, achieves, on realistic workloads, up to 4x speedup compared to a previous, highly optimized GPU port.

Chair/Author Details:

Gerhard Wellein (Chair) - Erlangen Regional Computing Center

Abdullah Gharaibeh - University of British Columbia

Matei Ripeanu - University of British Columbia

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The full paper can be found in the ACM Digital Library and IEEE Computer Society

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