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GPU Computing Gems Emerald Edition by Wen-mei W. Hwu

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Chapter 2. Large-Scale Chemical Informatics on GPUs
Imran S. Haque and Vijay S. Pande
In this chapter we present the design and optimization of GPU implementations of two popular chemical similarity techniques: Gaussian shape overlay (GSO) and LINGO. GSO involves a data-parallel, arithmetically intensive iterative numerical optimization; we use it to examine issues of thread parallelism, arithmetic optimization, and CPU-GPU transfer overhead minimization. LINGO is a string similarity algorithm that, in its canonical CPU implementation, is bandwidth intensive and branch heavy, with limited data parallelism. We present an algorithmic redesign allowing GPU implementation of such a low arithmetic-intensity kernel and discuss techniques for memory ...

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