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Porting a commercial application to OpenCL: a case study

Published: 12 May 2014 Publication History

Abstract

The use of virtual screening to find new drug hits and leads has become commonplace within the pharmaceutical industry. 2D methods have largely been replaced by 3D ligand-based methods and by structure-based methods (docking) where a reliable protein structure is available. However, the computational cost of calculating 3D molecular similarities is much higher than that for 2D similarity methods, meaning that large amounts of computing power are needed to screen a reasonable number of virtual compounds in a useful time scale.
In recent years, the popularity of graphical processing units (GPUs) has increased in the area of high performance computing, mainly for their attractive cost to performance ratio and the appearance of stable GPU coding frameworks. They are a promising solution for computationally-intense problems such as virtual screening. In collaboration, the University of Bristol and Cresset have ported the blazeV10 virtual screening commercial application to OpenCL, a framework for writing programs that execute across heterogeneous platforms using both CPUs and GPUs.
We present results showing that our OpenCL port of blazeV10 can provide an up to 20-fold speedup when run on a recent off-the-shelf GPU, compared to a contemporary multi-core CPU. This not only reduces the time required to obtain results but also saves hardware cost and space. We discuss some of the difficulties encountered in porting this commercial application to work well across a range of CPUs and GPUs, present hardware comparisons, and give guidance on how to maximize performance while retaining full precision.

References

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T. Cheeseright, M. Mackey, J. Melville, and J. Vinter. FieldScreen: virtual screening using molecular fields. application to the DUD data set. J Chem Inf Model, 2008.
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T. Cheeseright, M. Mackey, S. Rose, and J. Vinter. Molecular field extrema as descriptors of biological activity: Definition and validation. J. Chem. Inf. Model., 2006.
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J. A. Grant and B. T. Pickup. A gaussian description of molecular shape. JPhysChem, 1995.
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T. D. Han and T. S. Abdelrahman. Reducing branch divergence in GPU programs. University of Toronto, 2011.
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I. S. Haque and V. S. Pande. Accelerating parallel evaluations of ROCS. Wiley InterScience, 2009.
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R. Karrenberg and S. Hack. Improving performance of OpenCL on CPUs. Saarland University, 2011.
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S. McIntosh-Smith, J. Price, R. B. Sessions, and A. A. Ibarra. High performance in silico virtual drug screening on many-core processors. International Journal of High Performance Computing Applications, 2014.
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E. Young. OpenCL 1.1 enhancements for multi-GPU performance. 2011.
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E. Zhang and et al. Streamlining GPU applications on the fly: thread divergence elimination through runtime thread-data remapping. Proc. of Supercomputing, 2010.

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Published In

cover image ACM Other conferences
IWOCL '14: Proceedings of the International Workshop on OpenCL 2013 & 2014
May 2014
86 pages
ISBN:9781450330077
DOI:10.1145/2664666
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

  • ARM: ARM
  • AMD
  • SAMSUNG: SAMSUNG
  • Khronos: Khronos Group
  • Xilinx: Xilinx Inc.
  • QI: Qualcomm Inc.
  • Codeplay: Codeplay Software Ltd.
  • Intel: Intel
  • StreamComputing: StreamComputing BV
  • Lithe: Lithe Technology
  • The University of Bristol: The University of Bristol
  • Altera Corp.: Altera Corporation
  • ArrayFire: ArrayFire
  • Imagination: Imagination Technologies Limited

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 12 May 2014

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IWOCL '14
Sponsor:
  • ARM
  • SAMSUNG
  • Khronos
  • Xilinx
  • QI
  • Codeplay
  • Intel
  • StreamComputing
  • Lithe
  • The University of Bristol
  • Altera Corp.
  • ArrayFire
  • Imagination
IWOCL '14: International Workshop on OpenCL 2013 & 2014
May 12 - 13, 2014
Bristol, United Kingdom

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