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DOE OSTI · 1819961

GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering

Kommera, Pranay Reddy·Ramakrishnaiah, Vinay (ORCID:0000000229254798)·Sweeney, Christine (ORCID:000000032352490X)·Donatelli, Jeffrey·Zwart, Petrus H. (ORCID:0000000333154092)
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Abstract

The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.

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97 MATHEMATICS AND COMPUTINGAMD GPUsCUDA programmingGPU accelerationHIP programmingNVIDIA GPUsfluctuation X-ray scatteringfluctuation X-ray scattering, multitiered iterative phasing, polar Fourier transform, spherical harmonic transform, GPU acceleration, CUDA Programming, HIP C++ Programming, NVIDIA GPUs, AMD GPUsmultitiered iterative phasingpolar Fourier transformspherical harmonic transform

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Kommera, Pranay Reddy, Ramakrishnaiah, Vinay (ORCID:0000000229254798), Sweeney, Christine (ORCID:000000032352490X), Donatelli, Jeffrey, Zwart, Petrus H. (ORCID:0000000333154092). 2021-07-30. GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering. https://doi.org/10.1107/s1600576721005744

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