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GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering
- Source :
- Journal of applied crystallography, vol 54, iss Pt 4, Journal of Applied Crystallography
- Publication Year :
- 2021
- Publisher :
- eScholarship, University of California, 2021.
-
Abstract
- The paper presents efforts to accelerate the multitiered iterative phasing (MTIP) algorithm on contemporary graphics processing units (GPUs). Application portability is demonstrated by accelerating the MTIP algorithm on NVIDIA and AMD GPUs using a single codebase.<br />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.
- Subjects :
- Matching (graph theory)
Iterative method
Computer science
Interface (Java)
spherical harmonic transform
Bioengineering
Software_PROGRAMMINGTECHNIQUES
General Biochemistry, Genetics and Molecular Biology
polar Fourier transform
Mathematical Sciences
CUDA
Software portability
Engineering
NVIDIA GPUs
Graphics
ComputingMethodologies_COMPUTERGRAPHICS
ComputerSystemsOrganization_PROCESSORARCHITECTURES
GPU acceleration
Research Papers
HIP programming
Computer Science::Performance
multitiered iterative phasing
Computer Science::Graphics
AMD GPUs
CUDA programming
Physical Sciences
Programming paradigm
Computer Science::Mathematical Software
fluctuation X-ray scattering
Central processing unit
Inorganic & Nuclear Chemistry
Algorithm
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Journal of applied crystallography, vol 54, iss Pt 4, Journal of Applied Crystallography
- Accession number :
- edsair.doi.dedup.....04ad50d8efcfe90311ad490845ea92bf