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A hybrid MPI-CUDA approach for nonequispaced discrete Fourier transformation
- Source :
- Computer Physics Communications. 258:107513
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
Abstract
- Nonequispaced discrete Fourier transformation (NDFT) is widely applied in all aspects of computational science and engineering. The computational efficiency and accuracy of NDFT has always been a critical issue in hindering its comprehensive applications both in intensive and in extensive aspects of scientific computing. In our previous work (2018, S.-C. Yang et al., Appl. Comput. Harmon. Anal. 44, 273), a CUNFFT method was proposed and it shown outstanding performance in handling NDFT at intermediate scale based on CUDA (Compute Unified Device Architecture) technology. In the current work, we further improved the computational efficiency of the CUNTTF method using an efficient MPI-CUDA hybrid parallelization (HP) scheme of NFFT to achieve a cutting-edge treatment of NDFT at super extended scale. Within this HP-NFFT method, the spatial domain of NDFT is decomposed into several parts according to the accumulative feature of NDFT and the detailed number of CPU and GPU nodes. These decomposed NDFT subcells are independently calculated on different CPU nodes using a MPI process-level parallelization mode, and on different GPU nodes using a CUDA threadlevel parallelization mode and CUNFFT algorithm. A massive benchmarking of the HP-NFFT method indicates that this method exhibit a dramatic improvement in computational efficiency for handling NDFT at super extended scale without loss of computational precision. Furthermore, the HP-NFFT method is validated via the calculation of Madelung constant of fluorite crystal structure, and thereafter verified that this method is robust for the calculation of electrostatic interactions between charged ions in molecular dynamics simulation systems.<br />16 pages, 16 figures
- Subjects :
- FOS: Computer and information sciences
Computer science
Computation
Fast Fourier transform
Network delay
Message Passing Interface
FOS: Physical sciences
General Physics and Astronomy
Parallel computing
Condensed Matter - Soft Condensed Matter
01 natural sciences
010305 fluids & plasmas
CUDA
Physics - Chemical Physics
0103 physical sciences
010306 general physics
Throughput (business)
Chemical Physics (physics.chem-ph)
Computational Physics (physics.comp-ph)
Transformation (function)
Hardware and Architecture
Soft Condensed Matter (cond-mat.soft)
Computer Science - Mathematical Software
Node (circuits)
Mathematical Software (cs.MS)
Physics - Computational Physics
Subjects
Details
- ISSN :
- 00104655
- Volume :
- 258
- Database :
- OpenAIRE
- Journal :
- Computer Physics Communications
- Accession number :
- edsair.doi.dedup.....04db53d2f1edb97e9dd8c204598f0f56