[Table of Contents]

Plasma and Fusion Research

Volume 8, 1403150 (2013)

Regular Articles

Computation-Communication Overlap Techniques for Parallel Spectral Calculations in Gyrokinetic Vlasov Simulations
Shinya MAEYAMA, Tomohiko WATANABE1), Yasuhiro IDOMURA, Motoki NAKATA, Masanori NUNAMI1) and Akihiro ISHIZAWA1)
Japan Atomic Energy Agency, Rokkasho 039-3212, Japan
1)
National Institute for Fusion Science, Toki 509-5292, Japan
(Received 11 July 2013 / Accepted 28 August 2013 / Published 15 November 2013)

Abstract

One of the important phenomena in magnetically-confined fusion plasma is plasma turbulence, which causes particle and heat transport and degrades plasma confinement. To address multi-scale turbulence including temporal and spatial scales of electrons and ions, we extend our gyrokinetic Vlasov simulation code GKV to run efficiently on peta-scale supercomputers. A key numerical technique is the parallel Fast Fourier Transform (FFT) required for parallel spectral calculations, where masking of the cost of inter-node transpose communications is essential to improve strong scaling. To mask communication costs, computation-communication overlap techniques are applied for FFTs and transpose with the help of the hybrid parallelization of message passing interface and open multi-processing. Integrated overlaps including whole spectral calculation procedures show better scaling than simple overlaps of FFTs and transpose. The masking of communication costs significantly improves strong scaling of the GKV code, and makes substantial speed-up toward multi-scale turbulence simulations.

Keywords

computation-communication overlap, parallel fast Fourier transform, parallel spectral calculation, MPI/OpenMP hybrid parallelization, Vlasov simulation

DOI: 10.1585/pfr.8.1403150

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This paper may be cited as follows:

Shinya MAEYAMA, Tomohiko WATANABE, Yasuhiro IDOMURA, Motoki NAKATA, Masanori NUNAMI and Akihiro ISHIZAWA, Plasma Fusion Res. 8, 1403150 (2013).