Compressing the time series of five dimensional distribution function data from gyrokinetic simulation using principal component analysis

Asahi, Yuichi; Fujii, Keisuke*; Heim, D. M.*; Maeyama, Shinya*; Garbet, X.*; Grandgirard, V.*; Sarazin, Y.*; Dif-Pradalier, G.*; Idomura, Yasuhiro; Yagi, Masatoshi*

Physics of Plasmas, 28(1), p.012304_1 - 012304_21, 2021/01

AA2020-0790.pdf:7.13MB

https://doi.org/10.1063/5.0023166

This article demonstrates a data compression technique for the time series of five dimensional distribution function data based on Principal Component Analysis (PCA). Phase space bases and corresponding coefficients are constructed by PCA in order to reduce the data size and the dimensionality. It is shown that about 83% of the variance of the original five dimensional distribution can be expressed with 64 components. This leads to the compression of the degrees of freedom from to . One of the important findings - resulting from the detailed analysis of the contribution of each principal component to the energy flux - deals with avalanche events, which are found to be mostly driven by coherent structures in the phase space, indicating the key role of resonant particles.

Turbulent generation of poloidal asymmetries of the electric potential in a tokamak

Donnel, P.*; Garbet, X.*; Sarazin, Y.*; Asahi, Yuichi; Wilczynski, F.*; Caschera, E.*; Dif-Pradalier, G.*; Ghendrih, P.*; Gillot, C.*

Plasma Physics and Controlled Fusion, 61(1), p.014003_1 - 014003_11, 2019/01

https://doi.org/10.1088/1361-6587/aae4fe

Poloidal asymmetries of the plasma flow are known to play a role in neoclassical transport. According to conventional neoclassical theory, the level of poloidal asymmetry of the electric potential is expected to be very small. In the present work, a general framework for the generation of axisymmetric structures of potential by turbulence is presented. Zonal flows, geodesic acoustic modes and convective cells are described by a single model. This is done by solving the gyrokinetic equation coupled to the quasi-neutrality equation. This calculation provides a predictive calculation of the frequency spectrum of flows given a specified forcing due to turbulence. It also shows that the dominant mechanism comes from zonal flow compression at intermediate frequencies, while ballooning of the turbulence Reynolds stress appears to be the main drive at low frequency.

Optimization of fusion kernels on accelerators with indirect or strided memory access patterns

Asahi, Yuichi*; Latu, G.*; Ina, Takuya; Idomura, Yasuhiro; Grandgirard, V.*; Garbet, X.*

IEEE Transactions on Parallel and Distributed Systems, 28(7), p.1974 - 1988, 2017/07

https://doi.org/10.1109/TPDS.2016.2633349

High-dimensional stencil computation from fusion plasma turbulence codes involving complex memory access patterns, the indirect memory access in a Semi-Lagrangian scheme and the strided memory access in a Finite-Difference scheme, are optimized on accelerators such as GPGPUs and Xeon Phi coprocessors. On both devices, the Array of Structure of Array (AoSoA) data layout is preferable for contiguous memory accesses. It is shown that the effective local cache usage by improving spatial and temporal data locality is critical on Xeon Phi. On GPGPU, the texture memory usage improves the performance of the indirect memory accesses in the Semi-Lagrangian scheme. Thanks to these optimizations, the fusion kernels on accelerators become 1.4x - 8.1x faster than those on Sandy Bridge (CPU).

Estimation of kinetic parameters based on chirping Alfvn Eigenmodes

Lesur, M.*; Idomura, Yasuhiro; Shinohara, Koji; Garbet, X.*

Proceedings of 23rd IAEA Fusion Energy Conference (FEC 2010) (CD-ROM), 8 Pages, 2011/03

Alfvn Eigenmodes (AEs) with frequency sweeping (chirping AEs) are analyzed based on the so-called Berk-Breizman (BB) model. Kinetic parameter regimes with chirping nonlinear solutions are delimited, and a new quasi-periodic chirping regime is found, where the quasi-period of chirping events depends on the linear growth rate. Fundamental kinetic parameters such as the linear drive and the external damping rate are estimated by fitting nonlinear chirping characteristics between the experiment and the BB model. This approach is applied to Toroidicity-induced AEs on JT-60U, which suggests the existence of modes far from marginal stability. Two collision models are considered, and it is shown that dynamical friction and velocity-space diffusion are essential to reproduce nonlinear features observed in experiments. The results are validated by recovering measured growth and decay of perturbation amplitude, and by estimating collision frequencies from experimental equilibrium data.

Gyrokinetic simulations of turbulent transport; Size scaling and chaotic behaviour

Villard, L.*; Bottino, A.*; Brunner, S.*; Casati, A.*; Chowdhury, J.*; Dannert, T.*; Ganesh, R.*; Garbet, X.*; Grler, T.*; Grandgirard, V.*; et al.

Plasma Physics and Controlled Fusion, 52(12), p.124038_1 - 124038_18, 2010/11

https://doi.org/10.1088/0741-3335/52/12/124038

Fully nonlinear features of the energetic beam-driven instability

Lesur, M.*; Idomura, Yasuhiro; Garbet, X.*

Physics of Plasmas, 16(9), p.092305_1 - 092305_12, 2009/09

https://doi.org/10.1063/1.3234249

A Review of internal transport barrier physics for steady-state operation of tokamaks

Connor, J. W.*; Fukuda, Takeshi*; Garbet, X.*; Gormezano, C.*; Mukhovatov, V.*; Wakatani, Masahiro*; ITB Database Group; ITPA Topical Group on Transport and Internal Barrier Physics*

Nuclear Fusion, 44(4), p.R1 - R49, 2004/04

https://doi.org/10.1088/0029-5515/44/4/R01

This paper first reviews the present state of theoretical and experimental knowledge regarding the formation and characteristics of ITBs in tokamaks. Specifically, the current status of theoretical modeling of ITBs is presented; then, an international ITB database based on experimental information extracted from some nine tokamaks is described and used to draw some general conclusions concerning the necessary conditions for ITBs to appear, comparing these with the theoretical models. The experimental situation regarding the steady-state, or at least quasi-steady-state, operation of tokamaks is reviewed and finally the issues and prospects for achieving such operational modes in ITER are discussed.

Acceleration of stencil-based fusion kernels

Asahi, Yuichi*; Latu, G.*; Ina, Takuya; Idomura, Yasuhiro; Grandgirard, V.*; Garbet, X.*

no journal, , 

Computation kernels of fusion plasma turbulence codes based on the Semi-Lagrangian scheme and the Finite-Difference scheme are optimized on latest many core processors such as GPGPU, XeonPhi, and FX100, and 1.4x-8.1x speedup is achieved. Affinity between different memory access patterns in each numerical scheme and difference memory-cache architectures on each hardware is studied, and different optimization techniques are developed for each architecture. On Xeon Phi, thread load balance is improved, and an optimization technique for effective local cache usage is developed. On GPGPU, an optimization technique using a texture memory and an implementation to reuse registers are developed. On the other hand, on FX100, it is found that the conventional optimization techniques for CPU work.

Benchmark test of full-f gyrokinteic codes

Asahi, Yuichi; Idomura, Yasuhiro; Ina, Takuya; Garbet, X.*; Grandgirard, V.*; Latu, G.*

no journal, , 

In the so-called delta-f gyrokinetic simulations, the scale separation between the equilibrium and fluctuation plasmas is assumed, and the time evolution is solved only for the fluctuation part. In contrast, in the full-f gyrokinetic simulations, both of the equilibrium and fluctuation plasmas are solved on the basis of the same first principle, where the self-consistent simulations for the equilibrium and fluctuation plasmas are possible. So far, there are a plenty number of cross-code benchmarks for delta-f gyrokinetic simulations, which helps to improve the robustness of the simulations. However, this is not the case for the full-f simulations since the complicated full-f physics makes benchmarks more difficult. In the presentation, we will show the progress of the full-f benchmarks and discuss the confronting issues.

Estimation of kinetic parameters based on chirping Alfven eigenmodes

Lesur, M.*; Idomura, Yasuhiro; Shinohara, Koji; Garbet, X.*

no journal, ,