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Journal Articles

Interactive steering on in situ particle-based volume rendering framework

Kawamura, Takuma; Hasegawa, Yuta; Idomura, Yasuhiro

Journal of Visualization, 27(1), p.89 - 107, 2024/02

Interactive in-situ steering is an effective tool for debugging, searching for optimal solutions, and analyzing inverse problems in fast and large-scale computational fluid dynamics (CFD) simulations. We propose an interactive in-situ steering framework for large-scale CFD simulations on GPU supercomputers. This framework employs in-situ particle-based volume rendering (PBVR), in-situ data sampling, and a file-based control that enables interactive communication of steering parameters, compressed particle data, and sampled monitoring data between supercomputers and user PCs. The parallelized PBVR is processed on the host CPU to avoid interference with CFD simulations on the GPU. We apply the proposed framework to a real-time plume dispersion analysis code CityLBM on GPU supercomputers. In the numerical experiment, we address an inverse problem to find a pollutant source from the monitoring data, and demonstrate the effectiveness of the human-in-the-loop approach.

Journal Articles

Continuous data assimilation of large eddy simulation by lattice Boltzmann method and local ensemble transform Kalman filter (LBM-LETKF)

Hasegawa, Yuta; Onodera, Naoyuki; Asahi, Yuichi; Ina, Takuya; Imamura, Toshiyuki*; Idomura, Yasuhiro

Fluid Dynamics Research, 55(6), p.065501_1 - 065501_25, 2023/11

We investigate the applicability of the data assimilation (DA) to large eddy simulations (LESs) based on the lattice Boltzmann method (LBM). We carry out the observing system simulation experiment of a two-dimensional (2D) forced isotropic turbulence, and examine the DA accuracy of the nudging and the local ensemble transform Kalman filter (LETKF) with spatially sparse and noisy observation data of flow fields. The advantage of the LETKF is that it does not require computing spatial interpolation and/or an inverse problem between the macroscopic variables (the density and the pressure) and the velocity distribution function of the LBM, while the nudging introduces additional models for them. The numerical experiments with $$256times256$$ grids and 10% observation noise in the velocity showed that the root mean square error of the velocity in the LETKF with $$8times 8$$ observation points ($$sim 0.1%$$ of the total grids) and 64 ensemble members becomes smaller than the observation noise, while the nudging requires an order of magnitude larger number of observation points to achieve the same accuracy. Another advantage of the LETKF is that it well keeps the amplitude of the energy spectrum, while only the phase error becomes larger with more sparse observation. From these results, it was shown that the LETKF enables robust and accurate DA for the 2D LBM with sparse and noisy observation data.

JAEA Reports

Optimized phase-field modeling using a modified conservative Allen-Cahn equation for two-phase flows

Sugihara, Kenta; Onodera, Naoyuki; Idomura, Yasuhiro; Yamashita, Susumu

JAEA-Research 2023-006, 47 Pages, 2023/10

JAEA-Research-2023-006.pdf:3.28MB

This report presents a new surface capturing method based on the phase field model for gas-liquid two-phase flows simulation. In the conventional phase field model, the interface correction strength parameter was determined from the maximum flow velocity in the computational domain, but because the interface correction was applied uniformly to the entire space, it was also applied to locations that did not require correction. In the new method, the phase field parameter or the intensity of the phase field model is extended to have a spatial distribution, allowing us to set the optimal parameters depending on the local flow velocity fields. We also propose a method to derive the optimal phase field parameter based on systematic parameter scans using error analysis of the interface advection test and bubble rising calculations. Through benchmark tests of gas-liquid two-phase flows, the proposed model is verified, and it is shown that the proposed model has higher accuracy than the conventional phase field model.

Journal Articles

Parameter optimization for urban wind simulation using ensemble Kalman filter

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Asahi, Yuichi; Inagaki, Atsushi*; Shimose, Kenichi*; Hirano, Kohin*

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 28, 4 Pages, 2023/05

We have developed a multi-scale wind simulation code named CityLBM that can resolve entire cities to detailed streets. CityLBM enables a real time ensemble simulation for several km square area by applying the locally mesh-refined lattice Boltzmann method on GPU supercomputers. On the other hand, real-world wind simulations contain complex boundary conditions that cannot be modeled, so data assimilation techniques are needed to reflect observed data in the simulation. This study proposes an optimization method for ground surface temperature bias based on an ensemble Kalman filter to reproduce wind conditions within urban city blocks. As a verification of CityLBM, an Observing System Simulation Experiment (OSSE) is conducted for the central Tokyo area to estimate boundary conditions from observed near-surface temperature values.

Journal Articles

Full-$$f$$ gyrokinetic simulations of ohmic L-mode plasmas in linear and saturated ohmic confinement regimes

Idomura, Yasuhiro; Dif-Pradalier, G.*; Garbet, X.*; Sarazin, Y.*; Tore Supra Teams*

Physics of Plasmas, 30(4), p.042508_1 - 042508_18, 2023/04

 Times Cited Count:0 Percentile:0.01(Physics, Fluids & Plasmas)

Two time slices in linear and saturated ohmic confinement (LOC and SOC) regimes in a Tore Supra ohmic L-mode discharge are analyzed using nonlinear global full-$$f$$ gyrokinetic simulations, and qualitative features of the LOC-SOC transition are reproduced. The exhaust of carbon impurity ions is caused by fast ion mixing, which is driven by the toroidal field stress. The intrinsic rotation develops in the opposite direction between the LOC and SOC phases, which is characterized by the different features of the mode asymmetry between trapped electron modes in the LOC phase and ion temperature gradient driven modes in the SOC phase, leading to the change of the profile shear stress. The energy fluxes of electrons and deuterium ions are dominant in the LOC and SOC phases, respectively, and the ratio of the energy confinement time between two phases agree with the experimental value.

Journal Articles

A New data conversion method for mixed precision Krylov solvers with FP16/BF16 Jacobi preconditioners

Ina, Takuya; Idomura, Yasuhiro; Imamura, Toshiyuki*; Onodera, Naoyuki

Proceedings of International Conference on High Performance Computing in Asia-Pacific Region (HPC Asia 2023) (Internet), p.29 - 34, 2023/02

Mixed precision Krylov solvers with the Jacobi preconditioner often show significant convergence degradation when the Jacobi preconditioner is computed in low precision such as FP16 and BF16. It is found that this convergence degradation is attributed to loss of diagonal dominance due to roundoff errors in data conversion. To resolve this issue, we propose a new data conversion method, which is designed to keep diagonal dominance of the original matrix data. The proposed method is tested by computing the Poisson equation using the conjugate gradient method, the general minimum residual method, and the biconjugate gradient stabilized method with the FP16/BF16 Jacobi preconditioner on NVIDIA V100 GPUs. Here, the new data conversion is implemented by switching the round-nearest, round-up, round-down, and round-towards-zero intrinsics in CUDA, and is called once before the main iteration. Therefore, the cost of the new data conversion is negligible. When the coefficients of matrix is continuously changed by scaling the linear system, the conventional data conversion based on the round-nearest intrinsic shows periodic changes of the convergence property depending on the difference of the roundoff errors between diagonal and off-diagonal coefficients. Here, the period and magnitude of the convergence degradation depend on the bit length of significand. On the other hand, the proposed data conversion method is shown to fully avoid the convergence degradation, and robust mixed precision computing is enabled for the Jacobi preconditioner without extra overheads.

Journal Articles

CityTransformer; A Transformer-based model for contaminant dispersion prediction in a realistic urban area

Asahi, Yuichi; Onodera, Naoyuki; Hasegawa, Yuta; Shimokawabe, Takashi*; Shiba, Hayato*; Idomura, Yasuhiro

Boundary-Layer Meteorology, 34 Pages, 2023/01

 Times Cited Count:0 Percentile:0.01(Meteorology & Atmospheric Sciences)

We develop a Transformer-based deep learning model to predict the plume concentrations in the urban area under uniform flow conditions. Our model has two distinct input layers: Transformer layers for sequential data and convolutional layers in convolutional neural networks (CNNs) for image-like data. Our model can predict the plume concentration from realistically available data such as the time series monitoring data at a few observation stations and the building shapes and the source location. It is shown that the model can give reasonably accurate prediction with orders of magnitude faster than CFD simulations. It is also shown that the exactly same model can be applied to predict the source location, which also gives reasonable prediction accuracy.

Journal Articles

Data assimilation of three-dimensional turbulent flow using lattice Boltzmann method and local ensemble transform Kalman filter (LBM-LETKF)

Hasegawa, Yuta; Onodera, Naoyuki; Asahi, Yuichi; Idomura, Yasuhiro

Dai-36-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 5 Pages, 2022/12

This study implemented and tested the ensemble data assimilation (DA) of turbulent flows using the lattice Boltzmann method and the local ensemble transform Kalman filter (LBM-LETKF). The computational code was implemented fully on GPUs. The test was carried out for the 3D turbulent flow around a square cylinder with $$2.3times10^{7}$$ meshes and 32 ensemble members using 32 GPUs. The time interval of the DA in the test was a half of the period of the Kalman vortex shedding. The normalized mean absolute errors (NMAE) of the lift coefficient were 132%, 148%, and 13.2% for the non-DA case, the nudging case (a simpler DA algorithm), and the LETKF case, respectively. It was found that the LETKF achieved good DA accuracy even though the observation was not frequent enough for the small scale turbulence, while the nudging showed systematic delays in its solution, and could not keep the DA accurately.

Journal Articles

Parameter optimization for turbulent boundary layer generation using ensemble Kalman filter

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Nakayama, Hiromasa

Dai-36-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 3 Pages, 2022/12

We have developed a wind simulation code named CityLBM to realize wind digital twins. Mesoscale wind conditions are given as boundary conditions in CityLBM by using a nudging data assimilation method. It is found that conventional approaches with constant nudging coefficients fail to reproduce turbulent intensity in long time simulations, where atmospheric stability conditions change significantly. We propose a dynamic parameter optimization method for the nudging coefficient based on an ensemble Kalman filter. CityLBM was validated against plume dispersion experiments in the complex urban environment of Oklahoma City. The nudging coefficient was updated to reduce the error of the turbulent intensity between the simulation and the observation. The mean error of velocity variance is reduced by $$sim$$10% compared to the conventional nudging method with a constant nudging coefficient.

Journal Articles

Gas-liquid two-phase flow analysis using multi-phase field method

Sugihara, Kenta; Onodera, Naoyuki; Idomura, Yasuhiro; Yamashita, Susumu

Dai-36-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 5 Pages, 2022/12

The conventional Allen-Cahn type multi-phase field method was modified to conserve not only the sum of the masses of all phases but also the mass of each phase. The interface advection calculations within a two-dimensional rotational velocity field were performed as a verification problem, and the conservation was successfully achieved. The proposed method was used to calculate the horizontally aligned pair of bubbles rising, and it was found that the bouncing phenomenon between bubbles can be calculated at 1/50 resolution of the high-resolution calculation by Zhang et al. using the volume of fluid method.

Journal Articles

Development of local-scale high-resolution atmospheric dispersion and dose assessment system

Nakayama, Hiromasa; Onodera, Naoyuki; Satoh, Daiki; Nagai, Haruyasu; Hasegawa, Yuta; Idomura, Yasuhiro

Journal of Nuclear Science and Technology, 59(10), p.1314 - 1329, 2022/10

 Times Cited Count:5 Percentile:86.35(Nuclear Science & Technology)

We developed a local-scale high-resolution atmospheric dispersion and dose assessment system (LHADDAS) for safety and consequence assessment of nuclear facilities and emergency response to nuclear accidents or deliberate releases of radioactive materials in built-up urban areas. This system is composed of pre-processing of input files, main calculation by local-scale high-resolution atmospheric dispersion model using large-eddy simulation (LOHDIM-LES) and real-time urban dispersion simulation model based on a lattice Boltzmann method (CityLBM), and post-processing of dose-calculation by simulation code powered by lattice dose-response functions (SIBYL). LHADDAS has a broad utility and offers superior performance in (1) simulating turbulent flows, plume dispersion, and dry deposition under realistic meteorological conditions, (2) performing real-time tracer dispersion simulations using a locally mesh-refined lattice Boltzmann method, and (3) estimating air dose rates of radionuclides from air concentrations and surface deposition in consideration of the influence of individual buildings and structures. This system is promising for safety assessment of nuclear facilities as an alternative to wind tunnel experiments, detailed pre/post-analyses of a local-scale radioactive plume dispersion in case of nuclear accidents, and quick response to emergency situations resulting from deliberate release of radioactive materials by a terrorist attack in an urban central district area.

Journal Articles

GPU implementation of local ensemble transform Kalman filter (LETKF) with two-dimensional lattice Boltzmann method

Hasegawa, Yuta; Onodera, Naoyuki; Asahi, Yuichi; Idomura, Yasuhiro

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 27, 4 Pages, 2022/06

We developed GPU implementation of ensemble data assimilation (DA) using the local ensemble transform Kalman filter (LETKF) with the lattice Boltzmann method (LBM). The performance test was carried out upto 32 ensembles of two-dimensional isotropic turbulence simulations using the D2Q9 LBM. The computational cost of the LETKF was less than or nearly equal to that of the LBM upto eight ensembles, while the former exceeded the latter at larger ensembles. At 32 ensembles, their computational costs per cycle were respectively 28.3 msec and 5.39 msec. These results suggested that further speedup of the LETKF is needed for practical 3D LBM simulations.

Journal Articles

Optimization of phase field variables in gas-liquid two-phase flow problems

Sugihara, Kenta; Onodera, Naoyuki; Idomura, Yasuhiro; Yamashita, Susumu

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 27, 5 Pages, 2022/06

The phase-field method has been successfully applied to various multi-phase flow problems as an interface tracking method for gas-liquid interfaces. However, the accuracy of the phase-field method depends on hyper-parameters, which are empirically adjusted for each problem. The phase-field method sustains sharp interfaces by the balance between the numerical viscosity of the advection term and the interface modification by the diffusion and anti-diffusion terms. Based on this fact, we propose a method for deriving the optimal hyper-parameters in a non-empirical manner by performing a basic error analysis of the interface advection.

Journal Articles

Parameter optimization for generating atmospheric boundary layers by using the locally mesh-refined lattice Boltzmann method

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Shimokawabe, Takashi*; Aoki, Takayuki*

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 27, 4 Pages, 2022/06

We have developed a wind simulation code named CityLBM to realize wind digital twins. Mesoscale wind conditions are given as boundary conditions in CityLBM by using a nudging data assimilation method. It is found that conventional approaches with constant nudging coefficients fail to reproduce turbulent intensity in long time simulations, where atmospheric stability conditions change significantly. We propose a dynamic parameter optimization method for the nudging coefficient based on a particle filter. CityLBM was validated against plume dispersion experiments in the complex urban environment of Oklahoma City. The nudging coefficient was updated to reduce the error of the turbulent intensity between the simulation and the observation, and the atmospheric boundary layer was reproduced throughout the day.

Journal Articles

Performance measurement of an urban wind simulation code with the Locally Mesh-Refined Lattice Boltzmann Method over NVIDIA and AMD GPUs

Asahi, Yuichi; Onodera, Naoyuki; Hasegawa, Yuta; Shimokawabe, Takashi*; Shiba, Hayato*; Idomura, Yasuhiro

Keisan Kogaku Koenkai Rombunshu (CD-ROM), 27, 5 Pages, 2022/06

We have ported the GPU accelerated Lattice Boltzmann Method code "CityLBM" to AMD MI100 GPU. We present the performance of CityLBM achieved on NVIDIA P100, V100, A100 GPUs and AMDMI100 GPU. Using the host to host MPI communications, the performance on MI100 GPU is around 20% better than on V100 GPU. It has turned out that most of the kernels are successfully accelerated except for interpolation kernels for Adaptive Mesh Refinement (AMR) method.

Journal Articles

Challenges of ab initio simulations to physics of burning plasma confinement

Watanabe, Tomohiko*; Idomura, Yasuhiro; Todo, Yasushi*; Honda, Mitsuru*

Nihon Genshiryoku Gakkai-Shi ATOMO$$Sigma$$, 64(3), p.152 - 156, 2022/03

Understanding of physical processes of particle, momentum, and thermal transports is essential for predicting the confinement performance of burning plasmas in ITER, which is targeting the scientific demonstration of magnetic confinement fusion. First principles based simulations on Fugaku disclosed physical mechanisms such as complex transport processes of multi-scale turbulence in deuterium-tritium plasmas and kinetic effects in energetic particle transport due to electromagnetic fluctuations. We promote further research and development of first principles based simulations towards the performance prediction of burning plasmas.

Journal Articles

GPU optimization of lattice Boltzmann method with local ensemble transform Kalman filter

Hasegawa, Yuta; Imamura, Toshiyuki*; Ina, Takuya; Onodera, Naoyuki; Asahi, Yuichi; Idomura, Yasuhiro

Proceedings of 13th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Heterogeneous Systems (ScalAH22) (Internet), p.10 - 17, 2022/00

The ensemble data assimilation of computational fluid dynamics simulations based on the lattice Boltzmann method (LBM) and the local ensemble transform Kalman filter (LETKF) is implemented and optimized on a GPU supercomputer based on NVIDIA A100 GPUs. To connect the LBM and LETKF parts, data transpose communication is optimized by overlapping computation, file I/O, and communication based on data dependency in each LETKF kernel. In two dimensional forced isotropic turbulence simulations with the ensemble size of $$M=64$$ and the number of grid points of $$N_x=128^2$$, the optimized implementation achieved $$times3.85$$ speedup from the naive implementation, in which the LETKF part is not parallelized. The main computing kernel of the local problem is the eigenvalue decomposition (EVD) of $$Mtimes M$$ real symmetric dense matrices, which is computed by a newly developed batched EVD in EigenG. The batched EVD in EigenG outperforms that in cuSolver, and $$times64$$ speedup was achieved.

Journal Articles

Development of a surface heat flux model for urban wind simulation using locally mesh-refined lattice Boltzmann method

Onodera, Naoyuki; Idomura, Yasuhiro; Hasegawa, Yuta; Nakayama, Hiromasa

Dai-35-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Rombunshu (Internet), 3 Pages, 2021/12

A detailed wind simulation is very important for designing smart cities. Since a lot of tall buildings and complex structures make the air flow turbulent in urban cities, large-scale CFD simulations are needed. We develop a GPU-based CFD code based on a Lattice Boltzmann Method (LBM) with a block-based Adaptive Mesh Refinement (AMR) method. In order to reproduce real wind conditions, the wind condition and ground temperature of the mesoscale weather forecasting model are given as boundary conditions. In this research, a surface heat flux model based on the Monin-Obukhov similarity theory was introduced to improve the calculation accuracy. We conducted a detailed wind simulation in Oklahoma City. By executing this computation, wind conditions in the urban area were reproduced with good accuracy.

Journal Articles

Tree cutting approach for domain partitioning on forest-of-octrees-based block-structured static adaptive mesh refinement with lattice Boltzmann method

Hasegawa, Yuta; Aoki, Takayuki*; Kobayashi, Hiromichi*; Idomura, Yasuhiro; Onodera, Naoyuki

Parallel Computing, 108, p.102851_1 - 102851_12, 2021/12

 Times Cited Count:1 Percentile:34.17(Computer Science, Theory & Methods)

The aerodynamics simulation code based on the lattice Boltzmann method (LBM) using forest-of-octrees-based block-structured local mesh refinement (LMR) was implemented, and its performance was evaluated on GPU-based supercomputers. We found that the conventional Space-Filling-Curve-based (SFC) domain partitioning algorithm results in costly halo communication in our aerodynamics simulations. Our new tree cutting approach improved the locality and the topology of the partitioned sub-domains and reduced the communication cost to one-third or one-fourth of the original SFC approach. In the strong scaling test, the code achieved maximum $$times1.82$$ speedup at the performance of 2207 MLUPS (mega- lattice update per second) on 128 GPUs. In the weak scaling test, the code achieved 9620 MLUPS at 128 GPUs with 4.473 billion grid points, while the parallel efficiency was 93.4% from 8 to 128 GPUs.

Journal Articles

Iterative methods with mixed-precision preconditioning for ill-conditioned linear systems in multiphase CFD simulations

Ina, Takuya*; Idomura, Yasuhiro; Imamura, Toshiyuki*; Yamashita, Susumu; Onodera, Naoyuki

Proceedings of 12th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems ScalA21) (Internet), 8 Pages, 2021/11

 Times Cited Count:0 Percentile:51.94

A new mixed-precision preconditioner based on the iterative refinement (IR) method is developed for preconditioned conjugate gradient (P-CG) and multigrid preconditioned conjugate gradient (MGCG) solvers in a multi-phase thermal-hydraulic CFD code JUPITER. In the IR preconditioner, all data is stored in FP16 to reduce memory access, while all computation is performed in FP32. The hybrid FP16/32 implementation keeps the similar convergence property as FP32, while the computational performance is close to FP16. The developed solvers are optimized on Fugaku (A64FX), and applied to ill-conditioned matrices in JUPITER. The P-CG and MGCG solvers with the new IR preconditioner show excellent strong scaling up to 8,000 nodes, and at 8,000 nodes, they are respectively accelerated up to 4.86$$times$$ and 2.39$$times$$ from the conventional ones on Oakforest-PACS (KNL).

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