arXiv subjects

Ziyu Du

Publications and source records attributed to Ziyu Du.

2 recordsLinked to original sources

arXiv2026

A performance portable fast Ewald summation for Stokes flow

We present GPU algorithms for Ewald summation methods for accelerating N-body Stokes flow problems in periodic domains. Like most N-body codes, Ewald sums use a near-field/far-field decomposition. The near field involves particle-to-particle (P2P) interactions. The far field primarily involves particle-to-grid (P2G) and grid-to-particle (G2P) interactions, as well as Fast Fourier Transforms. For each interaction, we investigate several algorithmic variants. Our implementation uses PyKokkos, a Python interface for the Kokkos C++ parallel programming framework, which supports portability to AMD/NVIDIA GPU and ARM/x86 CPU architectures. Double and single-precision numerical results, alongside analytical performance models, confirm the efficiency of our algorithms on AMD and NVIDIA GPU and on ARM and AMD CPU architectures. The P2P interaction achieves around 73% compute efficiency on NVIDIA H200, 84% on NVIDIA A100, 60% on AMD MI300, 52% on Grace CPU, and 68% on AMD Epyc CPU. A straightforward implementation of the P2G kernel can become a computational bottleneck. We introduce a novel P2G algorithm that achieves up to 16$\times$ speedup compared to a baseline GPU implementation. The overall Ewald sum code processes approximately 8 million particles per second on a H200 GPU, and about a half-million particles per second on a Grace CPU, for nine digits of accuracy. We also perform a multi-GPU weak scaling test on up to 256 million particles (64 GPUs) that shows bounded communication cost for all stages except the all-to-all particle sorting, which can be reduced to neighbor communication in the relevant time-stepping regime.

math.NA↗

arXiv2023

A synchronization-capturing multi-scale solver to the noisy integrate-and-fire neuron networks

The noisy leaky integrate-and-fire (NLIF) model describes the voltage configurations of neuron networks with an interacting many-particles system at a microscopic level. When simulating neuron networks of large sizes, computing a coarse-grained mean-field Fokker-Planck equation solving the voltage densities of the networks at a macroscopic level practically serves as a feasible alternative in its high efficiency and credible accuracy. However, the macroscopic model fails to yield valid results of the networks when simulating considerably synchronous networks with active firing events. In this paper, we propose a multi-scale solver for the NLIF networks, which inherits the low cost of the macroscopic solver and the high reliability of the microscopic solver. For each temporal step, the multi-scale solver uses the macroscopic solver when the firing rate of the simulated network is low, while it switches to the microscopic solver when the firing rate tends to blow up. Moreover, the macroscopic and microscopic solvers are integrated with a high-precision switching algorithm to ensure the accuracy of the multi-scale solver. The validity of the multi-scale solver is analyzed from two perspectives: firstly, we provide practically sufficient conditions that guarantee the mean-field approximation of the macroscopic model and present rigorous numerical analysis on simulation errors when coupling the two solvers; secondly, the numerical performance of the multi-scale solver is validated through simulating several large neuron networks, including networks with either instantaneous or periodic input currents which prompt active firing events over a period of time.

math.NA↗