arXiv subjects

Guangnan Feng

Publications and source records attributed to Guangnan Feng.

4 recordsLinked to original sources

arXiv2026

POLAR-PIC: A Holistic Framework for Matrixized PIC with Co-Designed Compute, Layout, and Communication

Particle-in-Cell (PIC) simulations are fundamental to plasma physics but often suffer from limited scalability due to particle-grid interaction bottlenecks and particle redistribution costs. Specifically, the particle-grid interaction computations have not taken full advantage of the emerging Matrix Processing Units (MPUs), the particle motion introduces irregular memory accesses, and the bulk-synchronous redistribution further destroys long-term data locality thereby limiting parallel efficiency. To address these inefficiencies, we present POLAR-PIC, a co-designed framework for large-scale PIC simulations that (i) reformulates Field Interpolation into an MPU-friendly outer-product form, (ii) maintains a physically ordered particle layout to preserve memory contiguity, and (iii) overlaps particle communication with Deposition to hide redistribution overhead. The evaluation on the pilot system of an Exascale supercomputer demonstrates that POLAR-PIC accelerates the entire particle-processing phase by up to 10.9x in uniform plasma and 4.4x in real-world laser-ion acceleration scenarios compared to the native WarpX reference pipeline on LX2. Ablation studies reveal that the speedups achieved by Interpolation and Deposition are 8.0x and 13.2x, respectively, and the asynchronous communication design sustains a 99.1% overlap ratio. In cross-platform comparisons, POLAR-PIC achieves 13.2% of theoretical peak efficiency on the CPU-based LS system, while WarpX reaches 9.6% on NVIDIA A800 GPUs. Notably, the scalability evaluation demonstrates that POLAR-PIC maintains 67.5% weak scaling efficiency on over 2 million cores under high-migration dynamic workloads, highlighting the importance of holistic co-design for future matrix-centric HPC systems.

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arXiv2026

Clinical-Injection Transformer with Domain-Adapted MAE for Lupus Nephritis Prognosis Prediction

Lupus nephritis (LN) is a severe complication of systemic lupus erythematosus that affects pediatric patients with significantly greater severity and worse renal outcomes compared to adults. Despite the urgent clinical need, predicting pediatric LN prognosis remains unexplored in computational pathology. Furthermore, the only existing histopathology-based approach for LN relies on multiple costly staining protocols and fails to integrate complementary clinical data. To address these gaps, we propose the first multimodal computational pathology framework for three-class treatment response prediction (complete remission, partial response, and no response) in pediatric LN, utilizing only routine PAS-stained biopsies and structured clinical data. Our framework introduces two key methodological innovations. First, a Clinical-Injection Transformer (CIT) embeds clinical features as condition tokens into patch-level self-attention, facilitating implicit and bidirectional cross-modal interactions within a unified attention space. Second, we design a decoupled representation-knowledge adaptation strategy using a domain-adapted Masked Autoencoder (MAE). This strategy explicitly separates self-supervised morphological feature learning from pathological knowledge extraction. Additionally, we introduce a multi-granularity morphological type injection mechanism to bridge distilled classification knowledge with downstream prognostic predictions at both the instance and patient levels. Evaluated on a cohort of 71 pediatric LN patients with KDIGO-standardized labels, our method achieves a three-class accuracy of 90.1% and an AUC of 89.4%, demonstrating its potential as a highly accurate and cost-effective prognostic tool.

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arXiv2026

Matrix-PIC: Harnessing Matrix Outer-product for High-Performance Particle-in-Cell Simulations

Particle-in-Cell (PIC) simulations spend most of their execution time on particle--grid interactions, where fine-grained atomic updates become a major bottleneck on traditional many-core CPUs. Recent CPU architectures integrate specialized Matrix Processing Units (MPUs) that efficiently support matrix outer-product operations, offering new opportunities to overcome this limitation. Leveraging this architectural shift, this work focuses on redesigning the current deposition step of PIC simulations under a matrix-centric execution model. We present MatrixPIC, the first holistic co-design of the deposition kernel, data layout, and incremental particle sorting tailored to the hybrid MPU--VPU SIMD model on modern CPUs. MatrixPIC introduces: (i)~a block-matrix formulation of the current deposition algorithm that maps naturally to MPU outer-product primitives; (ii)~a hybrid execution pipeline that combines MPU-based high-density accumulation with VPU-based data preparation and control flow; and (iii)~an $O(1)$-amortized incremental sorter based on a gapped packed-memory array to preserve data locality for efficient MPU execution. Evaluated on a next-generation HPC platform, MatrixPIC achieves significant performance gains. In Laser-Wakefield Acceleration (LWFA) simulations, it delivers up to $2.63\times$ speedup in total runtime. For third-order deposition, the core kernel is accelerated by $8.7\times$ over the baseline and $2.0\times$ over the best hand-optimized VPU implementation. Moreover, MatrixPIC reaches $83.08\%$ of theoretical CPU peak performance, nearly $2.8\times$ higher than a highly optimized CUDA kernel on a data center GPU. These results demonstrate the effectiveness of matrix-oriented co-design for accelerating PIC simulations on emerging CPU architectures.

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arXiv2024

UNR: Unified Notifiable RMA Library for HPC

Remote Memory Access (RMA) enables direct access to remote memory to achieve high performance for HPC applications. However, most modern parallel programming models lack schemes for the remote process to detect the completion of RMA operations. Many previous works have proposed programming models and extensions to notify the communication peer, but they did not solve the multi-NIC aggregation, portability, hardware-software co-design, and usability problems. In this work, we proposed a Unified Notifiable RMA (UNR) library for HPC to address these challenges. In addition, we demonstrate the best practice of utilizing UNR within a real-world scientific application, PowerLLEL. We deployed UNR across four HPC systems, each with a different interconnect. The results show that PowerLLEL powered by UNR achieves up to a 36% acceleration on 1728 nodes of the Tianhe-Xingyi supercomputing system.

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