arXiv subjects

Guangming Tan

Publications and source records attributed to Guangming Tan.

At least 37 records · Page 2Linked to original sources

arXiv2026

Research Paradigm of Materials Science Tetrahedra with Artificial Intelligence

The classical material tetrahedron that represents the Structure-Property-Processing-Performance-Characterization relationship is the most important research paradigm in materials science so far. It has served as a protocol to guide experiments, modeling, and theory to uncover hidden relationships between various aspects of a certain material. This substantially facilitates knowledge accumulation and material discovery with desired functionalities to realize versatile applications. In recent years, with the advent of artificial intelligence (AI) techniques, the attention of AI towards scientific research is soaring. The trials of implementing AI in various disciplines are endless, with great potential to revolutionize the research diagram. Despite the success in natural language processing and computer vision, how to effectively integrate AI with natural science is still a grand challenge, bearing in mind their fundamental differences. Inspired by these observations and limitations, we delve into the current research paradigm dictated by the classical material tetrahedron and propose two new paradigms to stimulate data-driven and AI-augmented research. One tetrahedron focuses on AI for materials science by considering the Matter-Data-Model-Potential-Agent diagram. The other demonstrates AI research by discussing Data-Architecture-Encoding-Optimization-Inference relationships. The crucial ingredients of these frameworks and their connections are discussed, which will likely motivate both scientific thinking refinement and technology advancement. Despite the widespread enthusiasm for chasing AI for science, we must analyze issues rationally to come up with well-defined, resolvable scientific problems in order to better master the power of AI.

cond-mat.mtrl-sci↗

arXiv2026

MatRIS: Toward Reliable and Efficient Pretrained Machine Learning Interatomic Potentials

Foundation MLIPs demonstrate broad applicability across diverse material systems and have emerged as a powerful and transformative paradigm in chemical and computational materials science. Equivariant MLIPs achieve state-of-the-art accuracy in a wide range of benchmarks by incorporating equivariant inductive bias. However, the reliance on tensor products and high-degree representations makes them computationally costly. This raises a fundamental question: as quantum mechanical-based datasets continue to expand, can we develop a more compact model to thoroughly exploit high-dimensional atomic interactions? In this work, we present MatRIS (\textbf{Mat}erials \textbf{R}epresentation and \textbf{I}nteraction \textbf{S}imulation), an invariant MLIP that introduces attention-based modeling of three-body interactions. MatRIS leverages a novel separable attention mechanism with linear complexity $O(N)$, enabling both scalability and expressiveness. MatRIS delivers accuracy comparable to that of leading equivariant models on a wide range of popular benchmarks (Matbench-Discovery, MatPES, MDR phonon, Molecular dataset, etc). Taking Matbench-Discovery as an example, MatRIS achieves an F1 score of up to 0.847 and attains comparable accuracy at a lower training cost. The work indicates that our carefully designed invariant models can match or exceed the accuracy of equivariant models at a fraction of the cost, shedding light on the development of accurate and efficient MLIPs.

cs.LG↗

arXiv2025

Pipelined Dense Symmetric Eigenvalue Decomposition on Multi-GPU Architectures

Large symmetric eigenvalue problems are commonly observed in many disciplines such as Chemistry and Physics, and several libraries including cuSOLVERMp, MAGMA and ELPA support computing large eigenvalue decomposition on multi-GPU or multi-CPU-GPU hybrid architectures. However, these libraries do not provide satisfied performance that all of the libraries only utilize around 1.5\% of the peak multi-GPU performance. In this paper, we propose a pipelined two-stage eigenvalue decomposition algorithm instead of conventional subsequent algorithm with substantial optimizations. On an 8$\times$A100 platform, our implementation surpasses state-of-the-art cuSOLVERMp and MAGMA baselines, delivering mean speedups of 5.74$\times$ and 6.59$\times$, with better strong and weak scalability.

cs.MS↗

arXiv2025

ElasticMM: Efficient Multimodal LLMs Serving with Elastic Multimodal Parallelism

Multimodal large language models (MLLMs) extend LLMs to handle images, videos, and audio by incorporating feature extractors and projection modules. However, these additional components -- combined with complex inference pipelines and heterogeneous workloads -- introduce significant inference overhead. Therefore, efficiently serving MLLMs remains a major challenge. Current tightly coupled serving architectures struggle to distinguish between mixed request types or adapt parallelism strategies to different inference stages, leading to increased time-to-first-token (TTFT) latency and poor resource utilization. To address this, we introduce Elastic Multimodal Parallelism (EMP), a new serving paradigm that elastically adapts to resource heterogeneity across request types and inference stages. Building upon EMP, we develop ElasticMM, an MLLM serving system that (1) separates requests into independent modality groups with dynamic resource allocation via a modality-aware load balancer; (2) decouples inference stages and enables parallelism adjustment and adaptive scaling via elastic partition scheduling; and (3) improves inference efficiency through unified multimodal prefix caching and non-blocking encoding. Experiments on diverse real-world datasets show that ElasticMM outperforms state-of-the-art (SOTA) serving systems, reducing TTFT by up to 4.2x and achieving 3.2-4.5x higher throughput while meeting service-level objectives (SLOs).

cs.DC↗

arXiv2025

Exploring Landscapes for Better Minima along Valleys

Finding lower and better-generalizing minima is crucial for deep learning. However, most existing optimizers stop searching the parameter space once they reach a local minimum. Given the complex geometric properties of the loss landscape, it is difficult to guarantee that such a point is the lowest or provides the best generalization. To address this, we propose an adaptor "E" for gradient-based optimizers. The adapted optimizer tends to continue exploring along landscape valleys (areas with low and nearly identical losses) in order to search for potentially better local minima even after reaching a local minimum. This approach increases the likelihood of finding a lower and flatter local minimum, which is often associated with better generalization. We also provide a proof of convergence for the adapted optimizers in both convex and non-convex scenarios for completeness. Finally, we demonstrate their effectiveness in an important but notoriously difficult training scenario, large-batch training, where Lamb is the benchmark optimizer. Our testing results show that the adapted Lamb, ALTO, increases the test accuracy (generalization) of the current state-of-the-art optimizer by an average of 2.5% across a variety of large-batch training tasks. This work potentially opens a new research direction in the design of optimization algorithms.

cs.LG↗

arXiv2025

SolarZip: An Efficient and Adaptive Compression Framework for Solar EUV Imaging Data

Context: With the advancement of solar physics research, next-generation solar space missions and ground-based telescopes face significant challenges in efficiently transmitting and/or storing large-scale observational data. Aims: We develop an efficient compression and evaluation framework for solar EUV data, specifically optimized for Solar Orbiter Extreme Ultraviolet Imager (EUI) data, significantly reducing data volume while preserving scientific usability. Methods: We systematically evaluated four error-bounded lossy compressors across two EUI datasets. However, the existing methods cannot perfectly handle the EUI datasets (with continuously changing distance and significant resolution differences). Motivated by this, we develop an adaptive hybrid compression strategy with optimized interpolation predictors. Moreover, we designed a two-stage evaluation framework integrating distortion analysis with downstream scientific workflows, ensuring that observational analysis is not affected at high compression ratios. Results: Our framework SolarZip achieved up to 800x reduction for Full Sun Imager (FSI) data and 500x for High Resolution Imager (HRI$_{\text{EUV}}$) data. It significantly outperformed both traditional and advanced algorithms, achieving 3-50x higher compression ratios than traditional algorithms, surpassing the second-best algorithm by up to 30%. Simulation experiments verified that SolarZip can reduce data transmission time by up to 270x while ensuring the preservation of scientific usability. Conclusions: The SolarZip framework significantly enhances solar observational data compression efficiency while preserving scientific usability by dynamically selecting optimal compression methods based on observational scenarios and user requirements. This provides a promising data management solution for deep space missions like Solar Orbiter.

astro-ph.IM↗

arXiv2025

Stencil-Lifting: Hierarchical Recursive Lifting System for Extracting Summary of Stencil Kernel in Legacy Codes

We introduce Stencil-Lifting, a novel system for automatically converting stencil kernels written in low-level languages in legacy code into semantically equivalent Domain-Specific Language (DSL) implementations. Targeting the efficiency bottlenecks of existing verified lifting systems, Stencil-Lifting achieves scalable stencil kernel abstraction through two key innovations. First, we propose a hierarchical recursive lifting theory that represents stencil kernels, structured as nested loops, using invariant subgraphs, which are customized data dependency graphs that capture loop-carried computation and structural invariants. Each vertex in the invariant subgraph is associated with a predicate-based summary, encoding its computational semantics. By enforcing self-consistency across these summaries, Stencil-Lifting ensures the derivation of correct loop invariants and postconditions for nested loops, eliminating the need for external verification. Second, we develop a hierarchical recursive lifting algorithm that guarantees termination through a convergent recursive process, avoiding the inefficiencies of search-based synthesis. The algorithm efficiently derives the valid summaries of stencil kernels, and its completeness is formally proven. We evaluate Stencil-Lifting on diverse stencil benchmarks from two different suites and on four real-world applications. Experimental results demonstrate that Stencil-Lifting achieves 31.62$\times$ and 5.8$\times$ speedups compared to the state-of-the-art verified lifting systems STNG and Dexter, respectively, while maintaining full semantic equivalence. Our work significantly enhances the translation efficiency of low-level stencil kernels to DSL implementations, effectively bridging the gap between legacy optimization techniques and modern DSL-based paradigms.

cs.SE↗

arXiv2025

Deep Learning-Enabled Supercritical Flame Simulation at Detailed Chemistry and Real-Fluid Accuracy Towards Trillion-Cell Scale

For decades, supercritical flame simulations incorporating detailed chemistry and real-fluid transport have been limited to millions of cells, constraining the resolved spatial and temporal scales of the physical system. We optimize the supercritical flame simulation software DeepFlame -- which incorporates deep neural networks while retaining the real-fluid mechanical and chemical accuracy -- from three perspectives: parallel computing, computational efficiency, and I/O performance. Our highly optimized DeepFlame achieves supercritical liquid oxygen/methane (LOX/\ce{CH4}) turbulent combustion simulation of up to 618 and 154 billion cells with unprecedented time-to-solution, attaining 439/1186 and 187/316 PFlop/s (32.3\%/21.8\% and 37.4\%/31.8\% of the peak) in FP32/mixed-FP16 precision on Sunway (98,304 nodes) and Fugaku (73,728 nodes) supercomputers, respectively. This computational capability surpasses existing capacities by three orders of magnitude, enabling the first practical simulation of rocket engine combustion with >100 LOX/\ce{CH4} injectors. This breakthrough establishes high-fidelity supercritical flame modeling as a critical design tool for next-generation rocket propulsion and ultra-high energy density systems.

cs.DC↗

arXiv2025

JingZhao: A Framework for Rapid NIC Prototyping in the Domain-Specific-Network Era

The network is becoming domain-specific, which requires on-demand design of the network protocols, as well as the microarchitecture of the NIC. However, to develop such a NIC is not that easy. Since the scissor gap between network speed and the growth of CPU frequency is expanding, most of the protocols need to be offloaded to hardware. The process of designing, verifying and optimizing a domain-specific NIC usually takes great effort, which hinders the rapid iteration of new protocols and algorithms. In this paper, we propose JingZhao, an open-sourced framework for NIC prototyping, which could be leveraged to rapidly implement and verify a domain-specific NIC. Using this framework, we implement a fully-functional RDMA NIC (RNIC). To the best of our knowledge, this represents the first open-source RDMA NIC solution with complete compatibility to the standard OFED communication library. The RNIC was also taped out using TSMC's 28nm process to validate our design. Our evaluation results show that new network functions can be easily integrated into the framework, and achieve nearly line-rate packet processing.

cs.NI↗

arXiv2025

FastDup: a scalable duplicate marking tool using speculation-and-test mechanism

Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as the gold-standard tool, its single-threaded implementation and reliance on global sorting result in significant computational and resource overhead, limiting its efficiency on large-scale datasets. Here, we introduce FastDup: a high-performance, scalable solution that follows the speculation-and-test mechanism. FastDup achieves up to 20x throughput speedup and guarantees 100\% identical output compared to Picard MarkDuplicates. FastDup is a C++ program available from GitHub (https://github.com/zzhofict/FastDup.git) under the MIT license.

q-bio.GN↗

arXiv2025

TSUE: A Two-Stage Data Update Method for an Erasure Coded Cluster File System

Compared to replication-based storage systems, erasure-coded storage incurs significantly higher overhead during data updates. To address this issue, various parity logging methods have been pro- posed. Nevertheless, due to the long update path and substantial amount of random I/O involved in erasure code update processes, the resulting long latency and low throughput often fail to meet the requirements of high performance applications. To this end, we propose a two-stage data update method called TSUE. TSUE divides the update process into a synchronous stage that records updates in a data log, and an asynchronous stage that recycles the log in real-time. TSUE effectively reduces update latency by transforming random I/O into sequential I/O, and it significantly reduces recycle overhead by utilizing a three-layer log and the spatio-temporal locality of access patterns. In SSDs cluster, TSUE significantly im- proves update performance, achieving improvements of 7.6X under Ali-Cloud trace, 5X under Ten-Cloud trace, while it also extends the SSD's lifespan by up to 13X through reducing the frequencies of reads/writes and of erase operations.

cs.DC↗

arXiv2025

Scaling Neural-Network-Based Molecular Dynamics with Long-Range Electrostatic Interactions to 51 Nanoseconds per Day

Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical phenomena such as protein folding and dipolar surface and maintaining ab initio accuracy. However, neural network inference and long-range force computation remain the major bottlenecks, severely limiting simulation speed. In this paper, we target DPLR, a state-of-the-art NNMD package that supports long-range electrostatics, and propose a set of comprehensive optimizations to enhance computational efficiency. We introduce (1) a hardware-offloaded FFT method to reduce the communication overhead; (2) an overlapping strategy that hides long-range force computations using a single core per node, and (3) a ring-based load balancing method that enables atom-level task evenly redistribution with minimal communication overhead. Experimental results on the Fugaku supercomputer show that our work achieves a 37x performance improvement, reaching a maximum simulation speed of 51 ns/day.

cs.DC↗

arXiv2025

FastCHGNet: Training one Universal Interatomic Potential to 1.5 Hours with 32 GPUs

Graph neural network universal interatomic potentials (GNN-UIPs) have demonstrated remarkable generalization and transfer capabilities in material discovery and property prediction. These models can accelerate molecular dynamics (MD) simulation by several orders of magnitude while maintaining \textit{ab initio} accuracy, making them a promising new paradigm in material simulations. One notable example is Crystal Hamiltonian Graph Neural Network (CHGNet), pretrained on the energies, forces, stresses, and magnetic moments from the MPtrj dataset, representing a state-of-the-art GNN-UIP model for charge-informed MD simulations. However, training the CHGNet model is time-consuming(8.3 days on one A100 GPU) for three reasons: (i) requiring multi-layer propagation to reach more distant atom information, (ii) requiring second-order derivatives calculation to finish weights updating and (iii) the implementation of reference CHGNet does not fully leverage the computational capabilities. This paper introduces FastCHGNet, an optimized CHGNet, with three contributions: Firstly, we design innovative Force/Stress Readout modules to decompose Force/Stress prediction. Secondly, we adopt massive optimizations such as kernel fusion, redundancy bypass, etc, to exploit GPU computation power sufficiently. Finally, we extend CHGNet to support multiple GPUs and propose a load-balancing technique to enhance GPU utilization. Numerical results show that FastCHGNet reduces memory footprint by a factor of 3.59. The final training time of FastCHGNet can be decreased to \textbf{1.53 hours} on 32 GPUs without sacrificing model accuracy.

cs.DC↗

arXiv2025

Large Scale Finite-Temperature Real-time Time Dependent Density Functional Theory Calculation with Hybrid Functional on ARM and GPU Systems

Ultra-fast electronic phenomena originating from finite temperature, such as nonlinear optical excitation, can be simulated with high fidelity via real-time time dependent density functional theory (rt-TDDFT) calculations with hybrid functional. However, previous rt-TDDFT simulations of real materials using the optimal gauge--known as the parallel transport gauge--have been limited to low-temperature systems with band gaps. In this paper, we introduce the parallel transport-implicit midpoint (PT-IM) method, which significantly accelerates finite-temperature rt-TDDFT calculations of real materials with hybrid function. We first implement PT-IM with hybrid functional in our plane wave code PWDFT, and optimized it on both GPU and ARM platforms to build a solid baseline code. Next, we propose a diagonalization method to reduce computation and communication complexity, and then, we employ adaptively compressed exchange (ACE) method to reduce the frequency of the most expensive Fock exchange operator. Finally, we adopt the ring\_based method and the shared memory mechanism to overlap computation and communication and alleviate memory consumption respectively. Numerical results show that our optimized code can reach 3072 atoms for rt-TDDFT simulation with hybrid functional at finite temperature on 192 computing nodes, the time-to-solution for one time step is 429.3s, which is 41.4 times faster compared to the baseline.

cond-mat.mtrl-sci↗

arXiv2024

ALKPU: an active learning method for the DeePMD model with Kalman filter

Neural network force field models such as DeePMD have enabled highly efficient large-scale molecular dynamics simulations with ab initio accuracy. However, building such models heavily depends on the training data obtained by costly electronic structure calculations, thereby it is crucial to carefully select and label the most representative configurations during model training to improve both extrapolation capability and training efficiency. To address this challenge, based on the Kalman filter theory we propose the Kalman Prediction Uncertainty (KPU) to quantify uncertainty of the model's prediction. With KPU we design the Active Learning by KPU (ALKPU) method, which can efficiently select representative configurations that should be labelled during model training. We prove that ALKPU locally leads to the fastest reduction of model's uncertainty, which reveals its rationality as a general active learning method. We test the ALKPU method using various physical system simulations and demonstrate that it can efficiently coverage the system's configuration space. Our work demonstrates the benefits of ALKPU as a novel active learning method, enhancing training efficiency and reducing computational resource demands.

physics.comp-ph↗

arXiv2024

Scaling Molecular Dynamics with ab initio Accuracy to 149 Nanoseconds per Day

Physical phenomena such as chemical reactions, bond breaking, and phase transition require molecular dynamics (MD) simulation with ab initio accuracy ranging from milliseconds to microseconds. However, previous state-of-the-art neural network based MD packages such as DeePMD-kit can only reach 4.7 nanoseconds per day on the Fugaku supercomputer. In this paper, we present a novel node-based parallelization scheme to reduce communication by 81%, then optimize the computationally intensive kernels with sve-gemm and mixed precision. Finally, we implement intra-node load balance to further improve the scalability. Numerical results on the Fugaku supercomputer show that our work has significantly improved the time-to-solution of the DeePMD-kit by a factor of 31.7x, reaching 149 nanoseconds per day on 12,000 computing nodes. This work has opened the door for millisecond simulation with ab initio accuracy within one week for the first time.

cs.DC↗

arXiv2024

Overcoming Memory Constraints in Quantum Circuit Simulation with a High-Fidelity Compression Framework

Full-state quantum circuit simulation requires exponentially increased memory size to store the state vector as the number of qubits scales, presenting significant limitations in classical computing systems. Our paper introduces BMQSim, a novel state vector quantum simulation framework that employs lossy compression to address the memory constraints on graphics processing unit (GPU) machines. BMQSim effectively tackles four major challenges for state-vector simulation with compression: frequent compression/decompression, high memory movement overhead, lack of dedicated error control, and unpredictable memory space requirements. Our work proposes an innovative strategy of circuit partitioning to significantly reduce the frequency of compression occurrences. We introduce a pipeline that seamlessly integrates compression with data movement while concealing its overhead. Additionally, BMQSim incorporates the first GPU-based lossy compression technique with point-wise error control. Furthermore, BMQSim features a two-level memory management system, ensuring efficient and stable execution. Our evaluations demonstrate that BMQSim can simulate the same circuit with over 10 times less memory usage on average, achieving fidelity over 0.99 and maintaining comparable simulation time to other state-of-the-art simulators.

cs.DC↗

arXiv2024

FNCC: Fast Notification Congestion Control in Data Center Networks

Congestion control plays a pivotal role in large-scale data centers, facilitating ultra-low latency, high bandwidth, and optimal utilization. Even with the deployment of data center congestion control mechanisms such as DCQCN and HPCC, these algorithms often respond to congestion sluggishly. This sluggishness is primarily due to the slow notification of congestion. It takes almost one round-trip time (RTT) for the congestion information to reach the sender. In this paper, we introduce the Fast Notification Congestion Control (FNCC) mechanism, which achieves sub-RTT notification. FNCC leverages the acknowledgment packet (ACK) from the return path to carry in-network telemetry (INT) information of the request path, offering the sender more timely and accurate INT. To further accelerate the responsiveness of last-hop congestion control, we propose that the receiver notifies the sender of the number of concurrent congested flows, which can be used to adjust the congested flows to a fair rate quickly. Our experimental results demonstrate that FNCC reduces flow completion time by 27.4% and 88.9% compared to HPCC and DCQCN, respectively. Moreover, FNCC triggers minimal pause frames and maintains high utilization even at 400Gbps.

cs.NI↗