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May 19

FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics

Graph neural network (GNN) potentials such as SchNet improve the accuracy and transferability of molecular dynamics (MD) simulation by learning many-body interactions, but remain slower than classical force fields due to fragmented kernels and memory-bound pipelines that underutilize GPUs. We show that a missing principle is making GNN-MD IO-aware, carefully accounting for reads and writes between GPU high-bandwidth memory (HBM) and on-chip SRAM. We present FlashSchNet, an efficient and accurate IO-aware SchNet-style GNN-MD framework built on four techniques: (1) flash radial basis, which fuses pairwise distance computation, Gaussian basis expansion, and cosine envelope into a single tiled pass, computing each distance once and reusing it across all basis functions; (2) flash message passing, which fuses cutoff, neighbor gather, filter multiplication, and reduction to avoid materializing edge tensors in HBM; (3) flash aggregation, which reformulates scatter-add via CSR segment reduce, reducing atomic writes by a factor of feature dimension and enabling contention-free accumulation in both forward and backward passes; (4) channel-wise 16-bit quantization that exploits the low per-channel dynamic range in SchNet MLP weights to further improve throughput with negligible accuracy loss. On a single NVIDIA RTX PRO 6000, FlashSchNet achieves 1000 ns/day aggregate simulation throughput over 64 parallel replicas on coarse-grained (CG) protein containing 269 beads (6.5x faster than CGSchNet baseline with 80% reduction of peak memory), surpassing classical force fields (e.g. MARTINI) while retaining SchNet-level accuracy and transferability.

  • 5 authors
·
Feb 13

Cuckoo-GPU: Accelerating Cuckoo Filters on Modern GPUs

Approximate Membership Query (AMQ) structures are essential for high-throughput systems in databases, networking, and bioinformatics. While Bloom filters offer speed, they lack support for deletions. Existing GPU-based dynamic alternatives, such as the Two-Choice Filter (TCF) and GPU Quotient Filter (GQF), enable deletions but incur severe performance penalties. We present Cuckoo-GPU, an open-source, high-performance Cuckoo filter library for GPUs. Instead of prioritizing cache locality, Cuckoo-GPU embraces the inherently random access pattern of Cuckoo hashing to fully saturate global memory bandwidth. Our design features a lock-free architecture built on atomic compare-and-swap operations, paired with a novel breadth-first search-based eviction heuristic that minimizes thread divergence and bounds sequential memory accesses during high-load insertions. Evaluated on NVIDIA GH200 (HBM3) and RTX PRO 6000 Blackwell (GDDR7) systems, Cuckoo-GPU closes the performance gap between append-only and dynamic AMQ structures. It achieves insertion, query, and deletion throughputs up to 378x (4.1x), 6x (34.7x), and 258x (107x) higher than GQF (TCF) on the same hardware, respectively, and delivers up to a 350x speedup over the fastest available multi-threaded CPU-based Cuckoo filter implementation. Moreover, its query throughput rivals that of the append-only GPU-based Blocked Bloom filter - demonstrating that dynamic AMQ structures can be deployed on modern accelerators without sacrificing performance.

ARCQuant: Boosting NVFP4 Quantization with Augmented Residual Channels for LLMs

The emergence of fine-grained numerical formats like NVFP4 presents new opportunities for efficient Large Language Model (LLM) inference. However, it is difficult to adapt existing Post-Training Quantization (PTQ) strategies to these formats: rotation-based methods compromise fine-grained block isolation; smoothing techniques struggle with significant 4-bit quantization errors; and mixed-precision approaches often conflict with hardware constraints on unified-precision computation. To address these challenges, we propose ARCQuant, a framework that boosts NVFP4 performance via Augmented Residual Channels. Distinct from methods that compromise block isolation or hardware uniformity, ARCQuant maintains a strictly unified NVFP4 format by augmenting the activation matrix with quantized residual channels. This design integrates the error compensation process directly into the matrix reduction dimension, enabling the use of standard, highly optimized GEMM kernels with minimal overhead. Theoretical analysis confirms that the worst-case error bound of our dual-stage NVFP4 quantization is comparable to that of standard 8-bit formats such as MXFP8. Extensive experiments on LLaMA and Qwen models demonstrate that ARCQuant achieves state-of-the-art accuracy, comparable to full-precision baselines in perplexity and downstream tasks. Furthermore, deployment on RTX 5090 and RTX PRO 6000 GPUs confirms practical benefits, achieving up to 3x speedup over FP16. Our code is available at https://github.com/actypedef/ARCQuant .

  • 6 authors
·
Jan 12

Scaling DoRA: High-Rank Adaptation via Factored Norms and Fused Kernels

Weight-Decomposed Low-Rank Adaptation (DoRA) extends LoRA by decoupling weight magnitude from direction, but its forward pass requires the row-wise norm of W + sBA, a computation that every major framework we surveyed implements by materializing the dense [d_out, d_in] product BA. At d_in = 8192 and rank r = 384, a single module's norm requires about 512 MB of transient working memory in bf16, making high-rank DoRA costly and often infeasible on common single-GPU setups once hundreds of adapted modules and checkpointing are involved. We present two systems contributions. A factored norm decomposes the squared norm into base, cross, and Gram terms computable through O(d_out r + r^2) intermediates, eliminating the dense product. Fused Triton kernels collapse the four-kernel DoRA composition into a single pass, reducing memory traffic by about 4x and using a numerically stable form that avoids catastrophic cancellation in the near-unity rescaling regime where magnitude scales concentrate in practice. Across six 8-32B vision-language models (VLMs) on three NVIDIA GPUs (RTX 6000 PRO, H200, B200) at r = 384 in bf16, the fused implementation is 1.5-2.0x faster than Hugging Face PEFT's DoRA implementation for inference and 1.5-1.9x faster for gradient computation (optimizer step excluded), with up to 7 GB lower peak VRAM. Microbenchmarks on six GPUs spanning four architecture generations (L40S, A100, RTX 6000 PRO, H200, B200, B300) confirm 1.5-2.7x compose-kernel speedup. Final-logit cosine similarity exceeds 0.9999 across all model/GPU pairs, and multi-seed training curves match within 7.1 x 10^-4 mean per-step loss delta over 2000 steps.

  • 2 authors
·
Mar 23 2

Profiling Large Language Model Inference on Apple Silicon: A Quantization Perspective

A systematic understanding of Apple Silicon is lacking in the current landscape of hardware efficiency; research focus is largely centered on accelerating GPUs for large-scale training or inference on CUDA devices. This paper investigates Apple Silicon's unique memory architecture that offers a unified memory integrating CPU and GPU memory and its implications for on-device LLM inference. We decipher myths about whether Apple Silicon is efficient for on-device inference compared to competitors such as NVIDIA GPUs by directly conducting latency and throughput comparison benchmarks. We explain the performance gap between them through profiling low level hardware metrics - ALU utilization, memory bandwidth, buffer usage, cache residency etc. at runtime. We draw several insights regarding performance bottlenecks such as dequantization overhead, compute throughput and memory bandwidth. We debunk existing false claims regarding large language model inference such as compressing models to lower bit precision is a defacto promise for faster inference across all hardware platforms. We find that the large unified memory enables Apple Silicon to be both cost effective and efficient against NVIDIA GPUs for ultra large language models. Our large scale evaluation on 5 hardware testbeds incorporating three Apple M-series devices: M2 Ultra, M2 Max and M4 Pro and two NVIDIA GPUs: NVIDIA RTX A6000, a multi GPU setup with 2xNVIDIA RTX A6000, 5 model scales ranging from 8B to 405B parameters and 14 quantization schemes gives an understanding of how Apple Silicon fits within the paradigm of on-device LLM inference. Our analysis reveals multiple resource interdependencies and unexpected findings, while also quantifying established insights. To the best of our knowledge, this study makes the first attempt to present a thorough characterization and analysis of Apple Silicon for on-device inference.

  • 2 authors
·
Aug 11, 2025

CudaForge: An Agent Framework with Hardware Feedback for CUDA Kernel Optimization

Developing efficient CUDA kernels is increasingly critical for AI applications such as large-scale LLM training. However, manual kernel design is both costly and time-consuming, motivating automatic approaches that leverage LLMs for code generation. Existing methods for automatic kernel generation, however, often produce low-efficiency kernels, incur high computational overhead, and fail to generalize across settings. In this work, we propose CudaForge, a training-free multi-agent workflow for CUDA kernel generation and optimization. Our workflow is inspired by the iterative workflow of human experts, which contains steps such as developing initial kernels, testing correctness, analyzing hardware feedback, and iterative improvement. More specifically, CudaForge employs two LLM agents: a Coder and a Judge, that iteratively generate, correct, and optimize CUDA kernels, while integrating hardware feedback such as Nsight Compute (NCU) metrics. In extensive evaluations, we show that CudaForge, by leveraging base models like OpenAI-o3, achieves 97.6\% correctness of generated kernels and an average 1.68times speedup over PyTorch baselines, substantially surpassing state-of-the-art models including OpenAI-o3 and Kevin on KernelBench.Beyond accuracy and speed, CudaForge demonstrates strong generalization across GPUs (A100, RTX 6000, 4090, 3090) and base models (OpenAI-o3, GPT-5, gpt-oss-120B, Claude-Sonnet-4, QwQ-32B), while maintaining high efficiency. In particular, generating an optimized kernel takes about 26.5 minutes on one RTX6000 and incurs about \ 0.3 API cost, which is significantly cheaper than existing agentic work that costs 6 H100 hours and 5 API cost per kernel. Our results highlight that multi-agent, training-free workflows can enable cost-effective, generalizable, and high-performance CUDA kernel optimization. Code available at https://github.com/OptimAI-Lab/CudaForge

  • 6 authors
·
Oct 23, 2025