Flash Sparse Attention: An Alternative Efficient Implementation of Native Sparse Attention Kernel

Recent progress in sparse attention mechanisms has demonstrated strong potential for reducing the computational cost of long-context training and inference in large language models (LLMs). Native Sparse Attention (NSA), a state-of-the-art approach, introduces natively trainable, hardware-aligned sparse attention that delivers substantial system-level performance gains while maintaining accuracy comparable to full attention. However, the kernel implementation of NSA relies on a query-grouping strategy that is efficient only with large Grouped Query Attention (GQA) sizes, whereas modern LLMs typically adopt much smaller GQA groups, which limits the applicability of this sparse algorithmic advance. In this work, we propose Flash Sparse Attention (FSA), which includes an alternative kernel design that enables efficient NSA computation across a wide range of popular LLMs with varied smaller GQA group sizes on modern GPUs. Compared to vanilla NSA kernel implementation, our empirical evaluation demonstrates that FSA achieves (i) up to 3.5$\times$ and on average 1.6$\times$ kernel-level latency reduction, (ii) up to 1.25$\times$ and 1.09$\times$ on average end-to-end training speedup on state-of-the-art LLMs, and (iii) up to 1.36$\times$ and 1.11$\times$ on average end-to-end prefill speedup on state-of-the-art LLMs. The source code is open-sourced and publicly available at https://github.com/Relaxed-System-Lab/Flash-Sparse-Attention.