Benefiting from the self-attention mechanism, Transformer models have attained impressive contextual comprehension capabilities for lengthy texts. The requirements of high-throughput inference arise as the large language models (LLMs) become increasingly prevalent, which calls for large-scale token parallel processing (LTPP). However, existing dynamic sparse accelerators struggle to effectively handle LTPP, as they solely focus on separate stage optimization, and with most efforts confined to computational enhancements. By re-examining the end-to-end flow of dynamic sparse acceleration, we pinpoint an ever-overlooked opportunity that the LTPP can exploit the intrinsic coordination among stages to avoid excessive memory access and redundant computation. Motivated by our observation, we present SOFA, a cross-stage compute-memory efficient algorithm-hardware co-design, which is tailored to tackle the challenges posed by LTPP of Transformer inference effectively. We first propose a novel leading zero computing paradigm, which predicts attention sparsity by using log-based add-only operations to avoid the significant overhead of prediction. Then, a distributed sorting and a sorted updating FlashAttention mechanism are proposed with cross-stage coordinated tiling principle, which enables fine-grained and lightweight coordination among stages, helping optimize memory access and latency. Further, we propose a SOFA accelerator to support these optimizations efficiently. Extensive experiments on 20 benchmarks show that SOFA achieves $9.5\times$ speed up and $71.5\times$ higher energy efficiency than Nvidia A100 GPU. Compared to eight SOTA accelerators, SOFA achieves an average $15.8\times$ energy efficiency, $10.3\times$ area efficiency and $9.3\times$ speed up, respectively.

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