The scaling law for large language models (LLMs) depicts that the path towards machine intelligence necessitates training at large scale. Thus, companies continuously build large-scale GPU clusters, and launch training jobs that span over thousands of computing nodes. However, LLM pre-training presents unique challenges due to its complex communication patterns, where GPUs exchange data in sparse yet high-volume bursts within specific groups. Inefficient resource scheduling exacerbates bandwidth contention, leading to suboptimal training performance. This paper presents Arnold, a scheduling system summarizing our experience to effectively align LLM communication patterns with data center topology at scale. An in-depth characteristic study is performed to identify the impact of physical network topology to LLM pre-training jobs. Based on the insights, we develop a scheduling algorithm to effectively align communication patterns with the physical network topology in modern data centers. Through simulation experiments, we show the effectiveness of our algorithm in reducing the maximum spread of communication groups by up to $1.67$x. In production training, our scheduling system improves the end-to-end performance by $10.6\%$ when training with more than $9600$ GPUs, a significant improvement for our training pipeline.