The rapid proliferation of large language models has driven the need for efficient GPU training clusters. However, ensuring high-performance training in these clusters is challenging due to the complexity of software-hardware interactions and the frequent occurrence of training anomalies. Since existing diagnostic tools are narrowly tailored to specific issues, there are gaps in their ability to address anomalies spanning the entire training stack. In response, we introduce XPUTIMER, a real-time diagnostic framework designed for distributed LLM training at scale. XPUTIMER first integrates a lightweight tracing daemon to monitor key code segments with minimal overhead. Additionally, it features a diagnostic engine that employs novel intra-kernel tracing and holistic aggregated metrics to efficiently identify and resolve anomalies. Deployment of XPUTIMER across 6,000 GPUs over eight months demonstrated significant improvements across the training stack, validating its effectiveness in real-world scenarios.