This paper presents an effort to overcome the complexities of production system I/O performance monitoring. We design Beacon, an end-to-end I/O resource monitoring and diagnosis system, for the 40960-node Sunway TaihuLight supercomputer, current ranked world No.3. Beacon simultaneously collects and correlates I/O tracing/profiling data from all the compute nodes, forwarding nodes, storage nodes and metadata servers. With mechanisms such as aggressive online+offline trace compression and distributed caching/storage, it delivers scalable, low-overhead, and sustainable I/O diagnosis under production use. Higher-level per-application I/O performance behaviors are reconstructed from system-level monitoring data to reveal correlations between system performance bottlenecks, utilization symptoms, and application behaviors. Beacon further provides query, statistics, and visualization utilities to users and administrators, allowing comprehensive and in-depth analysis without requiring any code/script modification. With its deployment on TaihuLight for around 18 months, we demonstrate Beacon's effectiveness with real-world use cases for I/O performance issue identification and diagnosis. It has successfully helped center administrators identify obscure design or configuration flaws, system anomaly occurrences, I/O performance interference, and resource under- or over-provisioning problems. Several of the exposed problems have already been fixed, with others being currently addressed. In addition, we demonstrate Beacon's generality by its recent extension to monitor interconnection networks, another contention point on supercomputers. Both Beacon codes and part of collected monitoring data are released.