Most Stable Raspberry Pi? 81% Better NTP with Thermal Management

Summary

I’ve written before about building microsecond-accurate NTP servers with Raspberry Pi and GPS PPS, and more recently about revisiting the setup in 2025. Both posts focused on the hardware setup and basic configuration to achieve sub-microsecond time synchronization using GPS Pulse Per Second (PPS) signals. But there was a problem. Despite having a stable PPS reference, my NTP server’s frequency drift was exhibiting significant variation over time. After months (years) of monitoring the system with Grafana dashboards, I noticed something interesting: the frequency oscillations seemed to correlate with CPU temperature changes. The frequency would drift as the CPU heated up during the day and cooled down at night, even though the PPS reference remained rock-solid. Like clockwork (no pun intended), I somehow get sucked back into trying to improve my setup every 6-8 weeks. This post is the latest on that never-ending quest. This post details how I achieved an 81% reduction in frequency variability and 77% reduction in frequency standard deviation through a combination of CPU core pinning and thermal stabilization. Welcome to Austin’s Nerdy Things, where we solve problems that 99.999% of people (and 99% of datacenters) don’t have. The Problem: Thermal-Induced Timing Jitter Modern CPUs, including those in Raspberry Pis, use dynamic frequency scaling to save power and manage heat. When the CPU is idle, it runs at a lower frequency (and voltage). When load increases, it scales up. This is great for power efficiency, but terrible for precision timekeeping. Why? Because timekeeping (with NTP/chronyd/others) relies on a stable system clock to discipline itself against reference sources. If the CPU frequency is constantly changing, the system clock’s tick rate varies, introducing jitter into the timing measurements. Even though my PPS signal was providing a mostly perfect 1-pulse-per-second reference, the CPU’s frequency bouncing around made it harder for chronyd to maintain a s...