Final configuration

chrony

/etc/chrony/conf.d/gps.conf

# Coarse NMEA time from gpsd. Labels WHICH second it is. Never the time source.
refclock SHM 0 refid GPS precision 1e-1 offset 0.0 delay 0.2 poll 3 noselect

# Kernel PPS: the precise source. Median-filter 10 pulses, lock to GPS for
# second-numbering, prefer it as the reference.
refclock PPS /dev/pps0 refid PPS precision 1e-9 poll 2 lock GPS filter 10 prefer

allow 10.0.0.0/8

Plus, in chrony.conf:

user root      # needed to read gpsd's SHM segments (mode 0600, root-owned)

Keep the internet servers

Leave a few upstream NTP servers configured. While the GPS cold-acquires after a power cut, chrony leans on them and serves slightly less precise time rather than no time — then demotes them the instant PPS becomes trustworthy. We watched it bridge a 165-second gap and promote itself back to Stratum 1 unattended. That graceful degradation is worth the four lines.

gpsd

/etc/default/gpsd

START_DAEMON="true"
USBAUTO="false"
DEVICES="/dev/ttyAMA0"
GPSD_OPTIONS="-n"        # -n = poll immediately. NEVER pin the baud with -s.

systemctl enable gpsd.service   # NOT just gpsd.socket — see below

Two ways gpsd will betray you

1. Socket activation isn’t enough. chrony reads gpsd’s shared memory, never its socket — so nothing triggers the daemon to start. If it seems to work anyway, something else is connecting to port 2947 and starting it for you. For us that was the dashboard: our monitoring page was load-bearing for the time server. Check with systemctl is-enabled gpsd.service.

2. Never pin the baud. The module reverts to 9600 on power loss, and a pinned gpsd then talks to a device that isn’t listening. Let it auto-probe.

Kernel cmdline

isolcpus=2,3 irqaffinity=0,1 nohz=off cpuidle.off=1 skew_tick=1

systemd affinities

cpu0 is sacred — it holds the PPS interrupt.

chrony.service.d/affinity.conf

[Service]
CPUSchedulingPolicy=rr
CPUSchedulingPriority=20
CPUAffinity=2

# gpsd.service.d/affinity.conf
[Service]
CPUAffinity=3

# everything else (dashboard, Caddy, exporters, cron…)
[Service]
CPUAffinity=1
Nice=10