Timing signals have been restored and the models on the cymac are running again.
Timing for the cryo lab CyMAC is supplied by a Silicon Labs 5340 eval board. It needs to be initialized by a Raspberry Pi. As far as I can tell, the root cause of this problem is that the Pi has not been configured to run the necessary initialization script automatically on startup. The other issue is that we have two Pis for timing in the lab (the second one controls the GPS receiver), and at first I had them mixed up.
The timing board connects to the Pi over the I2C bus. The command i2cdetect -y 1, on the correct Pi, confirmed a device with address 77 was present. This is an uninitialized timing board. After running the initialization script (./si5340init.py Si5340-RevD-RTSCLOCK-Registers.txt, found in /opt/rtcds/tst/x1/target/timing), the I2C address updated to 75, representing an initialized timing board. Then models on cymac1 could start and run normally.
To be fixed next time: run the init script automatically on startup, give the two Pis descriptive hostnames to make it clear which one controls what, and put the timing board and its Pi into a proper enclosure.
i2cdetect -y 1