The clock used for this host is a CNS Clock from http://www.cnssys.com.
The manual provides details on setting up NTP with built in support for the Motorola Oncore NTPD drivers. See attached PDF.
The instructions in the PDF will first have you put the CNS Clock into a site survey mode. Beware!! This mode will throw the 1PPS for the system out of sync and could mess up observing. It can take several hours for the CNS Clock to determine the location down to the threshold of < 5m.
This threshold is the best for doing precision timing with the CNS Clock (see PDF manual). CNS Clock can be initially setup with Tac32 software, available from http://www.cnssys.com
Use a 9pin pass through (non-cross over) cable.
See the manual for full pinout details.
As the reference location has been stored in the CNS Clock already, MODE 0 can be used when launching NTP (see /etc/ntp.oncore0
This assumes the set geo location is correct and start from there.