tl;dr: NTP servers and clients were never synchronized, are not synchronizing even with ntp... nodus is synchronized but uses chronyd; should we use chronyd everywhere?
Spent some time investigating the ntp synchronization. In the morning, after Anchal set up all the ntp servers / FE clients I tried restarting the rts IOPs with no success. Later, with Tega we tried the usual manual matching of the date between c1iscex and fb1 machines but we iterated over different n-second offsets from -10 to +10, also without success.
This afternoon, I tried debugging the FE and fb1 timing differences. For this I inspected the ntp configuration file under /etc/ntp.conf in both the fb1 and /diskless/root.jessie/etc/ntp.conf (for the FE machines) and tried different combinations with and without nodus, with and without restrict lines, all while looking at the output of sudo journalctl -f on c1iscey. Everytime I changed the ntp config file, I restarted the service using sudo systemctl restart ntp.service . Looking through some online forums, people suggested basic pinging to see if the ntp servers were up (and broadcasting their times over the local network) but this failed to run (read-only filesystem) so I went into fb1, and ran sudo chroot /diskless/root.jessie/ /bin/bash to allow me to change file permissions. The test was first done with /bin/ping which couldn't even open a socket (root access needed) by running chmod 4755 /bin/ping then ssh-ing into c1iscey and pinging the fb1 machine successfully. After this, I ran chmod 4755 /usr/sbin/ntpd so that the ntp daemon would have no problem in reaching the server in case this was blocking the synchronization. I exited the chroot shell and the ntp daemon in c1iscey; but the ntpstat still showed unsynchronised status. I also learned that when running an ntp query with ntpq -p if a client has succeeded in synchronizing its time to the server time, an asterisk should be appended at the end. This was not the case in any FE machine... and looking at fb1, this was also not true. Although the fb1 peers are correctly listed as nodus, the caltech ntp server, and a broadcast (.BCST.) server from local time (meant to serve the FE machines), none appears to have synchronized... Going one level further, in nodus I checked the time synchronization servers by running chronyc sources the output shows
controls@nodus|~> chronyc sources
210 Number of sources = 4
MS Name/IP address Stratum Poll Reach LastRx Last sample
^* testntp1.superonline.net 1 10 377 280 +1511us[+1403us] +/- 92ms
^+ 18.104.22.168 2 10 377 206 +8219us[+8219us] +/- 117ms
^+ tms04.deltatelesystems.ru 2 10 377 23m -17ms[ -17ms] +/- 183ms
^+ ntp.gnc.am 3 10 377 914 -8294us[-8401us] +/- 168ms
I then ran chronyc clients to find if fb1 was listed (as I would have expected) but the output shows this --
Hostname Client Peer CmdAuth CmdNorm CmdBad LstN LstC
========================= ====== ====== ====== ====== ====== ==== ====
501 Not authorised
So clearly chronyd succeeded in synchronizing nodus' time to whatever server it was pointed at but downstream from there, neither the fb1 or any FE machines seem to be synchronizing properly. It may be as simple as figuring out the correct ntp configuration file, or switching to chronyd for all machines (for the sake of homogeneity?)