this can be caused by NTP server being "not precise enough" for Data ONTAP. Check the KBs
https://kb.netapp.com/support/index?page=content&id=1012660 (the "ntpq" part can be run from ONTAP systemshell)
Just try using the Host name of the NTP server in Timed.servers rather than an Ip or Alias and check if it resolves the issue.
Hope this helps.
The most appropriate troubleshooting method for your problem would be as mentioned by Harry_Redl in his post. But that involves a series of commands to be executed from the systemshell. You may also need to check if any device in between your storage controller and the DC is blocking port 123. Increasing the verbosity of EMS logging facility may be helpful to get some clue. Have you opened a support case with NetApp? They should be able to help you with more troubleshooting and a fix.
Its a known issue with DOT8.x and Windows Operating systems that uses W32time NTP service ( https://kb.netapp.com/support/index?page=content&actp=LIST&id=2015314 ). I am not really a microsoft guy, but as far as I know, OS versions upto windows server2012 uses w32time as the timeserver. Its not a good idea to use a Windows server syncing to its own hardware clock as an NTP source. It becomes worse when your windows runs inside a Virtual Machine. I would not choose that as an option If I were you.
From microsoft's KB article ( https://support.microsoft.com/en-us/kb/939322 )
"We do not guarantee and we do not support the accuracy of the W32Time service between nodes on a network. The W32Time service is not a full-featured NTP solution that meets time-sensitive application needs. The W32Time service is primarily designed to do the following:
I did opened a support case with NeApp. They recommended the steps as recommended by Harry_Redl in his post.
The ntpq analyzed issue "Flash=400 peer_dist. Peer synchronization distance exceeded."
As recommend in https://kb.netapp.com/support/index?page=content&id=2015314&actp=LIST, changed the precision of time server , but am afraid still won't synchronize.
The case is opened with Netapp. They too are investigating and am awaiting update since last 5 days.
Did you check ntpq status again? is it still Flash=400 or did it change to something else?