The way I read "man ntpd"  (on Debian wheezy), we could (should?) replace 
ntpdate by
"ntpd -q"; and if we are going to run ntpd then ntpdate is unnecessary anyway.
If we have (or are going to have) ntpd, then we should simply skip 
/etc/network/if-up.d/ntpdate;
seeing how that depends on NTPSERVERS in /etc/ntp.conf or somesuch, I do not 
see that
/etc/network/if-up.d/ntpdate is ever any use.

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Touch seeded packages, which is subscribed to ntp in Ubuntu.
https://bugs.launchpad.net/bugs/288905

Title:
  /etc/init.d/ntp doesnt use ntpdate to ensure clocks are aligned before
  starting server.

Status in ntp package in Ubuntu:
  Confirmed

Bug description:
  Binary package hint: ntp

  Ubuntu: 8.04.1
  ntp: 1:4.2.4p4+dfsg-3ubuntu2

  Despite other comments on here that ntpdate should be run from ifup
  scripts there is still a fundamental issue.

  If due to failures such as #114505 not bringing up ntpd correctly if
  the clock drifts you have to ifdown, ifup an interface. On a major
  server thats just plain ridiculous...To fix the ntp daemon I have to
  pull down an ENTIRE network interface and stuff every service that is
  running on that interface - simply to fix ntpd.

  The alternative is that I have to either recognise and issue and then

  /etc/int.d/ntp stop
  ntpdate-debian 
  /etc/init.d/ntp start

  again silly - because an /etc/init.d/ntp restart should work - the
  point of running NTP is it syncs.

  Therefore I propose that the /etc/init.d/ntp script is patched to
  include running of 'ntpdate-debian' during startup of the ntp server.
  This is a far more fail-safe method of working instead of forcing the
  admin to have to remember to run ntpdate-debian in case the clock has
  drifted excessively.

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