ntp

正午頃に ntpd を起動

> ntpq -c peers
remote refid st t when poll reach delay offset jitter
==============================================================================
LOCAL(0) LOCAL(0) 10 l 91 64 0 0.000 0.000 4000.00
ntp1.jst.mfeed. 210.173.160.56 2 u 12 16 1 46.828 7.266 0.002
ntp2.jst.mfeed. 210.173.160.86 2 u 12 16 1 49.683 8.797 0.002
ntp3.jst.mfeed. 210.173.160.86 2 u 12 16 1 44.030 5.926 0.002
ntp.nc.u-tokyo. .GPS. 1 u 13 16 1 44.502 5.637 0.002
ns01.iij4u.or.j 202.232.0.1 4 u 10 16 1 43.893 6.097 0.002
ns11.iij4u.or.j 202.232.0.1 4 u 11 16 1 44.546 5.964 0.002

様子を見てみると、ntp2 や、ntp3.jst の offset が大きくなっている...

> ntpq -c peers
remote refid st t when poll reach delay offset jitter
==============================================================================
LOCAL(0) LOCAL(0) 10 l 44 64 1 0.000 0.000 0.002
+ntp1.jst.mfeed. 210.173.160.56 2 u 25 64 17 44.485 9.118 5.774
+ntp2.jst.mfeed. 210.173.160.86 2 u 25 64 17 49.554 11.431 5.204
+ntp3.jst.mfeed. 210.173.176.4 2 u 29 64 17 43.747 11.293 4.265
*ntp.nc.u-tokyo. .GPS. 1 u 22 64 17 44.502 5.637 8.179
ns01.iij4u.or.j 202.232.0.1 4 u 26 64 17 43.622 8.861 4.769
ns11.iij4u.or.j 202.232.0.1 4 u 27 64 17 43.435 8.869 4.778

さらに ntp2 や、ntp3.jst の offset が増加

> ntpq -c peers
remote refid st t when poll reach delay offset jitter
==============================================================================
LOCAL(0) LOCAL(0) 10 l 21 64 3 0.000 0.000 0.002
+ntp1.jst.mfeed. 210.173.160.56 2 u 5 16 37 44.485 9.118 11.051
-ntp2.jst.mfeed. 210.173.160.86 2 u 3 16 37 44.848 26.971 13.849
-ntp3.jst.mfeed. 210.173.160.86 2 u 6 16 37 43.744 26.367 16.579
*ntp.nc.u-tokyo. .GPS. 1 u 1 16 37 44.502 5.637 12.903
+ns01.iij4u.or.j 202.232.0.1 4 u 5 128 37 43.622 8.861 9.805
+ns11.iij4u.or.j 202.232.0.1 4 u 5 128 37 43.435 8.869 10.283

ntp1.jst の offset まで増加

> ntpq -c peers
remote refid st t when poll reach delay offset jitter
==============================================================================
LOCAL(0) LOCAL(0) 10 l 21 64 7 0.000 0.000 0.002
+ntp1.jst.mfeed. 210.173.160.56 2 u - 16 377 44.290 37.043 16.173
+ntp2.jst.mfeed. 210.173.160.86 2 u - 16 377 43.917 31.745 11.401
+ntp3.jst.mfeed. 210.173.160.86 2 u 3 16 377 43.660 33.803 15.138
*ntp.nc.u-tokyo. .GPS. 1 u 14 16 377 44.502 5.637 19.994
-ns01.iij4u.or.j 202.232.0.1 4 u 68 128 37 43.622 8.861 9.805
-ns11.iij4u.or.j 202.232.0.1 4 u 68 128 37 43.435 8.869 10.283

更には東大の offset も...

> ntpq -c peers
remote refid st t when poll reach delay offset jitter
==============================================================================
LOCAL(0) LOCAL(0) 10 l 59 64 7 0.000 0.000 0.002
+ntp1.jst.mfeed. 210.173.160.56 2 u 5 16 377 43.810 39.151 10.286
+ntp2.jst.mfeed. 210.173.160.86 2 u 6 16 377 43.887 39.222 10.646
+ntp3.jst.mfeed. 210.173.160.86 2 u 6 16 377 43.287 39.151 11.698
*ntp.nc.u-tokyo. .GPS. 1 u 1 16 377 44.539 16.900 18.697
-ns01.iij4u.or.j 202.232.0.1 4 u 106 128 37 43.622 8.861 9.805
-ns11.iij4u.or.j 202.232.0.1 4 u 106 128 37 43.435 8.869 10.283

プロバイダーの ntp の方がアクセスが少なく、安定してるようですね。プロバイダーの ntp server を使いましょう。
こういうのを誰か調べている人は居ないんでしょうか？ntp の log(peerstatus) をグラフ化すれば一発なんですけど。
ns01, ns11 の poll が 128 で、ポーリングしてないっぽいのは内緒。

ちなみに、ネットワークの距離は
ns11.iij4u.or.jp 9hop
ntp.nc.u-tokyo.ac.jp 14hop
ntp1.jst.mfeed.ad.jp 8hop
でした。