I have continued struggling with ptp4l  on the Supermicro 5015A-EHF-D525
with its e1000e-driven NICs. I have recompiled the LINUX 3.12 stable
kernel, set the timing config as:
CONFIG_HZ_PERIODIC=y
# CONFIG_NO_HZ_IDLE is not set

# CONFIG_NO_HZ_FULL is not set
# CONFIG_NO_HZ is not set
# CONFIG_HZ_100 is not set
# CONFIG_HZ_250 is not set
# CONFIG_HZ_300 is not set
CONFIG_HZ_1000=y
CONFIG_HZ=1000

Ptp4l sees big phase jumps, often in the path delay ("negative path delay
-35184372300862"  clockcheck: clock jumped forwared occurred 876 times in
the past 17 hours. See attached example.)  It eventually recovers but as
chronyd shows, the PHC has huge jitter.  Compared with the 1PPS from a Ubox
LEA-6T GPS (standard deviation 247ns, PPS1 below), my PHC is still not
functional.

ptp4l -f /root/PTP/ptp1.conf -i eth1 -l 7 -s -p /dev/ptp1
root@pluto:~/PTP# cat ptp1.conf
[global]
#
# Port Data set
#
logAnnounceInterval    1
logSyncInterval        1
logMinDelayReqInterval    1
logMinPdelayReqInterval    1
announceReceiptTimeout    4
#delayAsymmetry        0
#fault_reset_interval    4
#
#time_stamping    software
time_stamping    hardware
slaveOnly    1



MS Name/IP address         Stratum Poll Reach LastRx Last sample
===============================================================================
#- PHC0                          0   3   377     9    +23us[  +23us] +/-
949.1s <---- bad
#+ PPS1                          0   4   377    20    +36us[  +36us] +/-
606ns
^* 10.10.10.20                   1   8   377   200  -6248ns[  -11us] +/-
1067us
^+ 10.10.10.214                  2  10   377   457    -96us[ -100us] +/-
783us

<<attachment: pps.png>>

<<attachment: phc.png>>

Attachment: ptp4.log
Description: Binary data

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