I am running a PTP slave where I start phc2sys and ptp4l with the following 
parameters:

phc2sys -d /dev/pps0 -s /dev/ptp0 -m -w
ptp4l -f /etc/ptp4l_slave.conf -i eth0 -A

/etc/ptp4l_slave.conf has the following in it:

[global]
twoStepFlag           1
verbose               1
time_stamping         hardware
slaveOnly             1
use_syslog            1
logging_level         6
summary_interval      2

I am seeing the following output constantly:

phc2sys[202.208]: PPS is not in sync with PHC (0.113732439)
phc2sys[203.208]: PPS is not in sync with PHC (0.113742830)
phc2sys[204.208]: PPS is not in sync with PHC (0.113744232)
phc2sys[205.208]: PPS is not in sync with PHC (0.113719010)
ptp4l[206.096]: rms  110 max  152 freq  +3080 +/-  82 delay 10856 +/-   9
...

I am also observing PPS signal from both the master and the slave on the scope 
and while they are synchronized, they are not in phase, in other words, they 
don't shift against each other, but one is offset relative to the other and 
this offset changes every time I reboot the slave.  I suspect that this is 
related to "PPS is not in sync with PHC" message that I am seeing.  I am 
running kernel 4.19.35.  Is there something wrong with the way I am starting 
phc2sys and ptp4l?  How do I get rid of "PPS is not in sync with PHC" messages? 
 I googled for this message, but didn't find much out there.

Thank you,
Irene.

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