NTP Configuration not being used

I am trying to set up a GPS NTP server on my SBC running Ubuntu 20.04 (headless) but I am having a configuration issue. When I reboot I get this:

$ ntpq -p

     remote           refid      st t when poll reach   delay   offset  jitter
==============================================================================
*_gateway        163.237.218.18   2 u   22   64    1    2.727    0.011   0.159

/etc/ntp.conf says:

pool 1.ubuntu.pool.ntp.org iburst
pool 2.ubuntu.pool.ntp.org iburst
pool 3.ubuntu.pool.ntp.org iburst

# Use Ubuntu's ntp server as a fallback.
#pool ntp.ubuntu.com

# Access control configuration; see /usr/share/doc/ntp-doc/html/accopt.html for
# details.  The web page <http://support.ntp.org/bin/view/Support/AccessRestrictions>
# might also be helpful.
#
# Note that "restrict" applies to both servers and clients, so a configuration
# that might be intended to block requests from certain clients could also end
# up blocking replies from your own upstream servers.

# By default, exchange time with everybody, but don't allow configuration.
restrict -4 default kod notrap nomodify nopeer noquery limited
restrict -6 default kod notrap nomodify nopeer noquery limited

# Local users may interrogate the ntp server more closely.
restrict 127.0.0.1
restrict ::1

# Needed for adding pool entries
restrict source notrap nomodify noquery

# Clients from this (example!) subnet have unlimited access, but only if
# cryptographically authenticated.
#restrict 192.168.123.0 mask 255.255.255.0 notrust


# If you want to provide time to your local subnet, change the next line.
# (Again, the address is an example only.)
#broadcast 192.168.123.255

# If you want to listen to time broadcasts on your local subnet, de-comment the
# next lines.  Please do this only if you trust everybody on the network!
#disable auth
#broadcastclient

# GPS Serial data reference
server 127.127.28.0 minpoll 4 maxpoll 4
fudge 127.127.28.0 time1 0.0 refid GPS

# GPS PPS reference
server 127.127.28.1 minpoll 4 maxpoll 4 prefer
fudge 127.127.28.1 refid PPS

/etc/ntp/step-tickers
is blank

I found on the internet a configuration for making a "device" that will run as a GPS timeserver and it said to do this:

$ su -
# killall -9 gpsd ntpd
# gpsd -n /dev/ttyXX
# sleep 2
# ntpd -gN
# sleep 2
# cgps 

and that works

root@ubuntu:/home/zach# ntpq -p
     remote           refid      st t when poll reach   delay   offset  jitter
==============================================================================
 0.ubuntu.pool.n .POOL.          16 p    -   64    0    0.000    0.000   0.000
 1.ubuntu.pool.n .POOL.          16 p    -   64    0    0.000    0.000   0.000
 2.ubuntu.pool.n .POOL.          16 p    -   64    0    0.000    0.000   0.000
 3.ubuntu.pool.n .POOL.          16 p    -   64    0    0.000    0.000   0.000
*SHM(0)          .GPS.            0 l    8   16    1    0.000  -40.232   0.000
 SHM(1)          .PPS.            0 l    -   16    0    0.000    0.000   0.000

any idea why i cannot get ntp to read /etc/ntp.conf at boot?

EDIT: I am unsure if gpsd is running at startup.

I did a dmesg | grep gps and nothing came up.

I then wrote a bash script with that killall line in it. I don't think it will run (@startup sh in crontab) though because it has to be elevated. I tried as init.d (i don't really know what I am doing there) and I get an error message audit: type=1400 audit(1636322022.316:45): apparmor="DENIED" operation="ptrace" profile="/usr/sbin/gpsd" pid=2794 comm="gpsd" requested_mask="read" denied_mask="read" peer="/usr/sbin/ntpd"


Ok, thanks to @ChristianEhrhardt, the use of Chrony seems to have worked quite well for some reason unbeknownst to me.

I already have gpsd running so I didn't have to mess with that, but it is important to indicate here. I am using the GPS plugged in via USB and not PPS. The device is ttyACM0

I used several guides on the internet and i am not sure the exact steps I took but it went something like this:

sudo apt install chrony

and then I had to configure the .conf file

sudo nano /etc/chrony/chrony.conf

I figured out that in order to make the GPS timeserver actually serve time to other computers I had to uncomment as below. I have serveral subnets so I opened it wide up

#Allow to be a NTP server 
allow 192.168.0.0/24

I needed to add my GPS source so I added:

#GPS Sources
refclock SHM 0 refid GPS precision 1e-1 offset 0 delay 0 stratum 2
refclock SOCK /var/run/chrony.ttyACM0.sock refid PPS

I know that restarting services is a thing, but I prefer the reboot.

sudo reboot now

Then I enabled it as a service

systemctl enable chrony

Then I checked to make sure it worked

chronyc sources

And lastly I verified that it was serving time to other computers. I went to a different machine and checked ntpq -p

and TA-DA