This guide will help you create an NTP server using the PC Enginges APU system board, the Versalogic GPS module and the StartTech serial port module. I'm using the ATOM PPS refclock source, because PPS is'nt provided via /dev/ttyACM0.

• PC Engines APU1 system board.
• PC Engines APU1c schematics.

• Versalogic VL-MPEu-G2 Reference Manual.
• Neo-7 Data Sheet.
• u-blox 7 Receiver Description: Including Protocol Specification V14.

• Mini PCI Express Serial Card specs.
• Mini PCI Express Serial Card manual.

• Upgrade APU BIOS using PXE or USB.
• Install an mSATA SSD.
• Install the Versalogic GPS module.
• Install the StarTech serial port module.
• Connect Versalogic TIME_PULSE, GND (pin 2, 3) to serial DCD, GND (pin 1, 5).
• Connect U.FL - SMA pig-tail to GPS module and connect the active GPS antenna.

• Install Voyage linux using PXE (network) or USB.
• After installation, log in as root (password voyage) and remount read/write.

  # remountrw

• Create non root user.

  useradd username
  passwd username

• Change hostname /etc/hosts /etc/hostname, configure network.
• Change apt mirrors in /etc/apt/…
• Install prerquisites.

  apt-get install dialog setserial

• Update.

  apt-get update
  apt-get upgrade

• Configure time zone.

  dpkg-reconfigure tzdata

• Configure locale.

  apt-get install locales
  dpkg-reconfigure locales

• Edit Voyage Linux config to enable writing to ntp drift file. Edit /etc/default/voyage-util

  VOYAGE_SYNC_DIRS="var/lib/ntp"

• Install gpsd.

  apt-get install gpsd gpsd-clients

• Reconfigure gpsd, add -n option

  dpkg-reconfigure gpsd

• We need to compile NTP to enable ATOM PPS support.

  (apt-get remove ntp)
  
  cd /root
  apt-get install dpkg-dev dialog devscripts fakeroot pps-tools
    
  apt-get source ntp && apt-get build-dep ntp
    
  cd ntp-4.2.6.p5+dfsg
  debuild -us -uc
  
  cd ..  
  dpkg --install ntp_4.2.6.p5+dfsg-2_i386.deb
  dpkg --install ntp-doc_4.2.6.p5+dfsg-2_all.deb

• Configure NTPd to run at the highest priority. Edit /etc/default/ntp

  NTPD_OPTS='-g -N'

• Create PPS device and set low_latency. Add udev rules. Create /etc/udev/rules.d/gps.rules.

  KERNEL=="ttyS2", SYMLINK+="gps0"
  KERNEL=="ttyS2", RUN+="/bin/setserial -v /dev/%k low_latency"
  KERNEL=="ttyS2", RUN+="/usr/sbin/ldattach pps /dev/%k"

• Configure /etc/ntp/conf.

  # Allow more distance between GPS (USB) and Serial PPS.
  # Stratum level 12 when no ref source available
  tos mindist 0.100 orphan 12
  
  driftfile /var/lib/ntp/ntp.drift
  leapfile  /var/lib/ntp/leap-seconds
  statsdir  /var/log/ntpstats/
  
  statistics loopstats peerstats clockstats
  filegen loopstats file loopstats type day enable
  filegen peerstats file peerstats type day enable
  filegen clockstats file clockstats type day enable
  
  # Local servers
  server ntp1.polaire.nl
  server ntp2.polaire.nl
  server ntp3.home.polaire.nl
  
  # ATOM PPS (/dev/pps0)
  server 127.127.22.0 minpoll 4 maxpoll 4
  fudge  127.127.22.0 refid PPS
  
  # GPS (USB /dev/ttyACM0)
  server 127.127.28.0 minpoll 4 maxpoll 4 prefer
  fudge 127.127.28.0 refid GPSd
  fudge 127.127.28.0 time1 0.063
  
  # By default, exchange time with everybody, but don't allow configuration.
  restrict -4 default kod notrap nomodify nopeer noquery
  restrict -6 default kod notrap nomodify nopeer noquery
  
  # Local users may interrogate the ntp server more closely.
  restrict 127.0.0.1
  restrict ::1

• Reboot and check results.

• Make sure gpsd and ntpd start at boot.

  update-rc.d ntp enable
  update-rc.d gpsd enable

• Test PPS reception.

  # ppswatch /dev/pps0
  trying PPS source "/dev/pps0"
  found PPS source "/dev/pps0"
  timestamp: 1403289214, sequence: 11, offset:  81613988
  timestamp: 1403289214, sequence: 11, offset:  81613988
  timestamp: 1403289215, sequence: 12, offset:  81607583
  timestamp: 1403289215, sequence: 12, offset:  81607583
  timestamp: 1403289216, sequence: 13, offset:  81609303
  timestamp: 1403289216, sequence: 13, offset:  81609303
  timestamp: 1403289217, sequence: 14, offset:  81601958
  ^C

• Check ntpq status. The 'o' means, PPS is working.

  $ ntpq -p
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
   ntp1.polaire.nl .PZF.            1 u   47   64    1    0.270   12.367   0.001
   ntp2.polaire.nl 95.97.208.29     2 u   48   64    1    0.293   12.720   0.001
   ntp3.home.polai .DCF.            1 u   47   64    1    0.300   13.941   0.001
  oPPS(0)          .PPS.            0 l    -   16    7    0.000   12.355   0.102
  *SHM(0)          .GPSd.           0 l    2   16    7    0.000    1.188   1.431
  
  # After a while...
  
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
  +ntp1.polaire.nl .PZF.            1 u   56   64  377    0.292   -0.099   0.075
  -ntp2.polaire.nl 95.97.208.29     2 u   50   64  377    0.289    0.638   0.086
  +ntp3.home.polai .DCF.            1 u   41   64  377    0.237    1.656   0.048
  oPPS(0)          .PPS.            0 l   15   16  377    0.000    0.027   0.003
  *SHM(0)          .GPSd.           0 l   16   16  377    0.000   -8.657   2.708

Automatic download of new leap second file.

• Install lftp.

  apt-get install lftp

• Create leap second download script /usr/local/bin/get_leap.sh
• Change executable mode

  chmod +x /etc/cron.weekly/leapsecond

The module is in a embedded device and you cannot run Windows on the APU system board. The following directions will let you pass through the serial device to a Windows computer over the network. Then you will be able to run the u-center GNSS evaluation software for Windows.

• Install socat.

  apt-get install socat

• Stop NTPd and gpsd.

  service ntp stop
  service gpsd stop

• Connect serial to TCP port.

  socat file:/dev/ttyACM0,raw,echo=0 tcp-l:3006,fork&

I'm using Windows 7 in this example.

• The com0com.sys is a test-signed kernel-mode driver that will not load by default. NOTE: Enabling test signing will impair computer security. To enable test signing, enter command:

  bcdedit.exe -set TESTSIGNING ON

• Reboot
• Download and install com0com and com2tcp http://sourceforge.net/projects/com0com/files/?source=navbar
• Launch setup to determine virtual com port pair. In my case it's COM5 ⇔ COM6
• Start cmd.exe, run:

  com2tcp.exe --ignore-dsr \\.\COM6 1.2.3.4 3006

• Download and install u-center http://www.u-blox.com/en/evaluation-software/u-center.html
• Run u-center, go to Receiver → Port → COM5
• Receiver → Generation → u-blox 7

• SBAS → Subsystem: Disabled.
• (not supported by u-blox 7) TMODE2 → Survey-in. If the position is known, the receiver can provide an accurate time solution by tracking only one satellite. For an unknown position, the receiver needs a minimum of four satellites to calculate a position fix and to solve for a timing solution. This is known as survey-in and can be chosen using the UBX-CFG-TMODE2 message. It is recommended to use survey-in only for non-moving platform applications. For optimal performance a known fixed position of the antenna should be used.
• NAV5 → Dynamic Model: Stationary
• NAV5 → Min SV Elevation: 10
• Save config, restart receiver. Receiver → Action → Cold start