Enable PPS support in Raspian

DUNE has a task called Supervisors.ClockPPS that is used to dicipline the clock from both IMC::GpsFix messages and a PPS source. To get this to work, the kernel has to be compiled with two options not currently enabled by default:

CONFIG_PPS (“PPS support” in “make menuconfig”)
CONFIG_NTP_PPS (“PPS kernel consumer support” in “make menuconfig”)

sudo apt install git bc bison flex libssl-dev

mkdir ppskernel
cd ppskernel
git clone https://github.com/raspberrypi/linux.git
cd linux
make mrproper
zcat /proc/config.gz > .config
make oldconfig

Then comes the hard part, setting the options. Normally this is straight forward, but due to some options only showing when others are disabled, it may be a little tricky.

Run make menuconfig

Go to General setup ---> Timers subsystem ---> and disable Old Idle dynticks config, then enter Timer tick handling and change it to Periodic timer ticks (constant rate, no dynticks)
Turn on PPS support: PPS kernel consumer support is the option that should have become visible after changing the timer settings. If not, save and reload make menuconfig.
Enter Device Drivers —> PPS support —>

          <M> PPS support  
          [ ]    PPS debugging messages
          [*]    PPS kernel consumer support   
                 *** PPS clients support ***         
          < >    Kernel timer client (Testing client, use for debug)
          <M>    PPS line discipline
          <M>    PPS client using GPIO
                 *** PPS generators support ***

Save and exit. To verify, check the .config file that has been created in the same folder (nano .config). These options should be present somewhere in the file:

CONFIG_PPS=y
CONFIG_NTP_PPS=y
#
# Timers subsystem
#
CONFIG_TICK_ONESHOT=y
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_HIGH_RES_TIMERS=y
# CONFIG_PREEMPT_NONE is not set
CONFIG_PREEMPT_VOLUNTARY=y
# CONFIG_PREEMPT is not set

make -j4
make modules

Gain superuser privileges and transfer a copy of the new kernel to the boot partition:

sudo -i
cd ~pi/ppskernel/linux-rpi-[kernel version number].y
make modules_install
cp ./arch/arm/boot/zImage /boot/kernel_new.img

Tell the system to use this new kernel by adding kernel=kernel_new.img to /boot/config.txt .
Reboot

Open /boot/config.txt again, and dtoverlay=pps-gpio,gpiopin=[GPIOPIN] where GPIOPIN is the PPS signal.
Load kernel module: sudo modprobe pps-gpio

Test

apt-get install pps-tools
sudo ppstest /dev/pps0

Expected result is something like:

trying PPS source "/dev/pps0"
found PPS source "/dev/pps0"
ok, found 1 source(s), now start fetching data...
source 0 - assert 1572772437.999997402, sequence: 6168 - clear  0.000000000, sequence: 0
source 0 - assert 1572772438.999997803, sequence: 6169 - clear  0.000000000, sequence: 0
source 0 - assert 1572772440.000000924, sequence: 6170 - clear  0.000000000, sequence: 0
source 0 - assert 1572772440.999998834, sequence: 6171 - clear  0.000000000, sequence: 0
source 0 - assert 1572772442.000001424, sequence: 6172 - clear  0.000000000, sequence: 0
source 0 - assert 1572772442.999999478, sequence: 6173 - clear  0.000000000, sequence: 0
source 0 - assert 1572772444.000000128, sequence: 6174 - clear  0.000000000, sequence: 0
source 0 - assert 1572772444.999999537, sequence: 6175 - clear  0.000000000, sequence: 0
source 0 - assert 1572772446.000000578, sequence: 6176 - clear  0.000000000, sequence: 0

If successful, make permanent by opening /etc/modules and adding pps-gpio to the end.
Running a DUNE configuration with Supervisors.ClockPPS should now work