An update - I haven't got round to testing new PRU code. However, this:

Setting and getting the timeout:
For some drivers it is possible to modify the watchdog timeout on the
fly with the SETTIMEOUT ioctl, those drivers have the WDIOF_SETTIMEOUT
flag set in their option field. The argument is an integer
representing the timeout in seconds. The driver returns the real
timeout used in the same variable, and this timeout might differ from
the requested one due to limitation of the hardware. 
>From 
here: 
https://github.com/philenotfound/beagleboneblack-kernel/blob/master/Documentation/watchdog/watchdog-api.txt

Looks relevant. Does anyone know if the Watchdog driver supports on the fly 
timeout adjustment?

On Tuesday, 4 June 2019 10:57:40 UTC+1, Hugh Frater wrote:

My experience of working directly with the i2c and eqep parts of the 
> silicon from within the PRU suggest that register access to the watchdog 
> peripheral would be both easy and reliable. It's simply a #define and you 
> can then access the register contents directly from within the PRU. 
>
> I will write some test code to reconfigure the watchdog and report back.
>
> On Tuesday, 4 June 2019 02:02:37 UTC+1, lazarman wrote:
>>
>> I'd ask the question are these register's accessable from the PRU my 
>> experience is dated and I'm not a Linux guy but most OS protect Access to 
>> certain registers I briefly looked at TRM the WDOG is enabled by default 
>> probably during boot. To set it or change the clock source you disable it 
>> which I doubt Linux would like from PRU side  but maybe I'm wrong. I'd look 
>> at the interconnect block diagram to see if PRU has access to the 
>> registers. Google am335x watchdog c code I see discussion about Kernel 
>> configuration. Typically on non Linux ARM side project TI provided quite a 
>> bit of example code for customer boot code options that's where I always 
>> start but that code isn't always in the public  domain and in your case 
>> isn't relavent after Linux takes over you may have to let ARM Linux side 
>> handle it. I'd look at PRU register memory map unless someone in here has 
>> done it from PRU. 
>> Good luck
>>
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>>
>> On Mon, Jun 3, 2019 at 7:07 AM, Hugh Frater
>> <hugh....@gmail.com> wrote:
>> Where does one go to tune the watchdog timer? Is it a 
>> kernel-recompilation-required thing, or can it be done through uBoot?
>>
>> Or.... should I just use my PRU code to tune the watchdog control 
>> register when it boots? This would be the easiest option for me, if someone 
>> can point me at the correct area if the AM335XTRM? I had a look in there 
>> and couldn't find the correct registers.
>>
>> I'd like it to run about 10 seconds if possible for my application.
>>
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