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Ok Peter, so that is resetting my original understanding. But I have been unable to get the index pulse, which is clearly present in halscope to trigger the position reset.

The way index works on LinuxCNC with quadrature encoders is that when LinuxCNC (or some hal component)
wants a encoder reset at the next index occurrence, it sets the index-enable pin. This arms the encoder counter
hardware so at the next index, two things happen, the encoder position is reset to 0, and the index enable pin
is set false, so LinuxCNC or the controlling hal component knows that the index has been detected (and position zeroed)

I will install LinuxCNC onto a random (not-super-ancient) HDD.

I hope it goes well.

Weird.

FreeBSD seems faster.

Why would they switch to Debian?

landoneilers wrote:

Why TrueNAS over FreeBSD?

(I know TrueNAS is based on FreeBSD, but still)

It's not, new version is Debian as far as i can gather from the boot time info.

landoneilers wrote:

I have never seen a motherboard with more than 4 SATA ports.

I've always had with more than 4 as they also had a separate SATA controller with RAID, still have 2 with 6 SATA ports, and all Enterpise towers also have 6 or 8 ports (HP Z420 and Z600)

Yes I will, I did take some photos and know what's the system PLC/System they use, I'll have to come back I hope later today to upload some photos about it.

Does HDD cache size have any impact?

Also, probably important to mention that I created this post because I read this one:
forum.linuxcnc.org/36-using-this-forum-q...bility-and-structure

Some of the assets are common to both sites (like the LinuxCNC logo).

And I don't understand the purpose of the DigitalOcean server at all, though I'm sure there is one.

Just curious about the rationale behind the setup, I guess.

HDD read/write has no impact on latency.which measures hardware performance, network latency is important for mesa/ethercat systems.
The buffering of gcode will be sufficient to cover HDD speed.
Using a SSD is  a great boost in performance and I usually install one when refurbing a machine. Recently I didn't on a 8 core i7 & I really noticed how much longer Debian took to install. 

Use the one you say is ideal

Why TrueNAS over FreeBSD?

(I know TrueNAS is based on FreeBSD, but still)

I have never seen a motherboard with more than 4 SATA ports.

I don't really need NAS, though that is a cool idea, I suppose.

This is a snapshot of latency of that PC when I tested servomotors.

I'll try exact same former procedures ( I have written something important about disabling eoe, and recalling everything as much as possible ) with former PC today.

Thank you so much for your every skillful reply.
 

I tried to run through this and see what I could see, with your partial cut file being a mess, it's hard for me to guess at where you are trying to start and what is going on. Can you post the actual cut file?

Also, what version of QtPlasmaC are you running? need the entire number in the window header.

landoneilers wrote:

500GB WD Blue HDD (16MB cache) (The ideal choice, I have like 6 extra ones)

Get an old mainboard/CPU/MEM and plug all 6 to it, see bellow

landoneilers wrote:

256 SanDisk SSD (I only have 4).

Use for LinuxCNC machines, much better latency/access times compared to mechanical drives, and much faster.

landoneilers wrote:

500GB WD Blue HDD (32MB cache) (Less plentiful than the 16MB caache drives, but I don't really need this drive for anything).

Use this one to install TrueNAS and plug it into the same old PC mentioned above with the other 6 drives, you get a nice 2.5TB NAS with fault tolerance for one failed drive.