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If a PC running Linux breaks, try putting the old hard drive in the new computer.

It actually works perfectly 99% of the time!

Why did you install 2.9?

Which version of 2.9? 2.9.4?

How does your PC control the machine?

That sorted it. Just #'d out the two PYVCP lines. Looking back over the build thread it was using probe basic so that's probably the issue.
I now have axis running with one encoder that's reading! Fantastic. Don't have any motor control though. I can move the motor shaft and get count and motion on the simulator display but with the machine enabled I can't jog. The sim shows movement but no shaft rotation.

I'm also getting a Linuxcnc notification "LCEC: Invalid appTimePeriod of 0 for master 0 (should be 1000000)."

A quick search on the forum suggests that relates to:
in the ini file but it's set to 1000000 already.

watching the "DRO" the z axis zeros then moves, hits the index, zeros, and then hits the estop. I have the offset set to 0 so it should just stop correct?

in testing the "Z" axis right now I have it passing the index point, it turns off the enable signal, seems to hesitate for a split second before continuing to the estop hard limit

Is index-enable connected to both motion and the driver?

If the encoder index  (something like hm2_cardname.0.encoder.00.index-enable)
has been set but is not ever cleared when the index location has been passed,
that suggests a hardware issue with the index signal itself.

After an impressively quick iterative process Lcvette and TurBoss managed to fix all the errors I encountered in this thread.

I'm sure they'll announce an updated development version shortly including these fixes.

It does set the index enable currently it just sails right by it when homing

Hi 
I am planning on using the same motor and driver for my mill until I upgrade to a larger motor.  would you be able to share your . ini  .hal  and . xml file of your configuration any what mode you set on the driver if you got it running? 
Thanks will 

Could official firmware for example for 6i25 or 7i92 currently accept 224bits via smart serial from slave?

Yes if the sserialb firmware is installed

Are you compiling from source because 2.9.6 doesn't work properly with the XHCWHB component?
If so then see this thread:

forum.linuxcnc.org/21-axis/57364-axis-co...-9-6?start=10#336658

if not, then you can get a list of the missing build dependencies

cd linuxcnc-dev
./debian configure no-docs
dpkg-checkbuilddeps

Do the encoders not match any of the Mesa absolute-encoder types?

linuxcnc.org/docs/stable/html/man/man9/h...%20Interface%20(SSI)

The manual turret looks like a prime candidate for motorisation...

Or get an industrial robot arm to operate the manual tool changer for you.

Look at the pins supplied by halui.

linuxcnc.org/docs/html/gui/halui.html

You might need to force home-sw-in high, so that it always thinks it's on the switch, and then it will set the index-enable.

ie, in the HAL file:
sets joint.0.home-sw-in 1

Hi Andy, I've been running a 25,000ns relatively successfully. Which is why I've been scratching my head so much. However, actually thinking out loud on here had me thinking it had to be electrical. So I dug out the oscilloscope and probed the signal. The cheap Chinese sensors had a 20k pull up resistor which was far too strong and was causing the pulse width to be way too long. So at 1900 the signal went from a pulse train to just "on".

I've swapped out the resistor and now getting good clean pulses read by the Pi with a stable speed reading up to 4000rpm.

Thank you for your suggestions as they have pointed me in the right direction. I'm in the process of modelling up a mount so i can mount two sensors to create a encoder that will do direction as you suggested.