@btmclain I see you have standstill current at 0% (M917 X0), have you tried commenting out this line, or increasing the standstill current value?

on my system when I add the M917 X0 I also get this clunk. Removing it and I have no clunk when tuning.

some background. I recently started playing with Duet, so I could be considered complete noob (though I have plenty of 3d printer and CNC experience)

I picked up a Duet mini5+, a 1HCL board (ver 1.0a), and a magnetic encoder (v0.3).
Upgraded the firmwares to 3.5.1
I've got it setup very minimally on the desk just getting used to the software/setup.

I'm trying to follow the guide, (still can't post links) but the Plugin never allows me to select a driver. "No data available"

I can move the motor in open and closed loop.
and even do a manual M569.5, then open the subsequent file in the plugin.
I just can't get the plugin to cause the recording/tuning moves.

I thought maybe it was my version, Started with RRF Version 3.5.1 on all, Updated to 3.5.4 on Mini 5+ 1HCL and DWC. uninstalled and reinstalled the ClosedLoop plugin 3.5.1. Same situation. Can move, can record, cannot get the plugin to cause the move.

is there something obvious i'm just missing?

Config.g

; Configuration file for RepRapFirmware on Duet 3 Mini 5+ Ethernet
; executed by the firmware on start-up

; General
G91 ; Relative coordinates
M83 ; relative extruder moves
M550 P"TestSaw" ; set hostname

; Network
M552 P192.168.1.14 S1 ; configure Ethernet adapter
M553 P255.255.255.0 ; set netmask
M554 P0.0.0.0 ; set gateway
M586 P0 S1 ; configure HTTP

; Wait a moment for the CAN expansion boards to become available
G4 S2

; Closed Loop Drivers
M569.1 P50.0 T3 E0.0:0.0 S200 R40 I0 D0 ; only magnetic shaft encoder

M569 P50.0 S1 D4 ; driver 123.0 goes forwards (extruder 0) FEED

; Axes
M584 E50.0 ; set axis mapping
M350 E16 ; configure microstepping 
M906 E800 ; set axis driver currents

; (micro)Steps/mm Calculation:
; E: Driver 16 microsteps
; E: Motor 400steps/rev (89080.1598:1) {6400}
; E: Belt Reduction 1/2 (0.5)(222.7003995:1) {12800}
; E: Harmonic Reduction 1/100 (0.01)(111.35019977:1) {12800000}
; E: Pinch Roller Radius 7.212148 mm (circ 45.3153) (1.1135:1) {28246.530421/mm}
; E: Encoder Roller Diameter 12.954 mm (circ 40.6962)(1,610.371484 ticks/mm)
M92 E28246.530421 ; configure microsteps per mm 
M566 E0 P1 ; set maximum instantaneous speed changes (mm/min)
M203 E17.7 I0.1 ; set maximum speeds (mm/min)
M201 E5462.962963 ; set accelerations (mm/s^2) 

; Kinematics
M669 K0 ; configure Cartesian kinematics

; Spindles
M950 R0 C"nil + io1.out" Q500 L60:10000 ; configure spindle #0 ;P"io1.out" 

; Tools
M563 P0 S"Blade" D0 F0 R0 ; create tool #0

; Miscellaneous
M453 ; select CNC mode
T0 ; select first tool

; Remove Requirement for homing
G92 E0 ;

This would also help me,
With BiSS-C I would be able to select an appropriate encoder for my desired setup (17+ bit resolution required)

There's a post I found where someone was supposedly able to "read" a BiSS-C encoder with SPI in the "SimpleFOCproject" community forum. (can't post links yet, but search for SPI BiSS-C SimpleFoc and it'll likely come up. )

@btmclain to do the tuning it needs to be in closed loop.

Generally you home the axis in open loop, move it to a "safe" location (not crashing the machine), set it to closed loop, then do the calibration.

I suggest you read the tuning documentation here

@btmclain By "manually" i mean not in a homing macro, but by sending the gcode manually either in the DWC console or connected SBC.
But after rereading your first post, I assume that's what you've done.

I think your issue may lie in the initial configuration of the encoder. the C parameter should be the number of cycles from the quadrature encoder per motor revolution.
I don't see anywhere you specify the motion relationship between motor and linear encoder, the linear encoder you specify has a 5um/pulse output, (20um/cycle)
With your C value of 1000 that works out to a movement of 20mm/motor rotation. is that correct?

Are you doing a small motor movement in open loop mode before attempting calibrations?

When playing with my setup I was able to somehow get the system to move in closed loop with only a magnetic encoder calibration, then I was able to confirm the linear encoder cycles/rotation value (i had to iterate a few times as the documentation says Pulses per revolution, I believe it should say cycles/revolution instead as that is what I ended up at to get the correct movement) Once I had the C value in the ballpark I was able to get the system to calibrate the Quadrature encoder (M569.6 V1) successfully.

Also, searching around the forum, it seems like this post might be the same issue, just with a delta printer instead of a simple z axis.

https://forum.duet3d.com/topic/36572/v2-0-consistently-increasing-probe-heights

@droftarts
I have tuned the Closed Loop parameters, though my system has backlash that requires me to have a lower Proportional value than most say is ideal for closed loop tuning setup (belt reduction to screw movement to linear movement, inherently there will be some backlash)

I do not reset the Z when probing, thus the s-1 on the G30, just report value.
I do however reset the Z at the start of the run from the average of 4 points on my tube (probe, save value, spin 90, probe, save value, spin 90, probe, save value, spin 90, probe, average values, set Z 0=average of values)
I was wondering if having the probe on the mainboard, not the 1HCL may be causing some of this, as inherently the motor controller will have to wait for the can message to stop movement, as opposed to potentially having an interrupt stopping movement immediately if it were on the 1HCL (i don't actually know how the 1HCL is coded with probing etc).
I did try the probe on the 1HCL at a previous time, but this tended in a "sticky" probe, where the probe would lock to 1000 or 0 and not change until I rebooted the board. This was on a previous firmware (3.6.0 beta2, vs 3.6.0-rc2+4), so may have been that causing the sticky probe, IDK.

I home in Open loop before moving to closed loop.

Another thought I had was maybe I'm so far into the decimals here that floating point math is causing issues. as my system only has 3mm overall Z travel maybe it'd be better to configure it as mm=um to cheat that up by a few orders of magnitude.

Config.g here.
config(3).g

I call this at the start of the Run to set Z 0
setZeroDepth.g

then this is called at each start of a cut
findContact.g

here's some raw logs I have parsed to get graphs from
eventlog4-24ClosedLoop.txt eventlog4-24OpenLoop.txt

Continuing with my project to control a tubing cutter with the Duet I have come across an interesting issue.

The issue is, over multiple probes the Z position seems to drift upwards (positive Z) in opposition to the raw encoder values in the 1HCL.

My blade is on an electrically isolated spindle, I have a simple probe setup between the blade and the tube. (essentially a microswitch probe)
My Z axis is run by a 1HCL board, with a quadrature encoder on the z axis, and a magnetic encoder on the motor.
The probe is on the Mini 5+ mainboard.

Quadrature encoder ticks per motor revolution is 189,
1 motor revolution is 0.318 mm

Operation is, probe to tubing, calculate depth required, feed z to depth required, then back out of the cut and feed/rotate the tubing to the next planned cut.

for testing I have a probing macro I call before each cut.
The script calls G30 S-1 Then calls M122 B50.0 immediately, then passes back to the previous script to calculate the cut depth.

I have parsed the M122 results with the "Stopped at height" results from the G30 and graphed them.
note: Quadrature encoder ticks per motor revolution is 189, 1 motor revolution is 0.318 mm
2nd Note: Encoder ticks should trend upwards slightly, as blade wear causes more movement before tube contact
In Closed Loop Mode

Note in purple the encoder ticks are very consistent only varying by ~43 individual ticks over the range, Logically the Z value should only vary by 0.072mm as opposed to it's ~0.35mm variation

Note in red, the ticks seem more noisy, it's due to my ineptitude in excel and setting ranges on the graph. Overall min/max is only 50 ticks, meaning 0.084mm variance as opposed to the shown 0.18mm variance.

The skew is worrying to me, but what is more concerning is the difference in closed vs open loop operation while probing.
Why would open loop be 2x more skew to the Z value compared to closed loop?

I'm very new to the Duet, so if anyone has any suggestions on what may be happening, or have easier ways to do the probing/evaluation than the parsing, I'm all ears.

@dc42
This makes sense. I didn't consider the homea.g being the cause as it had worked fine before. Though I didn't confirm I had the right axis referenced.

Good catch on this. and sorry for taking time on a bug that's not really a bug.

you could use a 3state inverting line driver to generate a rough differential signal, then convert it back to single ended at the end with something like defined here. https://www.analog.com/media/en/technical-documentation/application-notes/an78fs.pdf

but might not be worth the effort, and using shielded twisted pair probably easiest.

@dc42
Loaded rc2+4, error is still present

Console output here from uploading firmware, updating config.g back to the previous U axis definition, then G28 A

4/17/2025, 7:17:00 AM: : Board 50 starting firmware update
4/17/2025, 7:17:24 AM: Connection established
4/17/2025, 7:18:19 AM: Upload of config.g successful after 0s
4/17/2025, 7:18:33 AM: Connection interrupted, attempting to reconnect...: Network error: Request timed out
4/17/2025, 7:18:35 AM: Connection established
4/17/2025, 7:18:46 AM: G28 A: homea.g Call
Error: Code 7 move error: info=-2.147e+9, seg: s=16775844 t=2147483647 d=-2147483648.00 u=-1.0000e+0 a=0.0000e+0 f=0f
4/17/2025, 7:18:55 AM: M122: === Diagnostics ===
RepRapFirmware for Duet 3 Mini 5+ version 3.6.0-rc.2+4 (2025-04-17 08:23:50) running on Duet 3 Mini5plus Ethernet (standalone mode)
Board ID: G5729-TU8LU-F65J0-409NU-3F03Z-7U6T6
Used output buffers: 1 of 40 (19 max)
=== RTOS ===
Static ram: 94764
Dynamic ram: 116336 of which 16 recycled
Never used RAM 30280, free system stack 110 words
Tasks: NETWORK(1,ready,21.1%,178) ETHERNET(5,nWait 7,0.1%,578) HEAT(3,nWait 6,0.0%,371) TMC(4,nWait 6,0.8%,99) CanReceiv(6,nWait 1,0.0%,818) CanSender(5,nWait 7,0.0%,336) CanClock(7,delaying,0.0%,337) MAIN(1,running,75.5%,675) IDLE(0,ready,1.6%,29) USBD(3,blocked,0.0%,147) AIN(4,delaying,0.8%,261), total 99.8%
Owned mutexes:
=== Platform ===
Last reset 00:00:31 ago, cause: software
Last software reset at 2025-04-17 07:18, reason: User, Gcodes spinning, available RAM 30280, slot 1
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0400f000 BFAR 0xe000ed38 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
MCU temperature: min 30.2, current 31.2, max 31.2
Supply voltage: min 23.9, current 24.0, max 24.0, under voltage events: 0, over voltage events: 0, power good: yes
Heap OK, handles allocated/used 99/37, heap memory allocated/used/recyclable 2048/696/0, gc cycles 0
Events: 0 queued, 0 completed
Date/time: 2025-04-17 07:19:27
Slowest loop: 56.79ms; fastest: 0.16ms
=== Storage ===
Free file entries: 18
SD card 0 detected, requested/actual speed: 25.0/24.0MBytes/sec
SD card longest read time 3.4ms, write time 6.0ms, max retries 0
=== Move ===
Segments created 3, maxWait 22309ms, bed comp in use: none, height map offset 0.000, hiccups added 0/0 (0.00/0.00ms), max steps late 0, ebfmin 0.00, ebfmax 0.00
Pos req/act/dcf: 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00
No step interrupt scheduled
Driver 0: standstill, SG min 0, r/w errs 0/1, ifcnt 43, reads/writes 1603/15, timeouts 0, DMA errs 0, CC errs 0
Driver 1: standstill, SG min 0, r/w errs 0/1, ifcnt 41, reads/writes 1605/13, timeouts 0, DMA errs 0, CC errs 0
Driver 2: standstill, SG min 0, r/w errs 0/1, ifcnt 41, reads/writes 1604/13, timeouts 0, DMA errs 0, CC errs 0
Driver 3: standstill, SG min 0, r/w errs 0/1, ifcnt 32, reads/writes 1607/10, timeouts 0, DMA errs 0, CC errs 0
Driver 4: standstill, SG min 0, r/w errs 0/1, ifcnt 32, reads/writes 1608/10, timeouts 0, DMA errs 0, CC errs 0
Driver 5: not present
Driver 6: not present
=== DDARing 0 ===
Scheduled moves 1, completed 1, LaErrors 0, Underruns [0, 0, 0]
Segments left 1, axes/extruders owned 0x00000013, drives owned 0x00000013
Code queue is empty
=== DDARing 1 ===
Scheduled moves 0, completed 0, LaErrors 0, Underruns [0, 0, 0]
Segments left 0, axes/extruders owned 0x00000000, drives owned 0x00000000
Code queue is empty
=== Heat ===
Bed heaters -1 -1 -1 -1, chamber heaters -1 -1 -1 -1, ordering errs 0
=== GCodes ===
Movement locks held by HTTP, null
HTTP is idle in state(s) 2 5, running macro
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
File2 is idle in state(s) 0
Queue2 is idle in state(s) 0
=== CAN ===
Messages queued 156, received 249, lost 0, ignored 0, errs 2680, boc 0
Longest wait 277ms for reply type 6041, peak Tx sync delay 10687, free buffers 26 (min 25), ts 148/145/0
Tx timeouts 0,0,2,0,0,0 last cancelled message type 30 dest 127
=== Network ===
Slowest loop: 14.42ms; fastest: 0.03ms
Responder states: MQTT(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0)
HTTP sessions: 1 of 8
= Ethernet =
Interface state: active
Error counts: 0 0 0 0 0 0
Socket states: 6 6 2 2 2 0 0 0 0

Came across this error today with rc2 (no plus), still present with rc2+1
Not certain if it's just how weird my system is, or if it's an actual bug.

When attempting to home my A axis I get this error, UNLESS the home switch is already triggered.
If the homing switch is already triggered the axis homes just fine, but subsequent home commands run the motor at what sounds like 10X speed which the motor can't do and just squeals.
If at this point I physically move the axis to the home switch, at which point the homing sequence completes without error.

I can home my Z axis without issue.

I have found that if I define what I have called my U axis in the past, as the Y axis, then the error does not occur.
This is weird to me, as it's the A axis homing that causes the error, I do not have endstops for the U/Y axis.

I'm suspecting it is something to do with me not defining/using the X or Y axis, which you'd not really see in any normal setup.... though I do not know why that should be a problem.

Using Y instead of U is not a large issue for me, but I figured I'd better notify of what I found in case it is a bug instead of just me doing stupid things.

Error code:

Error: Code 7 move error: info=-2.147e+9, seg: s=10412661 t=2147483647 d=-2147483648.00 u=-1.0000e+0 a=0.0000e+0 f=0f

M122:

4/16/2025, 9:44:45 AM: M122: === Diagnostics ===
RepRapFirmware for Duet 3 Mini 5+ version 3.6.0-rc.2+1 (2025-04-09 16:55:47) running on Duet 3 Mini5plus Ethernet (standalone mode)
Board ID: G5729-TU8LU-F65J0-409NU-3F03Z-7U6T6
Used output buffers: 1 of 40 (19 max)
=== RTOS ===
Static ram: 94764
Dynamic ram: 116432 of which 16 recycled
Never used RAM 30184, free system stack 110 words
Tasks: NETWORK(1,ready,21.3%,145) ETHERNET(5,nWait 7,0.1%,578) HEAT(3,nWait 6,0.0%,371) TMC(4,nWait 6,0.8%,99) CanReceiv(6,nWait 1,0.0%,796) CanSender(5,nWait 7,0.0%,336) CanClock(7,delaying,0.0%,353) MAIN(1,running,74.7%,675) IDLE(0,ready,2.0%,29) USBD(3,blocked,0.0%,147) AIN(4,delaying,0.8%,261), total 99.7%
Owned mutexes:
=== Platform ===
Last reset 00:00:25 ago, cause: software
Last software reset at 2025-04-16 09:33, reason: User, Gcodes spinning, available RAM 30196, slot 1
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x00000000 BFAR 0xe000ed38 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
MCU temperature: min 28.2, current 29.5, max 29.5
Supply voltage: min 23.9, current 24.0, max 24.0, under voltage events: 0, over voltage events: 0, power good: yes
Heap OK, handles allocated/used 99/37, heap memory allocated/used/recyclable 2048/696/0, gc cycles 0
Events: 1 queued, 1 completed
Date/time: 2025-04-16 09:44:44
Slowest loop: 80.95ms; fastest: 0.16ms
=== Storage ===
Free file entries: 18
SD card 0 detected, interface speed: 22.5MBytes/sec
SD card longest read time 3.3ms, write time 3.9ms, max retries 0
=== Move ===
Segments created 3, maxWait 13801ms, bed comp in use: none, height map offset 0.000, hiccups added 0/0 (0.00/0.00ms), max steps late 0, ebfmin 0.00, ebfmax 0.00
Pos req/act/dcf: 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00 0.00/0/0.00 -2147483648.00/-2/-1.00 0.00/0/0.00
No step interrupt scheduled
Driver 0: standstill, SG min 0, r/w errs 0/1, ifcnt 29, reads/writes 1296/15, timeouts 0, DMA errs 0, CC errs 0
Driver 1: standstill, SG min 0, r/w errs 0/1, ifcnt 27, reads/writes 1298/13, timeouts 0, DMA errs 0, CC errs 0
Driver 2: standstill, SG min 0, r/w errs 0/1, ifcnt 27, reads/writes 1297/13, timeouts 0, DMA errs 0, CC errs 0
Driver 3: standstill, SG min 0, r/w errs 0/1, ifcnt 21, reads/writes 1300/10, timeouts 0, DMA errs 0, CC errs 0
Driver 4: standstill, SG min 0, r/w errs 0/1, ifcnt 21, reads/writes 1301/10, timeouts 0, DMA errs 0, CC errs 0
Driver 5: not present
Driver 6: not present
=== DDARing 0 ===
Scheduled moves 1, completed 0, LaErrors 0, Underruns [0, 0, 0]
Segments left 0, axes/extruders owned 0x00000013, drives owned 0x00000013
Code queue is empty
=== DDARing 1 ===
Scheduled moves 0, completed 0, LaErrors 0, Underruns [0, 0, 0]
Segments left 0, axes/extruders owned 0x00000000, drives owned 0x00000000
Code queue is empty
=== Heat ===
Bed heaters -1 -1 -1 -1, chamber heaters -1 -1 -1 -1, ordering errs 0
=== GCodes ===
Movement locks held by HTTP, null
HTTP is idle in state(s) 2 5, running macro
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
File2 is idle in state(s) 0
Queue2 is idle in state(s) 0
=== CAN ===
Messages queued 137, received 227, lost 0, ignored 0, errs 1, boc 0
Longest wait 277ms for reply type 6041, peak Tx sync delay 489, free buffers 26 (min 25), ts 120/119/0
Tx timeouts 0,0,0,0,0,0
=== Network ===
Slowest loop: 14.75ms; fastest: 0.04ms
Responder states: MQTT(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0)
HTTP sessions: 1 of 8
= Ethernet =
Interface state: active
Error counts: 0 0 0 0 0 0
Socket states: 6 6 2 2 2 0 0 0 0

M122 B50.0 does not complete

config.g that errors

; Configuration file for RepRapFirmware on Duet 3 Mini 5+ Ethernet
; executed by the firmware on start-up

; General
G91 ; Relative coordinates
;M83 ; relative extruder moves
M550 P"TestSaw" ; Tool Number in future NV01234567-999

; Network
M552 P192.168.1.14 S1 ; configure Ethernet adapter
M553 P255.255.255.0 ; set netmask
M554 P192.168.1.1 ; set gateway
M586 P0 S1 ; configure HTTP

; Wait a moment for the CAN expansion boards to become available
G4 S2

; Closed Loop Drivers
M569.1 P50.0 T1 C189.384649 E7.5:50.0 S200 R30 I10 D0.01 V250 A30000 ; quadrature encoder and magnetic encoder. 188.08049125 187.911371 185.905911 
M569 P50.0 S1 D2 

; Open Loop Drivers
M569 P0.0 S1 D2 ; Clamp Driver
M569 P0.1 S1 D2 ; Rotate Driver
M569 P0.2 S1 D2 ; Feed Driver

; Axes
M584 Z50.0 U0.2 A0.0 B0.1 ; set axis mapping
M350 Z16 U16 A16 B16 ; configure microstepping 
M906 Z800 U800 A1300 B1500; set axis driver currents
;M917 Z0

; (micro)Steps/mm Calculation:
; Z: Driver 1 microsteps
; Z: Motor 200steps/rev
; Z: Belt Reduction 1/2 (0.5)
; Z: Lead Screw Reduction 1.27 mm/Rotation (note,encoder reads here at 1.184759:1 ratio and 4um/cycle)
; Z: Motion Ratio 1.996311786:1
; B: Driver 16 microsteps
; B: Motor 200steps/rev
; B: Belt Reduction 25/60 (0.4166666)
; A: Driver 16 microsteps
; A: Motor 200steps/rev, direct coupled
; E: Driver 16 microsteps
; E: Motor 400steps/rev (89080.1598:1)
; E: Belt Reduction 1/2 (0.5)(222.7003995:1)
; E: Harmonic Reduction 1/100 (0.01)(111.35019977:1) step = 0.009 deg
; E: Pinch Roller Radius 7.212148 mm (circ 45.3153) (1.1135:1) 0.12587583333 mm/deg (0.0011328825 mm/step)
; E: Encoder Roller Diameter 12.954 mm (circ 40.6962)
M92 Z10060.153887 U28455.406926 A8.8888 B21.333333 ; steps/mm microsteps/mm E14123.2652106 for 200step motor 628.75961790625 E28246.5304212
M566 Z0 U1 A0 B1 P1 ; set maximum instantaneous speed changes (mm/min)
M203 Z270 U100 A210939.6 B703126.08 I0.001 ;set maximum speeds (mm/min)
M201 Z235.8796 U500 A50863.59954 B11593.69048 ; set accelerations (mm/s^2)
M208 Z-0.65:1.5 U-2147483647:2147483647  A0:180 B-2147483647:2147483647 ; axis Limits
; Kinematics
M669 K0 ; configure Cartesian kinematics

; Endstop and Probe
M574 Z2 P"!50.io0.in" S1 ; configure Z axis endstop inverted
M574 A1 P"^!out3.tach" S1 ; configure A axis endstop with pullup, inverted
M558 P8 C"^!io1.in" H1:0.01 F12.425:0.0363255 T100 K0 A10 S0.00127 B0 ; configure blade probe with pullup, inverted
G31 K0 Z0 P500

; Spindle configuration
M950 R0 C"nil + out0" L12000

;Coolant Pump Configuration
M950 F0 C"out1"

; Tools
M563 P0 S"Blade" F0 R0 ; create tool #0

; Miscellaneous
M453 ; select CNC mode
T0 ; select first tool

; Remove Requirement for homing
G92 E0 B0 ;

; setup display
M918 P2 E4 F2000000           ; Fysetc 12864mini
M950 E1 C"io3.out" T1 U3       ; create a RGB Neopixel LED strip with 3 LEDs on the Duet 3 Mini 5+ 12864_EXP1 header
M150 E1 R125 U0 B125 P125 S1 F1  ; display led blue R=Green, U=Red, B=Blue
M150 E1 R0 U0 B0 P0 S1 F1  ; left encoder led red
M150 E1 R0 U0 B0 P0 S1 F0  ; right encoder led green

;wait for things to be ready
G4 S1

;start logging
M929 S3 ; S3:DEBUG S2:INFO S1:WARN

;load variables
M98 P"0:/macros/general/commands/loadVariables.g"

homea.g

; homea.g
; called to home the A axis
;
if {exists(global.debugOn)}
	if {global.debugOn = 1}
		M118 P0 S"homea.g Call" L3
; anything here to make sure it's safe

; homing moves
var aTravel = move.axes[3].max - move.axes[3].min + 360 ; calculate how far Z can travel plus degrees
G91 ; relative positioning
G1 F{global.clampHomeSpeed}
G1 H1 A{-var.aTravel} F{global.clampHomeSpeed} ; coarse home in the -A direction
G1 H2 A5 F{global.clampHomeSpeed} ; move back 5degrees
G1 H1 A-1 F{global.clampHomeSpeed} ; fine home in the -A direction

G90 ; Absolute Positioning
G1 A{global.clampCloseDegrees} F{global.clampingSpeed}
set global.clampStatus = 1

G4 P1

if {exists(global.debugOn)}
	if {global.debugOn = 1}
		M118 P0 S"homea.g Return" L3

homez.g

; homez.g
; called to home the Z axis
;
; generated by RepRapFirmware Configuration Tool v3.5.8 on Mon Jan 06 2025 08:00:55 GMT-0700 (Mountain Standard Time)
if {exists(global.debugOn)}
	if {global.debugOn = 1}
		M118 P0 S"homez.g Call" L3
; anything here to make sure it's safe

; homing moves
var zTravel = move.axes[2].max - move.axes[2].min + 0.5 ; calculate how far Z can travel plus 0.5mm
var zHalfMax = move.axes[2].max / 2 ; calculate half the max of Z travel

G91 ; relative positioning
G1 H1 Z{var.zTravel} F{global.depthHomeSpeed * 10} ; coarse home in the -Z direction
G1 H2 Z-0.5 F{global.depthHomeSpeed * 10} ; move back 0.5mm
G1 H1 Z1 F{global.depthHomeSpeed} ; fine home in the -Z direction

G1 H2 Z{-var.zHalfMax} F100
; setup closed loop
M569 P50.0 D4
G4 P50
;M569.6 P50.0 V2
;G4 P500
M569.6 P50.0 V1
G4 P1

if {exists(global.debugOn)}
	if {global.debugOn = 1}
		M118 P0 S"homez.g Return" L3

config.g that does not error

; Configuration file for RepRapFirmware on Duet 3 Mini 5+ Ethernet
; executed by the firmware on start-up

; General
G91 ; Relative coordinates
M83 ; relative extruder moves
M550 P"TestSaw" ; set hostname

; Network
M552 P192.168.1.14 S1 ; configure Ethernet adapter
M553 P255.255.255.0 ; set netmask
M554 P0.0.0.0 ; set gateway
M586 P0 S1 ; configure HTTP

; Wait a moment for the CAN expansion boards to become available
G4 S2

; Closed Loop Drivers
M569.1 P50.0 T1 C189.384649 E7.5:50.0 S200 R30 I10 D0.01 V250 A30000 ; quadrature encoder and magnetic encoder. 188.08049125 187.911371 185.905911 
M569 P50.0 S1 D2 

; Open Loop Drivers
M569 P0.0 S1 D2 ; Clamp Driver
M569 P0.1 S1 D2 ; Rotate Driver
M569 P0.2 S1 D2 ; Feed Driver

; Axes
M584 Z50.0 Y0.2 A0.0 B0.1 ; set axis mapping
M350 Z16 Y16 A16 B16 ; configure microstepping 
M906 Z800 Y800 A1300 B1500; set axis driver currents
M917 Z0 ; standstill current percentage

; (micro)Steps/mm Calculation:
; Z: Driver 1 microsteps
; Z: Motor 200steps/rev
; Z: Belt Reduction 1/2 (0.5)
; Z: Lead Screw Reduction 1.27 mm/Rotation (note,encoder reads here at 1.184759:1 ratio and 4um/cycle)
; Z: Motion Ratio 1.996311786:1
; B: Driver 16 microsteps
; B: Motor 200steps/rev
; B: Belt Reduction 25/60 (0.4166666)
; A: Driver 16 microsteps
; A: Motor 200steps/rev, direct coupled
; E: Driver 16 microsteps
; E: Motor 400steps/rev (89080.1598:1)
; E: Belt Reduction 1/2 (0.5)(222.7003995:1)
; E: Harmonic Reduction 1/100 (0.01)(111.35019977:1) step = 0.009 deg
; E: Pinch Roller Radius 7.212148 mm (circ 45.3153) (1.1135:1) 0.12587583333 mm/deg (0.0011328825 mm/step)
; E: Encoder Roller Diameter 12.954 mm (circ 40.6962)
M92 Z10060.153887 Y28455.406926 A8.8888 B21.333333 ; steps/mm microsteps/mm E14123.2652106 for 200step motor 628.75961790625 E28246.5304212
M566 Z0 Y1 A0 B1 P1 ; set maximum instantaneous speed changes (mm/min)
M203 Z270 Y100 A210939.6 B703126.08 I0.001 ;set maximum speeds (mm/min)
M201 Z235.8796 Y500 A10000 B11593.69048 ; set accelerations (mm/s^2) A50863.59954
M208 Z-0.65:1.5 Y-2147483647:2147483647 A0:180 B-2147483647:2147483647 ; axis Limits
; Kinematics
M669 K0 ; configure Cartesian kinematics

; Endstop and Probe
M574 Z2 P"!50.io0.in" S1 ; configure Z axis endstop inverted
M574 A1 P"^!out3.tach" S1 ; configure A axis endstop with pullup inverted
M558 P8 C"^!io1.in" H1:0.01 F12.425:0.0363255 T100 K0 A10 S0.00127 B0 ; configure blade probe
G31 K0 Z0 P500 ; set probe status set probe 0 to 0 when value over 500

; Spindle configuration
M950 R0 C"nil + out0" L12000

;Coolant Pump Configuration
M950 F0 C"out1"

; Tools
M563 P0 S"Blade" F0 R0 ; create tool #0

; Miscellaneous
M453 ; select CNC mode
T0 ; select first tool

; Remove Requirement for homing
G92 B0 ;

; setup display
M918 P2 E4 F2000000           ; Fysetc 12864mini
M950 E1 C"io3.out" T1 U3       ; create a RGB Neopixel LED strip with 3 LEDs on the Duet 3 Mini 5+ 12864_EXP1 header
M150 E1 R125 U0 B125 P125 S1 F1  ; display led blue R=Green, U=Red, B=Blue
M150 E1 R0 U0 B0 P0 S1 F1  ; left encoder led red
M150 E1 R0 U0 B0 P0 S1 F0  ; right encoder led green

;wait for things to be ready
G4 S1

;start logging
M929 S3 ; S3:DEBUG S2:INFO S1:WARN

;load variables
M98 P"0:/macros/general/commands/loadVariables.g"

@btmclain I see you have standstill current at 0% (M917 X0), have you tried commenting out this line, or increasing the standstill current value?

on my system when I add the M917 X0 I also get this clunk. Removing it and I have no clunk when tuning.

@btmclain By "manually" i mean not in a homing macro, but by sending the gcode manually either in the DWC console or connected SBC.
But after rereading your first post, I assume that's what you've done.

I think your issue may lie in the initial configuration of the encoder. the C parameter should be the number of cycles from the quadrature encoder per motor revolution.
I don't see anywhere you specify the motion relationship between motor and linear encoder, the linear encoder you specify has a 5um/pulse output, (20um/cycle)
With your C value of 1000 that works out to a movement of 20mm/motor rotation. is that correct?

Are you doing a small motor movement in open loop mode before attempting calibrations?

When playing with my setup I was able to somehow get the system to move in closed loop with only a magnetic encoder calibration, then I was able to confirm the linear encoder cycles/rotation value (i had to iterate a few times as the documentation says Pulses per revolution, I believe it should say cycles/revolution instead as that is what I ended up at to get the correct movement) Once I had the C value in the ballpark I was able to get the system to calibrate the Quadrature encoder (M569.6 V1) successfully.

Have you tried the calibration steps manually?

once you have the magnetic encoder calibrated once you should not have to calibrate it again unless you change the mounting or magnet.