EDIT: I1 and pullup removed from code
I spent an hour or so reading the different posts to find how to wire and set Pinda2 probe on the tool board v1.1 of my new CoreXY machine. So here is some info for others to use. This will work for other inductive sensors, just do not connect temp1 connector
Wiring

Configuration

; Z-Probe
M671 X-31.39:250:531.36 Y18:433.3:18 S10       ; Locations left, center, right   
M558 P8 C"121.io2.in"  H0.7 F1000 T6000 A20 S0.005 ; PINDA set Z probe type to switch and the dive height + speeds
M308 S2 P"121.temp1" A"PINDA" Y"thermistor" T100000 B3950
G31 P500 X-3.20 Y0 Z2.5                                    ; set Z probe trigger value, offset and trigger height
M557 X20:485 Y41:360 P7                             ; define mesh grid

Here is the probe repeatability test result

6/6/2021, 9:26:30 AM	G32 bed probe heights: -0.001 -0.003 -0.003 -0.002 -0.002 -0.003 -0.002 -0.003 -0.002 -0.003 -0.001 -0.003 -0.003 -0.003 -0.002 -0.002 -0.001 -0.001 -0.002 -0.001 -0.000 -0.001 -0.002 -0.002 -0.002, mean -0.002, deviation from mean 0.001

@baua1024 With 3.4 I got this error only once for 48 hour printing already
My chamber heater is this link text
run trough SSR, I am using standard E3d V^ thermistor
this is my config line

M308 S2 A"Chamber" P"temp2" Y"thermistor" T100000 B4725 C7.06e-8
M950 H2 C"out2" T2                                 ;
M307 H2 A11 C99000 D2000 B1   ; 
M141 H2
M143 H2 S70

@mackiez Hi, Mine is highly modified with H2 extruder and 0.9 steppers on X and Y, so my curent config is not going to help . Here it is my config when I first set duet wifi on Sapphire pro. It is almost stock here , only Bltouch and E3d V6 block and heater with original heatsink and Chimera heatbreak

; General preferences
G90                                     ; send absolute coordinates...
M83                                     ; ...but relative extruder moves
M550 P"TP BOX1.0a"                      ; set printer name
M667 S1                                 ; select CoreXY mode
; Network
M552 S1                                 ; enable network
M586 P0 S1                              ; enable HTTP
M586 P1 S0                              ; disable FTP
M586 P2 S0                              ; disable Telnet
; Drives
M569 P0 S0                              ; physical drive 0 goes forwards
M569 P1 S0                              ; physical drive 1 goes forwards
M569 P2 S0                              ; physical drive 2 goes backwards
M569 P3 S0                             ; physical drive 3 goes forwards
M584 X0 Y1 Z2 E3                        ; set drive mapping
M350 X16 Y16 Z16 E16 I1                 ; configure microstepping with interpolation
M92 X80.0 Y80.0 Z1600.00 E395.00      ; set steps per mm
M566 X800.00 Y800.00 Z12.00 E300.00     ; set maximum instantaneous speed changes (mm/min)
M203 X18000.00 Y18000.00 Z500.00 E6000.00 ; set maximum speeds (mm/min)
M201 X2500.00 Y2500.00 Z100.00 E1500.00     ; set accelerations (mm/s^2)
M906 X900 Y900 Z900 E1000 I30         ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                 ; Set idle timeout
; Axis Limits
M208 X0 Y0 Z0 S1                        ; set axis minima
M208 X210 Y210 Z200 S0                  ; set axis maxima
; Endstops
M574 X1 Y2 Z1 S0                        ; set active low and disabled endstops
; Z-Probe
M558 P5 H5 F120 T6000                   ; set Z probe type to switch and the dive height + speeds
G31 P500 X0 Y0 Z2.5                     ; set Z probe trigger value, offset and trigger height
M557 X15:215 Y15:195 S20                ; define mesh grid
; Heaters
M307 H0 B0 S1.00                        ; disable bang-bang mode for the bed heater and set PWM limit
M305 P0 T100000 B4138 R4700             ; set thermistor + ADC parameters for heater 0
M143 H0 S120                            ; set temperature limit for heater 0 to 120C
M305 P1 T100000 B4138 R4700             ; set thermistor + ADC parameters for heater 1
M143 H1 S280                            ; set temperature limit for heater 1 to 280C
; Fans
M106 P0 S0 I0 F500 H-1                  ; set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S1 I0 F500 H-1                ; set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned on
; Tools
M563 P0 D0 H1 F0                        ; define tool 0
G10 P0 X0 Y0 Z0                         ; set tool 0 axis offsets
G10 P0 R0 S0                            ; set initial tool 0 active and standby temperatures to 0C
; Custom settings are not defined

@sebkritikel https://www.youtube.com/watch?v=ImSpw3hpFJg

Most probably it is some mistake in panel due manual operation, that made me change from - to + tool offset. It seems it is ok now

@frederik you may consider Pinda probe , it is 5 v

I just finished building MULDEX 3d printer. It js a Rep Rap style project with 3 Z and 400x300 buildplate and kinematic coupling with . Corexyu kinematics, 2 independent dual extruders and duet wifi with duex and paneldue.

@mackiez Could you photo your controller wiring and your end-stops on the frame

yes
first print finished with tool1 (left)
here is my new config
It is with PRF3.11 and I think It will work with PRF3.22 too

G90                                             ; send absolute coordinates...
M83                                             ; ...but relative extruder moves
M550 P"Muldex"                                  ; set printer name


; Network
M552 S1                                        ; enable network
M586 P0 S1                                      ; enable HTTP
M586 P1 S0                                      ; disable FTP
M586 P2 S0                                      ; disable Telnet

; Drives
M569 P0 S0                                      ; X physical drive 0 goes backwards
M569 P1 S0                                      ; Y right physical drive 1 goes backwards
M569 P2 S1                                      ; Y left physical drive 2 goes forwards
M569 P3 S1                                      ; U physical drive 3 goes forwards
M569 P4 S1                                     ; E1 physical drive 4 goes backwards
M569 P5 S1                                      ; Z left physical drive 5 goes backwards
M569 P6 S1                                     ; Z center physical drive 6 goes backwards
M569 P7 S0                                      ; Z right physical drive 7 goes forwards
M569 P8 S1                                      ; E2 physical drive 8 goes forwards

M584 X0 Y1:2 U3 Z5:6:7 E4:8                     ; set drive mapping

M350 X16 U16 Y16 Z16 E16:16 I1                                                           ; configure microstepping with interpolation
M92 X199.7 U200 Y199.8:199.8 Z799.2:799.2:799.2 E813.07:830.00                        ; set steps per mm (1760nimble)
M566 X1000.00 U1000.00 Y1000.00:1000.00 Z80.00:80.00:80.00 E100.00:100.00                ; set maximum instantaneous speed changes (mm/min)(Nimble 40)
M203 X12000.00 U12000.00 Y12000.00:12000.00 Z1000.00:1000.00:1000.00 E4200.00:4200.00    ; set maximum speeds (mm/min)
M201 X1310.00 U1310.00 Y1310.00:1310.00 Z35.00:35.00:35.00 E800.00:800.00                    ; set accelerations (mm/s^2)(500)(Nimble 120)
M906 X900 U900 Y900:900 Z900:900:900 E1000:1000 I30                                        ; set motor currents (mA) and motor idle factor in per cent(Nimble 500)
M84 S120                                                                                  ; Set idle timeout

; Axis Limits
M208 X-18 Y0 U40 Z0 S1                          ; set axis min - adjust X to align nozzle
M208 X350 U422.7 Y333 Z300 S0                   ; set axis max 

M669 K0 Y1:-1:0:1				                ; select Markforged Kinematics Y to react with X and U

; Endstops
M574 X1 S1 P"xstop"                             ;X axis active high endstop switch
M574 Y2 S1 P"ystop+e1stop"                      ;Y Double max active high endstop switch
;M574 Y1 S4 ; configure sensorless endstop for low end on Y
M574 U2 S1 P"e0stop"                            ;U axis active high endstop switch
;M574 Z2 S4

;Stall Detection(no used)
;M574 Y1 S4                                     ; Y axis stall detection
;M915 P1:9 S3 F1 R0                             ; Y axis stall detection

; Z-Probe
M671 X-20.6:200:420.6 Y14.3:333.3:14.3 S10       ; Locations left, center, right          
M950 S0 C"duex.e6heat"                          ; create servo pin 0 for BLTouch
M558 P9 C"zprobe.in+zprobe.mod" H10 F600 A1 T12000   ; set Z probe type to bltouch and the dive height + speeds 
G31 P25 X-29 Y0 Z3.97                           ; set Z probe trigger value, offset and trigger height(lower number farther away)1.8build 1.7glass 
M557 X10:320 Y20:290 S60                       ; probe from X=10 to 390, Y=10 to 290mm with a mesh spacing of 20mm

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B4534 C9.565227e-8      ; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0                                            ; create bed heater output on bedheat and map it to sensor 0
M143 H0 S120                                                     ; set temperature limit for heater 0 to 120C
M307 H0 B0 S1.00                                                 ; disable bang-bang mode for the bed heater and set PWM limit
M140 H0                                                          ; map heated bed to heater 0
M308 S1 P"e0temp" Y"thermistor" T100000 B4725 C0 R4700  ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1                                             ; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S280                                                     ; set temperature limit for heater 1 to 280C
M307 H1 B0 S1.00                                                 ; disable bang-bang mode for heater  and set PWM limit
M308 S2 P"e1temp" Y"thermistor" T100000 B4725 C0 R4700 ; configure sensor 2 as thermistor on pin e1temp
M950 H2 C"e1heat" T2                                             ; create nozzle heater output on e1heat and map it to sensor 2
M143 H2 S280                                                     ; set temperature limit for heater 2 to 280C
M307 H2 B0 S1.00                                                 ; disable bang-bang mode for heater  and set PWM limit

; Fans
M950 F0 C"fan0" Q500                             ; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1                               ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"fan1" Q500                             ; create fan 1 on pin fan1 and set its frequency
M106 P1 S1 H1 T45                                ; set fan 1 value. Thermostatic control is turned on
M950 F2 C"fan2" Q500                             ; create fan 2 on pin fan2 and set its frequency
M106 P2 S0 H-1                                   ; set fan 2 value. Thermostatic control is turned off
M950 F3 C"duex.fan8" Q500                        ; create fan 3 on pin duex.fan8 and set its frequency
M106 P3 S1 H2 T45                                ; set fan 3 value. Thermostatic control is turned on

; LEDs
M950 F4 C"duex.fan6" ;Q500                       ; create LED 4 on pin duex.fan6 and set its frequency
M106 P4 S128 H-1                                 ; set LED 4 value. Thermostatic control is turned OFF
M950 F5 C"duex.fan7" ;Q500                       ; create LED 5 on pin duex.fan7 and set its frequency
M106 P5 S128 H-1                                 ; set LED 5 value. Thermostatic control is turned OFF

; Tools
M563 P0 D0 H1 F0 S"Left"                         ; define tool 0 Left 
G10 P0 X0 Y0 Z-2.55                             ; set tool 0 axis offsets y was .45
G10 P0 R0 S0                                     ; set initial tool 0 active and standby temperatures to 0C

M563 P1 D1 H2 X3 F2 S"Right"                     ; define tool 1 Right
G10 P1 X0 Y0 Z0                ; set tool 1 axis offsets - adjust Y to alignn nozzle
G10 P1 R0 S0                                     ; set initial tool 1 active and standby temperatures to 0C

;M563 P2 D0:1 H1:2 X0:3 F0:2 S"Copy"              ; define tool 2 Copy
;G10 P2 X90 Y0 U-90 S0 R0                         ; set tool 2 axis offsets (WAS 105)
;M567 P2 E1:1         
;M568 P2 S1 ; turn on mixing for tool 2           ; set mix ratio 100% on both extruders
;G10 L1 P1 X0.0 Y0.0 Z-2.55

M501                                             ; Record
M593 F66.6
T0 PO
M575 P1 S1 B57600                                ;Panel due 
;G92 Z150
;G91
;G1 Z0.1 f100
;G90

TO warp up
In the end I found that it is working both ways with or without pullup.
I ended up changing pinda2 to superpinda, as far I got one delivered and super panda is working flawlessly with the same config

@dc42 Thank you . I get this but these are on the machine. Any guidelines about PID tuning. I managed to make it today following the wiki guide and my graphs are more "noisy" is this to be expected. It is a big machine with 0.6 and 0.8revo nozzles. But I limit the acceleration a lot , hopin to improve this by going closed loop

@dc42 Does that mean 0.9 steppers will have problems running in closed loop ?

I think I found the culprit.
Originally due to heavy gantry my motors LDO-42STH60-MAC were runing at 1700 mA max current cutoff (2 Amps max)
I reduced the current to 1200 mA and now it is without vibrations in closed loop mode

 1/20/2025, 10:05:28 PM	m569.6 p50.0 v3
Driver 50.0 calibration check succeeded, measured backlash is -0.067 step
Residual encoder reading errors: min -5.0, max 11.3, rms 1.4
1/20/2025, 10:04:47 PM	m569.6 p50.0 v2
Driver 50.0 calibration succeeded, measured backlash is -0.074 step
Original encoder reading errors: min -13.8, max 14.1, rms 5.7
Corrections made: min -9.6, max 9.2, rms 5.6
1/20/2025, 10:04:11 PM	m17
1/20/2025, 10:04:05 PM	M906 X1200 Y1200 I0

I still do not know if these numbers are good

@jay_s_uk here is new calibration

and then the m122 p50.0

m122 b50
Diagnostics for board 50:
Duet EXP1HCL rev 1.0a or earlier firmware version 3.6.0-beta.3 (2025-01-15 18:54:31)
Bootloader ID: SAME5x bootloader version 2.4 (2021-12-10)
All averaging filters OK
Never used RAM 51588, free system stack 184 words
Tasks: EncCal(1,nWait 6,0.3%,183) Move(3,nWait 7,0.0%,167) CLSend(3,nWait 6,0.0%,149) TMC(4,nWait 6,66.5%,317) HEAT(2,nWait 6,0.1%,105) CanAsync(5,nWait 4,0.0%,66) CanRecv(3,nWait 1,0.0%,65) CanClock(5,nWait 1,0.0%,64) MAIN(1,running,32.0%,253) IDLE(0,ready,0.0%,29) AIN(2,nWait 2,1.2%,255), total 100.0%
Owned mutexes:
Last reset 00:05:44 ago, cause: software
Last software reset data not available
Moves scheduled 0, hiccups 0 (0.00/0.00ms), segs 0, step errors 0 (types 0x0), maxLate 0 maxPrep 0, ebfmin 0.00 max 0.00
Phase step loop runtime (us): min=26, max=65, frequency (Hz): min=4807, max=18292
Peak sync jitter -7/7, peak Rx sync delay 190, resyncs 0/0, next timer interrupt due in 2 ticks, enabled, next step interrupt due in 4036578614 ticks, disabled
VIN voltage: min 24.2, current 24.3, max 24.3
V12 voltage: min 12.0, current 12.0, max 12.1
MCU temperature: min 28.4C, current 29.1C, maDriver 0: pos 690, 320.0 steps/mm, position tolerance exceeded, failed to maintain position, SG min n/a, mspos 4, reads 25157, writes 8 timeouts 0
Last sensors broadcast 0x00000000 found 0 89 ticks ago, 0 ordering errs, loop time 0
CAN messages queued 2421, send timeouts 0, received 3688, lost 0, ignored 0, errs 0, boc 0, free buffers 38, min 38, error reg 0
dup 0, oos 0/0/0/0, bm 0, wbm 0, rxMotionDelay 0
Closed loop driver 0 mode: closed loop, pre-error threshold: 10.00, error threshold: 20.00, encoder type rotaryAS5047, position -1966
Encoder reverse polarity: no, full rotations -1, last angle 14418, minCorrection=-9.0, maxCorrection=9.2, agc 79, mag 4747, no error
Tuning mode: 0, tuning error: 0, collecting data: no
Accelerometer: none
I2C bus errors 0, naks 0, contentions 0, other errors 0

@jay_s_uk Reboot is fixed I uped the error in m596.1
It now just gives a warning when I send m17
if I reset the tuning 569.6 p50.0 v4 it goes away
so the problem seems to be 0.9 steppers
it performs calibration and after that goes in resonance

I am stupid these are 0.9 mottors
tried to edit M569.1 with S400 parameter and the calibration went well , but after that the motor entered in such big resonance in stoped position , that crashed the whole board

1/20/2025, 8:37:55 PM	Connection established
1/20/2025, 8:37:25 PM	Connection interrupted, attempting to reconnect...
Network error: Request timed out
1/20/2025, 8:37:17 PM	Warning: Driver 50.0 warning: position tolerance exceeded
1/20/2025, 8:37:16 PM	m17
1/20/2025, 8:36:28 PM	Warning: Driver 50.0 warning: position tolerance exceeded
1/20/2025, 8:36:27 PM	Connection established
1/20/2025, 8:36:12 PM	Connection interrupted, attempting to reconnect...
Network error: Request timed out
1/20/2025, 8:36:03 PM	m569.6 p50.0 v2
Driver 50.0 calibration succeeded, measured backlash is -0.084 step
Original encoder reading errors: min -12.3, max 14.8, rms 5.2
Corrections made: min -9.0, max 10.0, rms 5.1
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
Warning: Driver 50.0 warning: position tolerance exceeded
1/20/2025, 8:35:37 PM	m569.6 p50.0
Error: M569.6: Driver 50.0 calibration failed (no reason available)
1/20/2025, 8:35:14 PM	m569.1 p50.0
Encoder type: rotaryAS5047
Magnetic encoder motor steps/rev 400, agc 80, mag 4715
PID parameters P=100.0 I=0.000 D=0.000 V=1000.0 A=0.0, torque constant 1.00Nm/A
Warning/error threshold 1.00/2.00
1/20/2025, 8:35:03 PM	m17
1/20/2025, 8:34:47 PM	Upload of config.g successful after 0s
1/20/2025, 6:39:33 PM	Connection established

Just in case downgraded back to 3.5.4 and the result is the same

FAIL of the initial tuning
So after yestarday everythig was set in open loop and working , homing etc.
Today I remembered I have m3 treaded rods and managed to attach the first encoder
I unloaded the stepper ( removed the belt) and hit the wall
here is what I get

1/20/2025, 5:05:29 PM	M569.6 P50.0 V3
Error: M569.6: Driver 50.0 calibration failed (no reason available)
1/20/2025, 5:00:24 PM	M569.6 P50.0 V2
Error: M569.6: Driver 50.0 calibration failed, the measured motion was less than expected, measured counts/step is about 41.0
Warning: Driver 50.0 warning: tuning/calibration failed
1/20/2025, 4:59:51 PM	m17
1/20/2025, 4:59:29 PM	M569.6 P50.0 V2
Error: M569.6: Driver is not enabled
1/20/2025, 4:59:05 PM	Upload of config.g successful after 0s

Here is my config.g

; Configuration file for Duet 3 (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.2.3 on Thu May 27 2021 13:17:12 GMT+0300 (Eastern European Summer Time)

; General preferences 
G90                                                    ; send absolute coordinates...
M83                                                    ; ...but relative extruder moves
M550 P"CoreXY500"                                     ; set printer name
M669 K1                                                ; select CoreXY mode

; Network
M552 P192.168.1.27 S1                                       ; enable network and acquire dynamic address via DHCP
M586 P0 S1                                             ; enable HTTP
M586 P1 S0                                             ; disable FTP
M586 P2 S0                                             ; disable Telnet
G4 S2   ;wait for expansion boards to start


; Drives
M569.1 P50.0 T3 E1:2 R100 I0 D0 ; Configure the Duet 3 Expansion 1HCL board at CAN address 50 with a Duet 3 magnetic encoder, warn if 1 fullstep threshold exceeded, error if 2 full steps threshold exceeded.
M569 P50.0 D4 S1 ;
;M569 P0.0 S1                                           ; physical drive 0.0 goes forwards
M569 P0.1 S0                                    ; physical drive 0.1 goes forwards
M569 P0.3 S0
M569 P0.4 S1  
M569 P0.5 S1                                           ; physical drive 0.2 goes forwards
M569 P121.0 S1                                         ; physical drive 121.0 goes forwards
M584 X50.0 Y0.1 Z0.3:0.4:0.5 E121.0                             ; set drive mapping
M350 X16 Y16 Z16 E16 I1                                ; configure microstepping with interpolation
M92 X160.00 Y160.00 Z8280.00 E395.70                      ; set steps per mm
M350 X32 Y32 Z16 E16 I1
M566 X300.00 Y300.00 Z50.00 E120.00                    ; set maximum instantaneous speed changes (mm/min)
M203 X12000.00 Y12000.00 Z150.00 E1200.00                ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z20.00 E500.00                    ; set accelerations (mm/s^2)
M906 X1700 Y1700 Z1000 E800 I30                           ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                                ; Set idle timeout

; Axis Limits
M208 X-26 Y0 Z0 S1                                       ; set axis minima
M208 X500 Y330 Z365 S0                                 ; set axis maxima

; Endstops
M574 X1 S4                                             ; configure sensorless endstop for low end on X
M574 Y1 S4                                             ; configure sensorless endstop for low end on Y
M574 Z1 S2                                             ; configure Z-probe endstop for low end on Z
;M574 E1 S1
;Filament sensor BTT E1
M591 D0 P2 C"io8.in" S1 ;configure BTT smart filament sensor
; Z-Probe
M671 X-31.39:250:531.36 Y-18:433.3:-18 S10       ; Locations left, center, right   
M558 P8 C"121.io2.in"  H3 F1000 T6000 A20 S0.005 ; PINDA set Z probe type to switch and the dive height + speeds
;M308 S2 P"121.temp1" A"PINDA" Y"thermistor" T100000 B3950
;M950 H2 C"out1" T2                                 ; create nozzle heater output on 121.out0 and map it to sensor 1
;M307 H2 B0 S1.00                                       ; disable bang-bang mode for heater  and set PWM limit
;M141 H2
;M143 H2 S90                                           ; set temperature limit for heater 1 to 280C
G31 P500 X30 Y0 Z1.48                            ; set Z probe trigger value, offset and trigger height
M557 X20:450 Y5:320 P5                             ; define mesh grid

; Heaters
M308 S0 P"temp0" Y"thermistor" T100000 B4138           ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out0" T0 Q10                                     ; create bed heater output on out0 and map it to sensor 0
M307 H0 B0 S1                                      ; disable bang-bang mode for the bed heater and set PWM limit
M140 H0                                                ; map heated bed to heater 0
M143 H0 S130                                          ; set temperature limit for heater 0 to 120C
M308 S1 P"121.temp0" Y"thermistor" T100000 B4725 C7.060000e-8       ; configure sensor 1 as thermistor on pin 121.temp0
M950 H1 C"121.out0" T1                                 ; create nozzle heater output on 121.out0 and map it to sensor 1
M307 H1 B0 S1.00                                       ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S290     ; set temperature limit for heater 1 to 280C

M308 S2 A"Chamber" P"temp2" Y"thermistor" T100000 B4725 C7.06e-8
M950 H2 C"out2" T2                                 ; create nozzle heater output on 121.out0 and map it to sensor 1
M307 H2 R0.001 A11 C99999 D4000 B1   ; disable bang-bang mode for heater  and set PWM limit
M141 H2
M143 H2 S70

; Fans
M950 F0 C"121.out1"                               ; create fan 0 on pin 121.out1 and set its frequency
M106 P0 S0 B0.5 H-1                                         ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"121.out2" Q500                               ; create fan 1 on pin 121.out2 and set its frequency
M106 P1 S1 H1 T45                                      ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                                       ; define tool 0
G10 P0 X0 Y0 Z-0.15                                        ; set tool 0 axis offsets
G10 P0 R0 S0                                           ; set initial tool 0 active and standby temperatures to 0C

; Custom settings are not defined
M955 P121.0 I05 ;Accelerometer on Toolboard
; Miscellaneous
M575 P1 S1 B57600                                      ; enable support for PanelDue
M572 D0 S0.045 ; PA for ABS GD filament 0.4 nozzle
M501                                                   ; load saved parameters from non-volatile memory
M911 S22.5 R23.5 P"M913 X0 Y0 G91 M83 G1 Z3 E-5 F1000" ; set voltage thresholds and actions to run on power loss

and here are diagnostics right after the error
system

	m122
=== Diagnostics ===
RepRapFirmware for Duet 3 MB6HC version 3.6.0-beta.3 (2025-01-16 19:09:36) running on Duet 3 MB6HC v1.01 (standalone mode)
Board ID: 08DJM-9P63L-DJMSS-6JKDA-3S86L-1BDB9
Used output buffers: 1 of 40 (21 max)
=== RTOS ===
Static ram: 136892
Dynamic ram: 127588 of which 16 recycled
Never used RAM 79560, free system stack 200 words
Tasks: NETWORK(1,ready,28.2%,175) ETHERNET(5,nWait 7,0.1%,316) HEAT(3,nWait 6,0.0%,347) Move(4,nWait 6,0.0%,333) TMC(4,nWait 6,3.1%,375) CanReceiv(6,nWait 1,0.0%,794) CanSender(5,nWait 7,0.0%,334) CanClock(7,delaying,0.0%,350) MAIN(1,running,68.5%,103) IDLE(0,ready,0.0%,29) USBD(3,blocked,0.0%,149), total 100.0%
Owned mutexes:
=== Platform ===
Last reset 00:14:48 ago, cause: software
Last software reset at 2025-01-20 16:59, reason: User, Gcodes spinning, available RAM 78828, slot 2
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x00400000 BFAR 0x00000000 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
Aux0 errors 0,0,0
MCU temperature: min 25.3, current 26.1, max 26.3
Supply voltage: min 24.1, current 24.1, max 24.2, under voltage events: 0, over voltage events: 0, power good: yes
12V rail voltage: min 12.1, current 12.1, max 12.2, under voltage events: 0
Heap OK, handles allocated/used 99/1, heap memory allocated/used/recyclable 2048/12/0, gc cycles 0
Events: 1 queued, 1 completed
Date/time: 2025-01-20 17:13:57
Slowest loop: 3.22ms; fastest: 0.07ms
USB interrupts 2
=== Storage ===
Free file entries: 20
SD card 0 detected, interface speed: 25.0MBytes/sec
SD card longest read time 1.0ms, write time 0.0ms, max retries 0
=== Move ===
Segments created 0, maxWait 0ms, 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
next step interrupt due in 9 ticks, disabled
Driver 0: standstill, SG min n/a, mspos 8, reads 7783, writes 11 timeouts 0
Driver 1: standstill, SG min n/a, mspos 4, reads 7773, writes 21 timeouts 0
Driver 2: standstill, SG min n/a, mspos 8, reads 7783, writes 11 timeouts 0
Driver 3: standstill, SG min n/a, mspos 8, reads 7773, writes 21 timeouts 0
Driver 4: standstill, SG min n/a, mspos 8, reads 7773, writes 21 timeouts 0
Driver 5: standstill, SG min n/a, mspos 8, reads 7773, writes 21 timeouts 0
Phase step loop runtime (us): min=0, max=89, frequency (Hz): min=1666, max=2500
=== DDARing 0 ===
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
=== 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 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1, chamber heaters 2 -1 -1 -1 -1 -1 -1 -1, ordering err=== GCodes ===
Movement locks held by null, null
HTTP is idle in state(s) 0
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
=== Filament sensors ===
check 0 clear 6854308
Extruder 0 sensor: ok
=== CAN ===
Messages queued 7938, received 25025, lost 0, ignored 0, errs 0, boc 0
Longest wait 13ms for reply type 6018, peak Tx sync delay 376, free buffers 50 (min 49), ts 4213/4212/0
Tx timeouts 0,0,0,0,0,0
=== Network ===
Slowest loop: 3.10ms; fastest: 0.03ms
Responder states: MQTT(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0) Telnet(0)
HTTP sessions: 2 of 8
= Ethernet =
Interface state: active
Error counts: 0 0 0 1 0 0
Socket states: 6 2 2 2 2 0 0 0 0
=== Multicast handler ===
Responder is inactive, messages received 0, responses 0

for the 1hcl board attached with the encoder

m122 b50
Diagnostics for board 50:
Duet EXP1HCL rev 1.0a or earlier firmware version 3.6.0-beta.3 (2025-01-15 18:54:31)
Bootloader ID: SAME5x bootloader version 2.4 (2021-12-10)
All averaging filters OK
Never used RAM 51588, free system stack 182 words
Tasks: EncCal(1,nWait 6,0.0%,312) Move(3,nWait 7,0.0%,167) CLSend(3,nWait 6,0.0%,149) TMC(4,nWait 6,60.5%,317) HEAT(2,nWait 6,0.0%,105) CanAsync(5,nWait 4,0.0%,66) CanRecv(3,nWait 1,0.0%,65) CanClock(5,nWait 1,0.0%,64) MAIN(1,running,38.4%,315) IDLE(0,ready,0.1%,29) AIN(2,nWait 2,1.0%,255), total 100.0%
Owned mutexes:
Last reset 00:15:41 ago, cause: software
Last software reset data not available
Moves scheduled 0, hiccups 0 (0.00/0.00ms), segs 0, step errors 0 (types 0x0), maxLate 0 maxPrep 0, ebfmin 0.00 max 0.00
Phase step loop runtime (us): min=26, max=65, frequency (Hz): min=8720, max=18292
Peak sync jitter -7/9, peak Rx sync delay 187, resyncs 0/0, next timer interrupt due in 11 ticks, enabled, next step interrupt due in 3589150588 ticks, disabled
VIN voltage: min 24.2, current 24.3, max 24.3
V12 voltage: min 12.0, current 12.0, max 12.1
MCU temperature: min 28.2C, current 29.1C, mDriver 0: pos -1080, 320.0 steps/mm, not tuned/calibrated, tuning/calibration failed, SG min n/a, mspos 4, reads 21334, writes 21 timeouts 0
Last sensors broadcast 0x00000000 found 0 181 ticks ago, 0 ordering errs, loop time 0
CAN messages queued 7704, send timeouts 0, received 12134, lost 0, ignored 0, errs 0, boc 0, free buffers 38, min 38, error reg 0
dup 0, oos 0/0/0/0, bm 0, wbm 0, rxMotionDelay 0
Closed loop driver 0 mode: closed loop, pre-error threshold: 1.00, error threshold: 2.00, encoder type rotaryAS5047, position 5520
Encoder reverse polarity: no, full rotations 0, last angle 5523, minCorrection=0.0, maxCorrection=0.0, agc 87, mag 4700, no error
Tuning mode: 0, tuning error: 0x6, collecting data: no
Accelerometer: none
I2C bus errors 12, naks 0, contentions 0, other errors 0

Any help is very much appreciated

Happy to report in open loop it works as expected with the 2 HCL board
Homing works from the first try with 3.6 beta 3
Did not manage to test closed loop as my motors are 60 mm and the suitable screw is 80 mm M3 , that I did have only 1 pc left in the drawer. So tomorrow evening will be able to install encoders and test

@T3P3Tony Thank you
You are right about the timing. I am currently on 3.5.2 ( updated lastly because of the filament sensor on the main board feature when using tool board)
I will first try everything on 3.5.2 by manually setting the home position and will commission the setup. If everything plays as expected, we will go through switching to 3.6 beta 3
Your help here is one of the reasons duet ecosystem is my preferred for almost any project I do