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If you can measure the pitch then you might be able to find it here:
connectorbook.com/identification.html?N=..._full_size_rect_conn

But it looks like standard 0.1" pitch so many things might fit. I would try the "dupont" style.
connectorbook.com/identification.html?N=&n=shroudless_plugs

On the top Right menu of the boot screen I have options for: 
Default Xsession
Gnome classic on Xorg
Gnome Classic
Gnome on wayland
Xfce Session
Only the Default Xsession and the Xfce session works. The others give me a white screen that says "Oh no. Something has gone wrong and the system cannot recover. Please log out and try again". There is also a sweet little icon of a computer screen and a sad face. Much of the googling I have done suggests that onboard only works with a few window managers.
Thanks again

Got the inputs figured out.

1.  Program drive so all inputs are 'no function assigned'

2. Change xml input address HAL name:
3. Add bitslice to HAL, using the bit chart from the servo manual:
Now I can press buttons connected to the drive and all five inputs react in halshow.  Rather exciting...

Next step is to see if I can fumble through changing the PDOs to 'fixed' and somehow map the outputs.

Anyone have a clue what 'sub-index 1' means?
 

Hi All hope everyone is good.
So I am considering going the LinuxCNC with EtherCat  route as opposed to a Inovance EtherCat Controller route.
So the Motors are as Follower
3 x 4.4KW Servo Motors from JSS Motor with a EtherCat Drivers  3phase Units
3 X 1.5KW Servo Motors from JSS Motors with EtherCat Drivers 3phase Units with Brake
Would like to know if it possible to configure LinuxCNC to work with these motors and drivers
I also have 12 Analog Inputs(Endstops proximity endstops)
Also have a 32Inch Touch Monitor 

So first and foremost can I go the LinuxCNC route
what is  the best recommendations

I looked into ethercat options for i/o and found many different modules at many different price points. Because there is so much aviable prices are not too bad. Its also easy to connect more i/o to the ethercat chain.

With the 7i96s I have a smart serial aviable for expansion cards but its only one port. Multiple boards, I think need to be daisy chained, dont know how to tho. 

The atc will be controlled by pneumatics. If you mean the rack/magazin I will try to design a semi active one, similar to what Marius Hornberger built for his hammer cnc. There will be a rack that moves out of the way when not in use. I plan on making mine not purely mechanical tho.

I hope people already did similar builds and I just need to connect the dots, basicly taking parts I need to make a build out of it. Playing around in the dark is not exactly my aim. 

Since you mentioned price sensitivity, you might think about IO - both current and future needs.

Ethercat drives generally have onboard IO available which can be used as general purpose, but these aren't directly expandable without adding more drives.  Nor can drive onboard IO drive high-power outputs directly - you'll likely need some relays (or similar) to turn on pumps, air cylinders, etc.

If you need more IO than the drives offer you'll need to add an IO module, such as a Beckhoff or other vendor.  Or go with non-realtime IO based on some USB solution.

I haven't priced Ethercat IO modules, but I suspect they are more expensive per IO point than Mesa.  It might be instructive to set up a spreadsheet with all your current and future IO requirements and price out an Ethercat solution vs. Mesa.

Or perhaps both Ethercat and Mesa - this is also an option.

Another consideration is your (future) ATC - have you thought about how to control it?  Will it be a 'dumb' motor using a geneva mechanism, or a servo-controlled thing with a reudcer?  Or something else?

Reason I bring this up is that it might be helpful to find an example of an LCNC configuration which matches your intended hardware...are there any examples of an ATC using Ethercat available, or will you need to break new ground?  Same goes for your possible laser.

It all gets rather complicated, doesn't it?

The Fanuc A06B-6102-H211#H520 spindle module, the A06B-0855-B102 SVM3 A06B-6080-H304 spindle motor, and the A06B-0141-B077 1.0 kW 2.5A X, Y, and Z axis motor, model alphaC12/2000. Thank you.

What error?

Here is the full file

loadrt mux2 names=mux2_x,mux2_y,mux2_z
addf mux2_x servo-thread
addf mux2_y servo-thread
addf mux2_z servo-thread

loadrt wcomp names=plus_x_trigger,minus_x_trigger,plus_y_trigger,minus_y_trigger,plus_z_trigger,minus_z_trigger
addf plus_x_trigger servo-thread
addf minus_x_trigger servo-thread
addf plus_y_trigger servo-thread
addf minus_y_trigger servo-thread
addf plus_z_trigger servo-thread
addf minus_z_trigger servo-thread

# this is the deadzone for each axis to stop drift, also can make bigger to stop x/y axis moves easier without one triggering the other
setp plus_x_trigger.max 0.15
setp minus_x_trigger.min -0.15
setp plus_y_trigger.max 0.15
setp minus_y_trigger.min -0.15
setp plus_z_trigger.max 0.15
setp minus_z_trigger.min -0.15

loadrt lut5 names=jog_x_enable,jog_y_enable,jog_z_enable
addf jog_x_enable servo-thread
setp jog_x_enable.function 0x80
addf jog_y_enable servo-thread
setp jog_y_enable.function 0x80
addf jog_z_enable servo-thread
setp jog_z_enable.function 0x80

loadrt or2 names=or-x-jog,or-y-jog,or-z-jog
addf or-x-jog servo-thread
addf or-y-jog servo-thread
addf or-z-jog servo-thread

loadrt scale names=scale.x,scale.y,scale.z
addf scale.x servo-thread
addf scale.y servo-thread
addf scale.z servo-thread

# mine were 0-4.8v. Assuming a range of -1 to +1. 2/4.8=.416 z was way off balance and cannot see how to adjust so do it in sw
setp scale.x.offset -1.00
setp scale.x.gain .416
setp scale.y.offset -1.00
setp scale.y.gain .416
setp scale.z.offset -0.80
setp scale.z.gain .416

net x-scale <= hm2_7i76e.0.7i76.0.0.analogin0 => scale.x.in
net y-scale <= hm2_7i76e.0.7i76.0.0.analogin1 => scale.y.in
net z-scale <= hm2_7i76e.0.7i76.0.0.analogin2 => scale.z.in

# the mux is used to select 0 or the current value and is implementing the deadband. Cannot let the analog value through otherwise in interferes with jogging from ui
net gate-x-scale <= scale.x.out => plus_x_trigger.in minus_x_trigger.in mux2_x.in1
net gate-y-scale <= scale.y.out => plus_y_trigger.in minus_y_trigger.in mux2_y.in1
net gate-z-scale <= scale.z.out => plus_z_trigger.in minus_z_trigger.in mux2_z.in1

# may not be needed anymore
net x-is-homed <= halui.joint.0.is-homed => jog_x_enable.in-1
net y-is-homed <= halui.joint.1.is-homed => jog_y_enable.in-1
net z-is-homed <= halui.joint.2.is-homed => jog_z_enable.in-1

# only allow jogging if in the jog menu linuxcnc/gmoccapy seemed to complain in any other state
net machine-is-injog <= halui.mode.is-manual => jog_x_enable.in-0 jog_y_enable.in-0 jog_z_enable.in-0

# fixed for all axis multiplied from .15 to 1 from scale above. Change scale is difference needed for each axis
setp halui.axis.jog-speed 600
setp halui.joint.jog-speed 600

# wcomp is used here as deadband. Controls relevant jog plus or minus
net enable-x-jog-plus <= plus_x_trigger.over => halui.axis.x.plus or-x-jog.in0
net enable-x-jog-minus <= minus_x_trigger.under => halui.axis.x.minus or-x-jog.in1
net enable-y-jog-plus <= plus_y_trigger.over => halui.axis.y.plus or-y-jog.in0
net enable-y-jog-minus <= minus_y_trigger.under => halui.axis.y.minus or-y-jog.in1
net enable-z-jog-plus <= plus_z_trigger.over => halui.axis.z.plus or-z-jog.in0
net enable-z-jog-minus <= minus_z_trigger.under => halui.axis.z.minus or-z-jog.in1

# if all 3 conditions are met i.e. not in deadband, is homed and is manual then select mux and route analog value to axis
net jog-x-either <= or-x-jog.out => jog_x_enable.in-2
net enable-x-mux <= jog_x_enable.out => mux2_x.sel
net jog-x-speed <= mux2_x.out => halui.axis.x.analog

net jog-y-either <= or-y-jog.out => jog_y_enable.in-2
net enable-y-mux <= jog_y_enable.out => mux2_y.sel
net jog-y-speed <= mux2_y.out => halui.axis.y.analog

net jog-z-either <= or-z-jog.out => jog_z_enable.in-2
net enable-z-mux <= jog_z_enable.out => mux2_z.sel
net jog-z-speed <= mux2_z.out => halui.axis.z.analog

Thanks for your reply. Problem is, I want to be able to use a virtual keyboard, and onboard just does not work. Could it have something to do with the window manager? Others seem to be available in the boot menu, but when I try them they come up with an error. This is a fresh install.

I mentioned before I want to future proof. To claify: its not a what if but a kind of fixed advancement plan:
1. ATC toolchanger
2. 4th possibly 5th axis
3. Alternating size/ tooling.
4. Laser/Mill hybrid 
5. possibly multiple machines of the same build.

I have a small business and depending on how I expand I want this cnc to be able to grow with me. Once I have a system running there will only be minor changes doable as downtime would cost me double.

Forgive me for being extremely new at this.

I understand 'add it to the xml file' in general terms, but as I have no experience or context it's hard for me to determine exactly what/how to add something.

My test xml file has what appears to be variable PDOs: "pdo idx=1600" and pdo idx="1A00"

These appear to be variable PDOs, whatever that means, based on the chart taken from the manual:
 

However, the only place where digital outputs appear to be available is in the Fixed PDO section:
 

Can I add another section in the xml file for fixed PDO's? or do I have to pick one or the other?

Regarding bitslice... am I correct - generally - in that the drive sends a 'word' or string or something to LCNC with address "60FDh", and the value of that word can be interpreted using bitslice as the status of the drive's digital inputs?

If so, using the chart below is the key needed to configure bitslice in to HAL pins?
 
 

Not your drive but this XML shows you how to set the input type using sdoconfig
github.com/rodw-au/linuxcnc-cia402/blob/main/ethercat-conf.xml

You can obtain the PDO corresponding to IO by consulting the servo's manual, and then add it to the ethercat-config.xml file. The "bitslice" component may be required in the hal file.
I have tested it with Leadshine's servo before and it worked normally, but I didn't save the configuration file.