Building V3.1 using the arduino and cnc

I am trying to get the stepper motor to run the firmware loaded fine into the arduino. The first issue is when I start up my laptop the motors start running and then stop. The next thing is when I go to gperdict and engage the atrium all I get ithe thread is started, nothing else. Can someone help in these matters. I only have the elevation side built. also have anyone using the Raspberry Pi with the rotor,.using the USB to control the arduino.

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