To use the Atmel-ICE programmer on linux, make sure to add the following udev rule first:

sudo vi /etc/udev/rules.d/77-atmel-ice_jtag_swd.rules

And insert the following two lines:

# Atmel-ICE JTAG/SWD in-circuit debugger
SUBSYSTEM=="usb", ATTR{idVendor}=="03eb", ATTR{idProduct}=="2141", GROUP="dialout", MODE="666"

If required, add yourself to the dialout group (First verify with the groups command if you are already listed in that group)

(Optional) usermod -a -G dialout ${USER}

Reload udev rules:

sudo udevadm control --reload-rules 

The pinout from the Arduino Micro as seen from above is:

*   *   *   *   *   *   *   *   *   *   *   *   *   *   *   *   *

                                                           (SWITCH)

USB PORT   ARDUINO                                       (2) (4) (6)
            MICRO
                                                         (1) (3) (5)


*   *   *   *   *   *   *   *   *   *   *   *   *   *   *   *   *

The pinout from the 6-pin IDC connector from the cable that came with the Atmel-ICE as seen from the bottom:

    +-----+-----+-----+
    !  6  !  4  !  2  !
    +-----+-----+-----+
    !  5  !  3  !  1  !
    +-----+-----+-----+
          +++++++

To connect the Atmel-ICE to an Arduino Micro, use the cable that came with the Atmel-ICE. Insert the 50-mil 10-pin JTAG connector, at the “AVR” port (See marking at the top of the enclosure. It is the port which is at the right side, away from where the 3 LEDs are) at the Atmel-ICE and the other 6-pin IDC connector at the Arduino Micro.

The Arduino micro cannot be powered from the Atmel-ICE. An external 5v power is required.