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 top:

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

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.

When connected it should look like the following picture:

"$HOME/.arduino15/packages/arduino/tools/avrdude/6.3.0-arduino18/bin/avrdude" -C"$HOME/.arduino15/packages/arduino/tools/avrdude/6.3.0-arduino18/etc/avrdude.conf" -v -patmega32u4 -catmelice_isp -Pusb -Uflash:w:/tmp/arduino_build_987637/Blink.ino.hex:i

vrdude: Version 6.3-20201216
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch

         System wide configuration file is "$HOME/.arduino15/packages/arduino/tools/avrdude/6.3.0-arduino18/etc/avrdude.conf"
         User configuration file is "$HOME/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : usb
         Using Programmer              : atmelice_isp
avrdude: usbdev_open(): Found Atmel-ICE CMSIS-DAP, serno: J42700064543
avrdude: max packet size expected 912, but found 512 due to EP 0x01's wMaxPacketSize
avrdude: Found CMSIS-DAP compliant device, using EDBG protocol
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : JTAG3_ISP
         Description     : Atmel-ICE (ARM/AVR) in ISP mode
         Vtarget         : 5.0 V
         SCK period      : 125.00 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.02s

avrdude: Device signature = 0x1e9587 (probably m32u4)
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as CB
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "/tmp/arduino_build_987637/Blink.ino.hex"
avrdude: writing flash (3958 bytes):

Writing | ################################################## | 100% 16.21s

avrdude: 3958 bytes of flash written
avrdude: verifying flash memory against /tmp/arduino_build_987637/Blink.ino.hex:
avrdude: load data flash data from input file /tmp/arduino_build_987637/Blink.ino.hex:
avrdude: input file /tmp/arduino_build_987637/Blink.ino.hex contains 3958 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 16.24s

avrdude: verifying ...
avrdude: 3958 bytes of flash verified

avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as CB
avrdude: safemode: Fuses OK (E:CB, H:D8, L:FF)

avrdude done.  Thank you.