ATmega2560 wiring (stk500v2) bootloader flash writing stability issue

[mcuee]

Using the test hex file and it seems that the wiring bootloader has the same issue as the FT2232H based programmer.

• [bug #53703] FT232H based programmer returns all 0xFF when reading flash from atmega2560 #474 (comment)

Update: this hex file is not valid for this test. Now the issue is rather on the stability side,

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c wiring -P COM3 -p m2560 -D 
-U flash:w:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : wiring
avrdude.exe: stk500v2_ReceiveMessage(): timeout
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Wiring
             Description     : Wiring
             Programmer Model: AVRISP
             Hardware Version: 15
             Firmware Version Master : 2.10
             Vtarget         : 0.0 V
             SCK period      : 0.1 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.01s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\atmega2560_0x11000_offset.hex"
avrdude.exe: writing flash (261414 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 261414 bytes of flash written
avrdude.exe: verifying flash memory against .\atmega2560_0x11000_offset.hex:

Reading | ################################################## | 100% 0.01s

avrdude.exe: verification error, first mismatch at byte 0x11000
             0xff != 0x54
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

atmega2560_0x11000_offset.hex.txt

[mcuee]

Verified with AVR Dragon as well.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c dragon_isp -p m2560 -D 
-U flash:v:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : usb
             Using Programmer              : dragon_isp
avrdude.exe: usbdev_open(): Found AVRDRAGON, serno: 00A200001487
JTAG ICE mkII sign-on message:
Communications protocol version: 1
M_MCU:
  boot-loader FW version:        255
  firmware version:              7.39
  hardware version:              1
S_MCU:
  boot-loader FW version:        255
  firmware version:              7.39
  hardware version:              2
Serial number:                   00:a2:00:00:14:87
Device ID:                       AVRDRAGON
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : DRAGON_ISP
             Description     : Atmel AVR Dragon in ISP mode
             Vtarget         : 4.8 V
             SCK period      : 2.00 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.15s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: verifying flash memory against .\atmega2560_0x11000_offset.hex:

Reading | ################################################## | 100% 0.01s

avrdude.exe: verification error, first mismatch at byte 0x11000
             0xff != 0x54
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

[mcuee]

AVR Dragon seems to be okay.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c dragon_isp -p m2560  -D 
-U flash:w:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : usb
             Using Programmer              : dragon_isp
avrdude.exe: usbdev_open(): Found AVRDRAGON, serno: 00A200001487
JTAG ICE mkII sign-on message:
Communications protocol version: 1
M_MCU:
  boot-loader FW version:        255
  firmware version:              7.39
  hardware version:              1
S_MCU:
  boot-loader FW version:        255
  firmware version:              7.39
  hardware version:              2
Serial number:                   00:a2:00:00:14:87
Device ID:                       AVRDRAGON
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : DRAGON_ISP
             Description     : Atmel AVR Dragon in ISP mode
             Vtarget         : 4.8 V
             SCK period      : 2.00 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.15s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\atmega2560_0x11000_offset.hex"
avrdude.exe: writing flash (261414 bytes):

Writing | ################################################## | 100% 0.01s

avrdude.exe: 261414 bytes of flash written
avrdude.exe: verifying flash memory against .\atmega2560_0x11000_offset.hex:

Reading | ################################################## | 100% 0.00s

avrdude.exe: 261414 bytes of flash verified

avrdude.exe done.  Thank you.

And verfied with the Wiring bootloader as well.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c wiring -P COM3 -p m2560 -D 
-U flash:v:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : wiring
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Wiring
             Description     : Wiring
             Programmer Model: AVRISP
             Hardware Version: 15
             Firmware Version Master : 2.10
             Vtarget         : 0.0 V
             SCK period      : 0.1 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.01s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: verifying flash memory against .\atmega2560_0x11000_offset.hex:

Reading | ################################################## | 100% 0.00s

avrdude.exe: 261414 bytes of flash verified

avrdude.exe done.  Thank you.

[mcuee]

The test hex file is usng the ATmega2560 stk500v2 bootloader contents plus extra contents at 0x11000. The extra contents were generated by srec_cat.

$ srec_cat eepromtest.bin -offset 0x011000 -o eepromtest.srec
srec_cat: eepromtest.bin: 19: warning: no execution start address record

$ srec_cat eepromtest.srec  -o eepromtest_intel.hex -intel
srec_cat: eepromtest.srec: 19: warning: no execution start address record

$ cat eepromtest_intel.hex
:020000040001F9
:2010000054686520717569636B2062726F776E20666F78206A756D7073206F7665722074FE
:201020006865206C617A7920646F670A54686520717569636B2062726F776E20666F78206C
:201040006A756D7073206F76657220746865206C617A7920646F670A5468652071756963ED
:201060006B2062726F776E20666F78206A756D7073206F76657220746865206C617A7920C4
:20108000646F670A54686520717569636B2062726F776E20666F78206A756D7073206F76A5
:2010A000657220746865206C617A7920646F670A54686520717569636B2062726F776E20EE
:2010C000666F78206A756D7073206F76657220746865206C617A7920646F670A54686520B2
:2010E000717569636B2062726F776E20666F78206A756D7073206F76657220746865206C06
:20110000617A7920646F670A54686520717569636B2062726F776E20666F78206A756D7028
:2011200073206F76657220746865206C617A7920646F670A54686520717569636B20627269
:201140006F776E20666F78206A756D7073206F76657220746865206C617A7920646F670AFE
:2011600054686520717569636B2062726F776E20666F78206A756D7073206F76657220749D
:201180006865206C617A7920646F670A54686520717569636B2062726F776E20666F78200B
:2011A0006A756D7073206F76657220746865206C617A7920646F670A54686520717569638C
:2011C0006B2062726F776E20666F78206A756D7073206F76657220746865206C617A792063
:2011E000646F670A54686520717569636B2062726F776E20666F78206A756D7073206F7644
:00000001FF

[mcuee]

Not only wiring bootloader, the one provided by @stefanrueger here ( https://github.com/avrdudes/avrdude/files/8882669/atmega2560_v3.txt ) in #940 discussion has a problem as well. But the problem may be a bit different.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c arduino -P COM3 -p m2560 -D
 -U flash:w:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : arduino
avrdude.exe: ser_open(): can't open device "\\.\COM3": The system cannot find the file specified.

avrdude.exe: opening programmer "arduino" on port "COM3" failed

avrdude.exe done.  Thank you.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -c arduino -P COM6 -p m2560 -D -U flash:w:.\atmega2560_0x11000_offset.hex:i -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM6
             Using Programmer              : arduino
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Arduino
             Description     : Arduino
             Hardware Version: 7
             Firmware Version: 7.6

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\atmega2560_0x11000_offset.hex"
avrdude.exe: writing flash (261414 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 261414 bytes of flash written
avrdude.exe: verifying flash memory against .\atmega2560_0x11000_offset.hex:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verification error, first mismatch at byte 0x3fd00
             0x11 != 0x99
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

[stefanrueger]

avrdude.exe: verification error, first mismatch at byte 0x3fd00

You are trying to overwrite the bootloader. Your file is 261414 bytes long, i.e. does not fit into the available flash of 256k minus 768 bytes for the bootloader. My bootloader protects itself from being overwritten, but throws no error when writing (that costs too many code bytes :). You will notice during verification. The -c arduino programmer does not know about the size of the bootloader, so cannot do anything in this situation; my proposed urclock programmer knows about the available flash; its draft implementation complains with an appropriate error message and exits before attempting to write flash:

$ avrdude -qq -D -p m2560 -c urclock -b 115200 -P /dev/ttyUSB1 -U flash:w:atmega2560_0x11000_offset.hex:i
avrdude: ERROR, input [$11000, $3fd25] overlaps with bootloader [$3fd00, $3ffff]

[stefanrueger]

avrdude.exe: verification error, first mismatch at byte 0x11000

That is an interesting and unusual address for the first verification error. What I find intriguing is that apparently

$ .\avrdude.exe -c dragon_isp -p m2560 -D -U flash:v:.\atmega2560_0x11000_offset.hex:i -v

fails and that

$ .\avrdude.exe -c dragon_isp -p m2560 -D -U flash:w:.\atmega2560_0x11000_offset.hex:i -v

works?!? The only difference is 'v' and 'w' in the -U.

Perhaps try test files that fit below the bootloader?

[stefanrueger]

Your input file is to blame, I think.

$ srec_cat atmega2560_0x11000_offset.hex -intel -o - -c-arra dopp -Output_Word | tail -9 | head -4
srec_cat: atmega2560_0x11000_offset.hex: 470: warning: data records not in
    strictly ascending order (expected >= 0x3FD26, got 0x11000)
const unsigned long dopp_termination = 0x00000000;
const unsigned long dopp_start       = 0x00011000;
const unsigned long dopp_finish      = 0x0003FD26;
const unsigned long dopp_length      = 0x0002ED26;

[mcuee]

@stefanrueger
Apparently the file generated is not correct. The intention is not to test above 256KB but just above 0x11000 (a bit above 64KB) to test out the fix in #474 and here. The next step is then to test a bit above 128KB, and then probably a bit close to 256KB.

As for trying to overwrite the bootloader, that is kind of intentional -- to see how the bootloader behaves with -D.

The idea is really to put the offset to the test pattern into offset 0x11000 but apparently it is not correct to simply combine the following hex file with the bootloader hex file.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> cat .\eepromtest_intel.hex
:020000040001F9
:2010000054686520717569636B2062726F776E20666F78206A756D7073206F7665722074FE
:201020006865206C617A7920646F670A54686520717569636B2062726F776E20666F78206C
:201040006A756D7073206F76657220746865206C617A7920646F670A5468652071756963ED
:201060006B2062726F776E20666F78206A756D7073206F76657220746865206C617A7920C4
:20108000646F670A54686520717569636B2062726F776E20666F78206A756D7073206F76A5
:2010A000657220746865206C617A7920646F670A54686520717569636B2062726F776E20EE
:2010C000666F78206A756D7073206F76657220746865206C617A7920646F670A54686520B2
:2010E000717569636B2062726F776E20666F78206A756D7073206F76657220746865206C06
:20110000617A7920646F670A54686520717569636B2062726F776E20666F78206A756D7028
:2011200073206F76657220746865206C617A7920646F670A54686520717569636B20627269
:201140006F776E20666F78206A756D7073206F76657220746865206C617A7920646F670AFE
:2011600054686520717569636B2062726F776E20666F78206A756D7073206F76657220749D
:201180006865206C617A7920646F670A54686520717569636B2062726F776E20666F78200B
:2011A0006A756D7073206F76657220746865206C617A7920646F670A54686520717569638C
:2011C0006B2062726F776E20666F78206A756D7073206F76657220746865206C617A792063
:2011E000646F670A54686520717569636B2062726F776E20666F78206A756D7073206F7644
:00000001FF

$ srec_cat eepromtest_intel.hex -intel -o - -c-arra dopp -Output_Word | tail -9 | head -4
const unsigned long dopp_termination = 0x00000000;
const unsigned long dopp_start       = 0x00011000;
const unsigned long dopp_finish      = 0x00011200;
const unsigned long dopp_length      = 0x00000200;

[mcuee]

@stefanrueger
Redo the tests with your bootloader -- now the test hex file seems to be okay bu the it is okay.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c usbasp 
-U .\atmega2560_sr940_v3.hex -v

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : usb
             Using Programmer              : usbasp
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : usbasp
             Description     : USBasp, http://www.fischl.de/usbasp/

avrdude.exe: auto set sck period (because given equals null)
avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: NOTE: "flash" memory has been specified, an erase cycle will be performed
             To disable this feature, specify the -D option.
avrdude.exe: erasing chip
avrdude.exe: auto set sck period (because given equals null)
avrdude.exe: reading input file ".\atmega2560_sr940_v3.hex"
avrdude.exe: input file .\atmega2560_sr940_v3.hex auto detected as Intel Hex
avrdude.exe: writing flash (262144 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 262144 bytes of flash written
avrdude.exe: verifying flash memory against .\atmega2560_sr940_v3.hex:
avrdude.exe: input file .\atmega2560_sr940_v3.hex auto detected as Intel Hex

Reading | ################################################## | 100% 0.00s

avrdude.exe: 262144 bytes of flash verified

avrdude.exe done.  Thank you.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c arduino -P COM3 -D 
-U flash:w:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : arduino
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Arduino
             Description     : Arduino
             Hardware Version: 7
             Firmware Version: 7.6

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\eepromtest_intel.hex"
avrdude.exe: writing flash (70144 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 70144 bytes of flash written
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: 70144 bytes of flash verified

avrdude.exe done.  Thank you.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c arduino -P COM3 -D 
-U flash:v:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : arduino
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Arduino
             Description     : Arduino
             Hardware Version: 7
             Firmware Version: 7.6

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: 70144 bytes of flash verified

avrdude.exe done.  Thank you.

[mcuee]

But the stk500v2 wiring bootloader (with eeprom read fix) seems to still have a problem.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c usbasp 
-U .\stk500boot_v2_mega2560_eeprom_fix.hex

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: NOTE: "flash" memory has been specified, an erase cycle will be performed
             To disable this feature, specify the -D option.
avrdude.exe: erasing chip
avrdude.exe: reading input file ".\stk500boot_v2_mega2560_eeprom_fix.hex"
avrdude.exe: input file .\stk500boot_v2_mega2560_eeprom_fix.hex auto detected as Intel Hex
avrdude.exe: writing flash (261414 bytes):

Writing | ################################################## | 100% 0.01s

avrdude.exe: 261414 bytes of flash written
avrdude.exe: verifying flash memory against .\stk500boot_v2_mega2560_eeprom_fix.hex:
avrdude.exe: input file .\stk500boot_v2_mega2560_eeprom_fix.hex auto detected as Intel Hex

Reading | ################################################## | 100% 0.01s

avrdude.exe: 261414 bytes of flash verified

avrdude.exe done.  Thank you.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c wiring -P COM3 -D 
-U flash:w:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : wiring
avrdude.exe: wiring_open(): releasing DTR/RTS
avrdude.exe: wiring_open(): asserting DTR/RTS
avrdude.exe: ser_recv(): programmer is not responding
avrdude.exe: stk500v2_ReceiveMessage(): timeout
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Wiring
             Description     : Wiring
             Programmer Model: AVRISP
             Hardware Version: 15
             Firmware Version Master : 2.10
             Vtarget         : 0.0 V
             SCK period      : 0.1 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading |                                     | 0% 0.00savrdude.exe: stk500isp_read_byte(.., signature, 0x0, ...)
avrdude.exe: stk500isp_read_byte(): Sending read memory command: 
avrdude.exe: stk500isp_read_byte(.., signature, 0x1, ...)
Reading | #################                                  | 33% 0.01savrdude.exe: 
stk500isp_read_byte(.., signature, 0x2, ...)
Reading | ################################################## | 100% 0.01s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\eepromtest_intel.hex"
avrdude.exe: writing flash (70144 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 70144 bytes of flash written
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: verification error, first mismatch at byte 0x11000
             0xff != 0x54
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.



PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c wiring -P COM3 -D 
-U flash:v:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : wiring
avrdude.exe: wiring_open(): releasing DTR/RTS
avrdude.exe: wiring_open(): asserting DTR/RTS
avrdude.exe: ser_recv(): programmer is not responding
avrdude.exe: stk500v2_ReceiveMessage(): timeout
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Wiring
             Description     : Wiring
             Programmer Model: AVRISP
             Hardware Version: 15
             Firmware Version Master : 2.10
             Vtarget         : 0.0 V
             SCK period      : 0.1 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading |                                        | 0% 0.00savrdude.exe: stk500isp_read_byte(.., signature, 0x0, ...)
avrdude.exe: stk500isp_read_byte(): Sending read memory command: avrdude.exe: 
stk500isp_read_byte(.., signature, 0x1, ...)
Reading | #################                                  | 33% 0.01savrdude.exe: 
stk500isp_read_byte(.., signature, 0x2, ...)
Reading | ################################################## | 100% 0.01s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: verification error, first mismatch at byte 0x11000
             0xff != 0x54
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

[mcuee]

Using the optiboot bootloader from megacore from @MCUdude seems to be okay as weel.

:\Users\xiaof\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino18/bin/avrdude -
CC:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\hardware\avr\2.1.3/avrdude.conf -v 
-patmega2560 -cusbasp -Pusb -
Uflash:w:C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\hardware\avr\2.1.3/bootloaders/
optiboot_flash/bootloaders/atmega2560/16000000L/
optiboot_flash_atmega2560_UART0_115200_16000000L_B7_BIGBOOT.hex:i 
-Ulock:w:0x0f:m 

avrdude: 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 
"C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\hardware\avr\2.1.3/avrdude.conf"

         Using Port                    : usb
         Using Programmer              : usbasp
         AVR Part                      : ATmega2560
         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
Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x3f:
avrdude: load data lock data from input file 0x3f:
avrdude: input file 0x3f contains 1 bytes
avrdude: reading on-chip lock data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude: reading input file "0xfd"
avrdude: writing efuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of efuse written
avrdude: verifying efuse memory against 0xfd:
avrdude: load data efuse data from input file 0xfd:
avrdude: input file 0xfd contains 1 bytes
avrdude: reading on-chip efuse data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of efuse verified
avrdude: reading input file "0b11010110"
avrdude: writing hfuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of hfuse written
avrdude: verifying hfuse memory against 0b11010110:
avrdude: load data hfuse data from input file 0b11010110:
avrdude: input file 0b11010110 contains 1 bytes
avrdude: reading on-chip hfuse data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of hfuse verified
avrdude: reading input file "0xf7"
avrdude: writing lfuse (1 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xf7:
avrdude: load data lfuse data from input file 0xf7:
avrdude: input file 0xf7 contains 1 bytes
avrdude: reading on-chip lfuse data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of lfuse verified

avrdude done.  Thank you.

           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
           flash         65    10   256    0 yes    262144  256   1024  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 : usbasp
         Description     : USBasp, http://www.fischl.de/usbasp/

avrdude: auto set sck period (because given equals null)
avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x1e9801 (probably m2560)
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: auto set sck period (because given equals null)
avrdude: reading input file "C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\
hardware\avr\2.1.3/bootloaders/
optiboot_flash/bootloaders/atmega2560/16000000L/
optiboot_flash_atmega2560_UART0_115200_16000000L_B7_BIGBOOT.hex"
avrdude: writing flash (262144 bytes):

Writing | ################################################## | 100% -0.00s

avrdude: 262144 bytes of flash written
avrdude: verifying flash memory against C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\
hardware\avr\2.1.3/
bootloaders/optiboot_flash/
bootloaders/atmega2560/16000000L/
optiboot_flash_atmega2560_UART0_115200_16000000L_B7_BIGBOOT.hex:
avrdude: load data flash data from input file 
C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\hardware\avr\2.1.3/bootloaders/
optiboot_flash/bootloaders/atmega2560/16000000L/
optiboot_flash_atmega2560_UART0_115200_16000000L_B7_BIGBOOT.hex:
avrdude: input file C:\Users\xiaof\AppData\Local\Arduino15\packages\MegaCore\hardware\
avr\2.1.3/bootloaders/optiboot_flash/
bootloaders/atmega2560/16000000L/
optiboot_flash_atmega2560_UART0_115200_16000000L_B7_BIGBOOT.hex 
contains 262144 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 262144 bytes of flash verified
avrdude: reading input file "0x0f"
avrdude: writing lock (1 bytes):

Writing | ################################################## | 100% 0.01s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x0f:
avrdude: load data lock data from input file 0x0f:
avrdude: input file 0x0f contains 1 bytes
avrdude: reading on-chip lock data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of lock verified

avrdude done.  Thank you.


PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c arduino -P COM3 -D -U 
lash:w:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : arduino
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Arduino
             Description     : Arduino
             Hardware Version: 3
             Firmware Version: 8.0

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\eepromtest_intel.hex"
avrdude.exe: writing flash (70144 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 70144 bytes of flash written
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: 70144 bytes of flash verified

avrdude.exe done.  Thank you.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c arduino -P COM3 -D 
-U flash:v:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : arduino
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Arduino
             Description     : Arduino
             Hardware Version: 3
             Firmware Version: 8.0

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: 70144 bytes of flash verified

avrdude.exe done.  Thank you.

[mcuee]

BTW, programmer like usbasp and AVR Dragon have no issues.

In summary, only stk500v2 wiring bootloader has issues.

PS C:\work\avr\avrdude_test\avrdude-v7.0-windows-x64> .\avrdude.exe -p m2560 -c wiring -P COM3 -D 
-U flash:w:.\eepromtest_intel.hex:i -vv

avrdude.exe: Version 7.0
             Copyright (c) Brian Dean, http://www.bdmicro.com/
             Copyright (c) Joerg Wunsch

             System wide configuration file is "C:/work/avr/avrdude_test/avrdude-v7.0-windows-x64/avrdude.conf"

             Using Port                    : COM3
             Using Programmer              : wiring
avrdude.exe: wiring_open(): releasing DTR/RTS
avrdude.exe: wiring_open(): asserting DTR/RTS
avrdude.exe: ser_recv(): programmer is not responding
avrdude.exe: stk500v2_ReceiveMessage(): timeout
             AVR Part                      : ATmega2560
             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
             PollIndex                     : 3
             PollValue                     : 0x53
             Memory Detail                 :

                                               Block Poll               Page                       Polled
               Memory Type Alias    Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
               ----------- -------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
               eeprom                 65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
               flash                  65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
               lfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               hfuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               efuse                   0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               lock                    0     0     0    0 no          1    1      0  9000  9000 0x00 0x00
               calibration             0     0     0    0 no          1    1      0     0     0 0x00 0x00
               signature               0     0     0    0 no          3    1      0     0     0 0x00 0x00

             Programmer Type : Wiring
             Description     : Wiring
             Programmer Model: AVRISP
             Hardware Version: 15
             Firmware Version Master : 2.10
             Vtarget         : 0.0 V
             SCK period      : 0.1 us

avrdude.exe: AVR device initialized and ready to accept instructions

Reading |                            | 0% 0.00savrdude.exe: stk500isp_read_byte(.., signature, 0x0, ...)
avrdude.exe: stk500isp_read_byte(): Sending read memory command: 
avrdude.exe: stk500isp_read_byte(.., signature, 0x1, ...)
Reading | #################                                  | 33% 0.01savrdude.exe: 
stk500isp_read_byte(.., signature, 0x2, ...)
Reading | ################################################## | 100% 0.01s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: reading input file ".\eepromtest_intel.hex"
avrdude.exe: writing flash (70144 bytes):

Writing | ################################################## | 100% 0.00s

avrdude.exe: 70144 bytes of flash written
avrdude.exe: verifying flash memory against .\eepromtest_intel.hex:
avrdude.exe: load data flash data from input file .\eepromtest_intel.hex:
avrdude.exe: input file .\eepromtest_intel.hex contains 70144 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude.exe: verifying ...
avrdude.exe: verification error, first mismatch at byte 0x11000
             0xff != 0x54
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

Full debug log attached:
atmega2560_wiringbootloader_write_runlog.txt

[stefanrueger]

Would it be fair to summarise that a particular bootloader does not seem to work (stk500v2 wiring) with -c wiring, but other bootloaders do? So this could well be the bootloader that is unable to upload that file.

Have you tried input files that start at 0? Some bootloaders autoincrement the address and ignore any set extended address commands. In this case your input file should have been folded by the defective bootloader into the [0, 0xffff] space. Try to find where your input has been placed (read out the flash and look at it).

Anyway, AVRDUDE wouldn't be able to do anything about defective bootloaders...