The AVR ISP Mkii (no longer available) lists the ATMega2560:
Manual : http://www.atmel.com/Images/Atmel-42093-AVR-ISP-mkII_UserGuide.pdf
Not sure what the ISP clones do...
I never use the bootloader. Always use an ISPMKII since I spin my own PCB's. Don't want the USB thing... also I use a lot of Promini's...
One thing - if you buy chips from places like Digikey you'll need to set the fuses. I use AVR Burn O Mat - AVR8 Burn-O-Mat avrdude GUI
There's listing of the proper fuse settings for each type here - http://www.codingwithcody.com/2011/06/25/arduino-default-fuse-settings/
Console output programming an Arduino Mega2560 with blink using an actual AVR ISPMKii
Note that I use a slightly different fuse setting of D0 instead of D8 (since I usually want to preserve EEPROM contents during dev)
:
Using Port : usb
Using Programmer : stk500v2
avrdude: usbdev_open(): Found AVRISP mkII, serno: 000200103672
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
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 : STK500V2
Description : Atmel STK500 Version 2.x firmware
Programmer Model: AVRISP mkII
Hardware Version: 1
Firmware Version Master : 1.10
Vtarget : 5.0 V
SCK period : 8.00 us
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: reading input file "C:\Users\xxxxxx\AppData\Local\Temp\arduino_build_340018/Blink.ino.hex"
avrdude: writing flash (1462 bytes):
Writing | ################################################## | 100% 0.45s
avrdude: 1462 bytes of flash written
avrdude: verifying flash memory against C:\Users\xxxx\AppData\Local\Temp\arduino_build_340018/Blink.ino.hex:
avrdude: load data flash data from input file C:\Users\xxxxx\AppData\Local\Temp\arduino_build_340018/Blink.ino.hex:
avrdude: input file C:\Users\xxxxxx\AppData\Local\Temp\arduino_build_340018/Blink.ino.hex contains 1462 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 0.46s
avrdude: verifying ...
avrdude: 1462 bytes of flash verified
avrdude done. Thank you.