Yay you have finally moved on from 8-bit chips and are ready to try out some 32-bit hotness! Those ARM Cortex chips look fun, some have built in bluetooth, or 2.4ghz radios, or usb...all you have to do is learn how to program them.
OpenOCD
On your way to learning how to use your favorite new ARM Cortex you may have heard of OpenOCD. OpenOCD is the software that we will use to do the actual programming of chips. Unlike the AVR ISP programming protocol, every ARM chip is significantly different to program, with platform-unique commands, flash locations, fuse bits, settings, etc. Teasing out those details is a struggle and if you change chips you have to start all over even if both chips are, say, Cortex-M3 based!
Each chip fab tends to supply its own programming software - Atmel has Atmel Studio, Nordic has NRFGo, ST has ST Link - but often times that software is Windows only.
OpenOCD is great because its cross platform, open source, and has support for a vast number of chips & programmers.
You can use OpenOCD with dongle-programmers such as J-Link and ST-Link or even an FTDI chip. But, if you have a spare Raspberry Pi (and who doesn't these days?) you can use it as a native OpenOCD programmer with just a few wires.
It's also really fast to program chips natively, and if you have to program a mess of chips, it can make things speedy - an extra 30 seconds adds up when you're doing 1000!
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