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The soc thing is nothing new. People have been using processors (power pc, arms, x86 etc) alongside fpgas since the start of fpgas. Xilinx have had hard core cpus in their fpgas for at least 10 years (power pc, now arm), so altera are only now just catching up with Xilinx (10 year lag). Altera have really missed the boat on this, and the fact they farm Linux support off to rocketboards is quite telling (ie. Altera don't care much about the soc market).
Fpgas are good at number crunching, cpus good at control.
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I've noticed that the activities both here on this forum, as well as on rocketboards, is far less then what I'm used to with other development communities. I have a handful of unanswered posts both here and on rocketboards, which I find unfortunate. For this type of development and you're stuck, this community might not be the place to go to if you're in a hurry.
I'm not particular familiar with Xilinx, but do they have a better development community? Since "Altera lags 10 years behind Xilinx", is the development tool for this more mature on Xilinx? From other experience in our company, Xilinx and Altera has constantly been leaping over each other. One year Altera is better, Xilinx the next. In the big picture is really does not matter which you choose.
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Thanks Tricky! I'm so thankful for all the comments. I'm taking the Qsys and ARM training classes from Altera this June and I'll ask the instructor these questions and comments.
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There are free online training that you can sign up for. I had good experience taking a few of those and browsing through them to aquire some basic understanding before heading into the training classes. Helps to ask the productive questions to the instructor when he's there.