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This guide provides some quick instructions (still takes awhile to download, and set things up) on how to setup the AD-FMCMOTCON1-EBZ on either:
Instruction regarding the hardware connection can be found at:
Hardware connection user guide ZED board
Even thought this is Linux, this is a persistent file system. Care should be taken not to corrupt the file system -- please shut down things, don't just turn off the power switch. Depending on your monitor, the standard power off could be hiding. You can do this from the terminal as well with:
sudo shutdown -h now