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If I were to make a small change in Qsys and want to update the Device Tree, I can't seem to find where I would update that info for the linux build.
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Mike, I've been building the DTS separately and loading it on myself. To really do things correctly, you'd need to create a new Yocto BSP for your board based on the socfpga one, and then modify all of the recipes to pull the correct dts files, etc. What I do is build Linux and the kernel using Yocto, while the preloader and u-boot through the Altera tools. Really I could do a custom u-boot as well for other drivers, but I like how tightly coupled the preloader process is using the bsp-editor. You can see what I've done here:
http://www.alteraforum.com/forum/showthread.php?t=50270 The dts/dtb is purely based on the FPGA design and maybe preloader and is decoupled, so.... If you dig down in to the poky recipe structure, you can see that the default dtb is included in the linux-socfpga-ltsi (or other) repository. You could always create a recipe patch to have it use your own, instead, but why rebuild linux every time your devicetree changes? Just run the sopc2dts command and dump them wherever they need to go. Much easier. And you're more than welcome to ask me directly or post here-- people are quite helpful. Also:
http://rocketboards.org/foswiki/documentation/gsrd141sdcardarrowsockitedition#creating_sd_card_image_using_rebuilt_binaries and
http://rocketboards.org/foswiki/documentation/gsrd131programmingfpga#gsrd_fpga_configuration give much clearer ideas about what's actually going on.