Good questions. logi loader is what we recommend using as it is very dynamic in being able to load/reload files from bone user space. In order to automate FPGA configuration you can setup a bone boot script that automatically calls logi_loader to load a specific boot file on system boot. Here is a newer debian image for the bone that has the user space logi_loader: https://www.dropbox.com/s/4gmcpigtdpap5br/debian_jessie_24_07_2014.img.zip
You can directly load a bitfile into flash using the jtag port and xilinx impact tool. The Flash will be auto recognized and you can load your bitfile. In order for the FPGA to self boot from flash you will need to set the jumpers on teh backside of the logi-bone for self-config.
Alternatively there you could create an FPGA program that could load the Flash from the FPGA after passing it a config file from the bone. The xula boards have hdl source to do this.
Here are some low cost JTAG adapters from digilent inc. I think that there are some other alternative low cost options available on ebay and elsewhere as well.
@jpiat may be able to comment further on any other approaches for loading flash.
I'm good, we have some Xilinx tools here, the JTAG programming worked very well using Impact as you suggested, I loaded the blink test and now I can push my own bit file to the board and have it load automatically on power up.
For people reading this post later you need to short the JP3 and JP6 jumpers (on pcb R1.0) to set the FPGA into self-configuration mode and take the flash memory out of reset.
@darkhelmet Glad to hear it worked well for you. Just note that the pins connected to the Flash/FPGA are shared with the BBB. So, in order for the FPGA to self boot, these pins tristate on the bone will need to be set to the appropriate state. It sounds like by default they are not a problem - great!
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