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Quartus doesn't really matter
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Great, then that makes things a lot easier.
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we just need to be able to use a JAM player or similar to program the system and perhaps run self tests etc.
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Ok, then you'll be doing pretty much what I do.
Look at the schematic and various documents here:
http://www.ovro.caltech.edu/~dwh/carma_board/ (
http://www.ovro.caltech.edu/%7edwh/carma_board/)
For example, this doc discusses configuration and testing:
http://www.ovro.caltech.edu/~dwh/carma_board/fpga_configuration.pdf (
http://www.ovro.caltech.edu/%7edwh/carma_board/fpga_configuration.pdf)
Are you running Linux on your ARM processor? We run Linux on the PowerPC processor on the CARMA board. The MAX II devices on the board can only be programmed via JTAG, so we use a JAM Player port that runs on the x86 host PC, and accesses the JTAG chain via registers mapped to PCI. We did not bother to port it to the PowerPC, since the FPGA JTAG could be accessed with the PowerPC core held in reset. I don't think it would be too difficult to get it working on your ARM processor.
Since we also had the PowerPC JTAG port wired on the board, we let the JTAG programmer (BDI2000) take on some jobs, eg., programming the configuration flash, even though the FPGA could also have been used to perform that task (no point in duplicating effort though). Once the board is booted, the PCI interface can be used for reprogramming all devices on the board. The boards were manufactured with the MAX II devices and Flash programmed. Once they were booted in a compact PCI crate, the MAX II CPLDs were updated to the latest images using the Jam player, and the flash (with the SYS-FPGA, and PowerPC U-Boot images) was programmed.
Feel free to ask questions about the design.
Cheers,
Dave