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Depending on the configuration scheme chosen, the FPGA will always try to configure at power up. If there's a valid configuration image then it will always boot and assign the pins 'as per program'. I assume that's what you refer to.
However, you should always be able to take control of the FPGA, via JTAG. Occasionally BSDL files have faults in them. However, with a mature series, like Stratix II, this shouldn't be the case. Download the BSDL file again. Make sure you take it from the "stratix ii bsdl files (https://www.altera.com/support/support-resources/download/board-layout-test/bsdl/stratix2.html)" page. Cheers, AlexDear sir
I am doing a functional testing of PCB. Which having two BGA and both having JTAG access. Generally in other boundary scan device I am able to use I/O as a vertual external. It get configure as a input or output as per my programming through JTAG . But in this device it is getting predefine as per the program store in it. In vit (vertual interconnection test) track between two BGA are check for that both device pin should work like bidirectional but it is getting predefine either as a input or output as per designer programming.Dear Sir
I am using BGA package, and i do agree with you that family pin will not change via jtag. Anyway Today i erase the program of FPGA after that it is working fine. My problem is almost solved. But Still i wants to know the technical reason behind it if any. Thanks for support.I'm glad you're getting somewhere. I can't comment on the 'technical reason why' without knowing the specific issue, the specific pins and which BGA package you're using. If you need further help post those details here.
Cheers, Alex