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A user can send commands in the system console but I don't know if I can type at a rate of 1kHz! Can the design put values in the sdram by itself (maybe using a NIOS)?
What need is the quartus_stp? What difference with the system_console?
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You can write a Tcl script that can transfer the data. The "fastest" Tcl method is master_read_memory or master_write_memory. The fastest it can go is about 600kB/s.
You can transfer your data by either writing to one side of a FIFO and reading it via Tcl from the other, or perhaps a slightly easier solution to understand would be to capture a block of samples, and then read them out over Tcl, and then repeat that sequence. The JTAG-to-Avalon-MM tutorial describes how to simulate a Qsys system, so you can always try that too.
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Are you a professor or what is your work?
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I'm an engineer building FPGA-based hardware and high-speed ADC interface logic for radio astronomy signal processing. The slides I linked to show what I build.
Cheers,
Dave