Running NIOS program from external SDRAM

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How do I point the reset address to the EPCS address? There is no option in Qsys.

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You have to set it in Nios component properties

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Will the standard bootloader copy the code to the on-chip RAM or the external SDRAM? Must I modify it to tell it somehow?

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IIRC this is automatic, unless you have several code sections distributed across different memory devices.

If you configure the linker options to place all code sections in sdram (or sram, or whatever), you don't have to worry about.