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2. How to manually test the flash? Sorry cause I am starting from zero, so I am very new in this.
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Assuming your flash memory has a 16bit data interface
/* enter autoselect mode */
IOWR(EXT_FLASH_BASE, 0x555, 0xaa);
IOWR(EXT_FLASH_BASE, 0x2aa, 0x55);
IOWR(EXT_FLASH_BASE, 0x555, 0x90);
int Manufacturer_ID = IORD(EXT_FLASH_BASE, 0);
int Device_ID = IORD(EXT_FLASH_BASE, 1);
/* back to normal mode (memory data read) */
IOWR(EXT_FLASH_BASE, 0, 0xff);
Search the web for the specific flash memory datasheet to have further information and the ID codes.
About breakpoints and step into the code: what dev tools do you use?
If Nios IDE, you simply place the breakpoint by double clicking on the left side of source code window. Then the Nios program will stop there when the instruction is executed (you must start the code with Debug as... -> Nios hardware).
How are you debugging now?