Quartus Programmer works but Eclipse Flash Programmer doesn't work

Hi,

The Nios II processor and other IPs typically expect a stable internal FPGA clock. A raw external crystal (not a clock module) needs a PLL or oscillator circuit to become a usable internal clock. Without a PLL, the Nios system might not run, hence causing the “Target is broken” error.

Fix:

Add a PLL (ALTPLL) in Platform Designer and configure it:

• Input: 40 MHz

• Output: a stable clock (e.g., 50 MHz or 100 MHz)

• Connect this to the clock input of your Nios II system

Then regenerate the system and recompile your project.

Even if you have a clock input connected, if the FPGA fabric doesn't receive a valid toggling signal, Nios II won't start.

Test:

• Add a blinking LED logic driven by the same clock to verify the FPGA "sees" a running clock.

• Or use a SignalTap logic analyzer to probe clock toggling internally.

Run Quartus -> Tools -> System Console, then:
tcl, jtagconfig
bash, nios2-terminal
If the Nios II does not respond, it's likely not clocking or reset properly.

Verify:

• reset_n to the Nios II and other peripherals is correctly connected

• You’ve added a reset controller in Platform Designer

• The reset source is active-low and held long enough during power-up

After regenerating Platform Designer system:

• Go to Eclipse: Right click the BSP → Regenerate BSP

• Clean and build the ELF file again

• Then try to flash

Sometimes the Flash Programmer fails due to:

• Missing or incorrect Flash controller connection

• Try using Run → External Tools → Nios II Flash Programmer instead of Run Configuration