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Uh, I've deal with simple and cruel post-soviet russian board!;)))))) It's hardware are able to work in main purpose, nothing additional.
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In that case, you need to decide how to deal with thermal issues externally.
For example
1) Perform a power analysis of your design. Measure the power used by your design. Measure the temperature of your FPGA.
2) Make sure the FPGA has a heatsink and airflow over that heatsink. If the board is plugged into a VME chassis, then the chassis will provide the airflow. If you are not using it in a chassis, then you should add a fan, eg., a CPU fan. Of course, then you have to locate power for the fan ... so you might need to solder some wires to the board.
3) Bond a temperature sensor to the FPGA package. Monitor the temperature. If you can access a GPIO pin on the FPGA, then route an alert signal from your sensing circuit to the FPGA. If that signal asserts, then disable the logic in your design, eg., use it as a reset for the whole design, or as an enable to the power-hungry logic part of your design.
Cheers,
Dave