I am using arduino mega and ramps 1.4 for running my printer. Recently i have been facing an issue where the smart controller starts blinking randomly and the printer stops, i checked and found the arduino was really hot. After cooling it works again but after some time of printing the same issues starts all over again.
Please help how to fix this issue .

Edited 1 time(s). Last edit at 10/12/2016 07:29AM by rizulthkr.

Check the power and ground connections.
As it's getting hot due to excess current running though something aka a short which causes the MCU to shutdown.

Is the Arduino 16 pin chip getting hot? Is that what you meant?

This there anything on the smart controller that is shorting a positive connection, maybe dust causing high resistance ?

Does the fault occur when the hot end is on or the bed is heating and printer is not printing?

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Printer: Ormerod 2 (528.4) Duel extruder set-up with Aluminium X-Rib, RRPro Firmware v1.11-ch (2016-04-08)

It also can be a partial processor damage. When one of the output MOSFETs is broken, for example. Than you see the processor working but heating too much.