This suggests a temperature issue. recheck that you have assembled the system correctly and the heat-sink is making proper contact. Too much paste is as bad as not enough. Check out THIS guide for some good general advice on applying thermal paste.
Could also be a fan issue - unplugged, jammed, dirty etc.
To test the fan, turn power OFF, hold the eject button.
While holding the eject button, press and HOLD the power button till the power light is green. When you release the button the system should beep
The fan should run at FULL speed and eject any disc that is inside.
the fan should run for around 15 seconds and then stop.The ps3 should then beep 3x and flash a red light.
Power OFF and then power up normally to reset to normal mode after fan test.