Massive, long computations with large matrices, etc., can indeed heat my computer up, forcing my fan to kick on. I use a stationary system though, so it has a sufficient internal fan that can handle the load. So I have had this computer running flat out for multiple days at a time, with all cores in operation.
When my wife was using her laptop for some extensive work a few years back, we got her an external fan, one that the laptop would rest on. We also found and installed a temperature monitor application, one that could report the temperature in various components, so the graphics card temp, CPU temp, etc. You could see the difference with the external fan on.
At the very least, you might want to raise the laptop from the surface it rests on. Air flow under the case can allow it to cool down.
