If it does get too hot you may find krun useful:

krun: run command within temperature window
    
The command:
  krun 80 60 make test
will run the subcommand 'make test' while monitoring CPU temperatures;
if at any point the temperature goes above 80C, the subcommand (proces
+s
group) will be suspended until it falls below 60C, then allowed to res
+ume.
[download]

It relies on the 'sensors' library, which IIRC is available for Ubuntu as the lm-sensors package.