Thus, when you run a computation-intensive job in the background or remotely -- running at length in your absense -- "nice" the job so that it runs at a lower priority and doesn't interfere with work being done by the person actually sitting at the workstation console. Read the manual pages for ``nice'' and ``renice''.
For running large Mathematica or Matlab jobs in the background, use the command mathbg or matlabbg.
Don't generate huge data files in your home directory; use a subdirectory in /scratch. (Read about disk limits and /scratch space.)