I would recommend using a monitoring tool like Cacti or Ganglia if you are wondering how your systems are performing and want to look at historical utilization.
www.cacti.netwww.ganglia.infoI have used the data from cacti to help provide justification for cluster expansions and purchase of additional licenses based on utilization and projected growth.
As for your errors, it all depends on what that runtime error code means.
If your system if paging, either increased the ram or reduce the job size or the number of jobs on the machine. Paging just kills calculation efficiency and should be avoided. Using a monitoring tool I previously mentioned will help you track this usage.
Also, ensure that any programs you run are executing with a proper batch mode. Hopefully when the program is run in batch mode it will not pop up a dialog box for user input. If it does, open a bug ticket with the company to have it corrected! I have personally ran into this type of batch mode problem before on the Windows version of a program, where as the linux release was correct. It was a license about to expire warning of all things!