Note that this is not a case of Eclipse terminating, it is your program that is terminating. From your explanation, Eclipse appears to continue running.
The problem is likely that the file is not being found. When you start a process, it runs in a working directory. Files referenced by the program are looked for relative to that location. You can define the working directory where Eclipse launches your program on the Launch Config dialog (Run->Run Configurations). Changing this to the directory containing the file should help. You could also specify the absolute path to the file when prompted by the program.