You haven't described what kind of script you are running, or what language it is in, so it's hard to know how to answer you. You can compile your own PHP, for instance, and tweak things there... but the default PHP is already configured with a 90 MB limit.
It sounds to me as though the DreamHost "prockiller" is tracking down your process(es). Remember that DreamHost provides you access to a fully featured shell environment, but its primary purpose is the serving of webpages, not dataprocessing.
Have you tried running your script(s) heavily "niced"? You might also consider doing the data processing on your own machine, and just uploading your converted data to the server for use by your new script.
Without more detail about the script(s) you are running, and the error message(s) encountered, I can only suggest you contact support ... I do not know of a way to temporarily allocate more resources to a user on a shared server (DreamHost PS does allow this, however).