From Scott:

I have an additional question. I'd like to be able to use a directory hierarchy when executing these jobs. They require 2 input files per rupture, and 4 output files, so for a typical site of about 7000 ruptures, that's a lot of files in a single directory. However, if I specify the output files as "<directory>/<output file>", then I think they get registered in the RC with the directory as part of their LFN, which isn't what I want. Is there a way around this issue? Thanks!