 <p>I can't think of a good way to do this with qsub as there are no programmatic interfaces into the -o and -e options. There is, however, a way to accomplish what you want.</p> <p>Run your qsub with -o and -e pointing to /dev/null. Make the command you run be some type of wrapper that redirects it's own stdout and stderr to files in whatever fashion you want (i.e., your broken down directory structure) before it execs the real job.</p>