Maximizing number of open files

Hello,
I use OS X Lion 10.7 on a powerful mac pro (12 core, 96GB RAM), and attempting to run a scientific software I get the error message that too many files are open. I would like to make the maximum open files and processes on my system unlimited. I tried following some online advice, and checking the maximum processes processes available using the following command I get:
>launchctl limit
cpu unlimited unlimited
filesize unlimited unlimited
data unlimited unlimited
stack 8388608 67104768
core unlimited unlimited
rss unlimited unlimited
memlock unlimited unlimited
maxproc 709 1064
maxfiles 10000 10240
I tried to increase the limit of maxfiles, maxproc and stack by (for example):
>launchctl limit maxfiles 100000
but this doesn't make any difference. I would be grateful for your help regarding a permanent solution to this issue.