So you now are ok with the same script running as long as it's acting on different files? Then yes, that's just fine. Use flock, as discussed in the slides I linked to, to lock the files you are acting upon. That will ensure that multiple instances of your script cannot possibly touch the same file. If you do that, sure, there's nothing wrong with running the same script multiple times simultaneously against different data sets, so long as none of the instances attempt to write to the same file.