We've recently implemented a quota of 1 million files per 1TB of filesystem space. And yes, we had to clean up a number of groups' and individuals' spaces before implementing that. There seems to be a trend in the bioinformatics community for using the filesystem as a database. I think it's enabled partly by a lack of knowledge of scaling and speedup in the community, since so much stuff still runs on laptops and desktops. I'd really like to teach a basic scientific computing class at work to address those concepts, but that would take more time than I have right now.
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