The limit on the number of open file handles is the kind of thing that would traditionally force programmers to be creative in finding algorithms that scaled nicely despite the limit.
For example, if you store your output in an accumulating data structure instead of hundreds of files that are being kept open, and modularize the process of adding content to the data structure, there's just a little extra planning work to be done to establish a threshold for when data needs to be dumped to a given file so that the given chunk of memory can be reused. It's a matter of striking a balance between the amount of memory consumed and the number of times files must be opened and closed.
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