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Nobody has said it, but conversion from PDF to anything can be very time and CPU consuming. PDF is the very worst input format because everything is specified in fixed position on a page, which is no use at all when trying to convert to an ereader format.
You might be happier trying to convert only a few at a time....even one, if badly constructed from the ebook perspective can be a real drain. Unfortunately for you, calibre for supercomputers hasn't come out yet!
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