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Methods to create large pdf documents with a very large number of annotations

I need to create large pdf documents with a very large number of annotations.   It combines text with a keyword in context index:  each significant word in the full text links to the corresponding word in the context index and back again.

On a linux desktop with 32Gb, using perl PDF::API2  I can successfully create a document of 1000 pages with 750 annotations on each page.   More than this causes the process to hang, probably after exhausting RAM.