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I don't believe a lack of header files will present a problem. Certainly Mathematica does not ship with a bunch of header files - just 4 static libraries (ending in .a).

You could try downloading a binary for your system, then copying the atlas files from that.

Whilst it is true that ATLAS takes a long time to build and prints lots of things, I don't believe it is particularly memory hungry.

I think someone managed to build Sage in 512 MB. I've built it in under 2 GB. But if you have other things running on the machine at the same time, you might be pushing your luck just to far.