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Introduction to Computer Organization with x86-64 Assembly Language and GNU/Linux is a college textbook intended for first- or second-year computer science students. It could also be used by professional programmers as a primer to 64-bit assembly language of the x86. Available both in pdf and paperback at
http://www.lulu.com/spotlight/bobplantz. It has been used in the classroom for several years.
Free preview copy (first seven chapters) is available at
http://bob.cs.sonoma.edu.