A year ago, Victor Eijkhout from TACC posted an early draft of his book, Introduction to High Performance Scientiﬁc Computing. Freshly updated, the book is now available for download or you can get a nicely bound hard copy from Lulu.
I think Eijkhout does a great job of covering the bases for computational scientists. I have a copy at home and I keep it handy as a reference.
The book also features tutorials on LaTeX, Unix, Compilers and libraries, Managing code with Make, Source control, and Programming practices. Course slides are also available for download.