What scientists must know about hardware to write fast code

This document is hosted at https://viralinstruction.com/posts/hardware/. An older, outdated version is hosted at https://biojulia.net/.

It is written as a Pluto notebook. If you can, I recommend running the code in a Pluto notebook so you can play around with it and learn. Alternatively, you can read the HTML file in your browser.

PR's (to the notebook file!) are welcome.

This notebook covers:

• Why you must limit your disk read/writes
• What a CPU cache is, and how to use it effectively
• Memory alignment
• How to read assembly code and why you must do it
• Why you should reduce allocations
• Why immutable datastructures ususally are fastest
• SIMD vectorization
• Struct of arrays vs array of structs
• Specialized CPU instructions
• Function inlining
• Loop unrolling
• Branch prediction
• The effects of memory dependencies in the CPU pipeline
• Multithreading
• Why GPUs are fast at some things and slow at others