AWS Setup & Config

Goals

I want to create an AMI for structure prediction, protein modeling and docking with the following (or maybe multiple images).  Possible software includes

• NAMD and/or Gromacs
• Some homology modeling code
• HMMer
• Dock and/or Autodock
• ...

What else?

AMI Creation

So far I've only played around with pre-built stacks, so time to do some building.

The EC2 Getting Started Guide is a must

Since I am primarily using Ubuntu, spending a lot of time reading material by Eric Hammond

• EC2 images from scratch
• Rebundling EC2 images
• Automating EC2 instance set up with user-data scripts

Also check out Eric's OSCON talk

Instance launching and management

Lots of resources here, including the EC2 Getting Started Guide and the rest of the AWS docs.  Here is a list of tools I use/recommend or am simply keeping in the back pocket cause I like the looks of them

• Chef - Probably the leader of the pack in high end config management
  • Chef-deploy
  • All the cookbooks from 37 signals
• Various tools from Matt Wood
  • Vehicle Assembly
  • Mission Control
  • Launchpad
• Sumo - Single EC2 instances (blog post)
• Rubber - For complex Ruby on Rails setups
• Cloud-Crowd - Distributed computing, especially for doc processing.  very very nice documentation
• Pool Party - Manage cloud deployments
• EC2Cluster - Rails REST web service and dashboard UI for launching MPI clusters on Amazon EC2 and running user submitted jobs