Update examples

[jrlagrone]

Update examples so they are consistent with usage on M3 and/or the SuperPOD

• Organize examples into categories (as best as we're able, e.g. chemistry, fluid dynamics, physics, AI/ML, etc.)
• Make all job requests specify all resources needed and give an explanation of why the particular values were chosen when possible
  • all jobs request memory
  • all jobs request cores
  • all jobs request run time
  • no jobs use exclusive without a good reason
• Add links to software home pages and documentation, when available
• Identify examples that no longer work (E.g. we don't have the software installed anymore)