Software in the HPC

• 1. Module System
  • 1.1. Where can I find installed software?
  • 1.2. How can I find specific Python or R packages?
  • 1.3. How can I find old software?
  • 1.4. How can I find legacy software?
  • 1.5. The toolchain of software packages
• 2. Graphical applications
  • 2.1. X11 forwarding
  • 2.2. Remote desktop sharing
• 3. Specific Use Cases
  • 3.1. AlphaFold
  • 3.2. Ansys Fluent
  • 3.3. CESM/CIME
  • 3.4. ColabFold
  • 3.5. CP2K
  • 3.6. GAMESS-US
  • 3.7. GAP
  • 3.8. Gaussian
  • 3.9. GaussView
  • 3.10. GROMACS
  • 3.11. MATLAB
  • 3.12. matplotlib
  • 3.13. OpenFold
  • 3.14. ORCA
  • 3.15. PyTorch
  • 3.16. R
  • 3.17. SRA-Toolkit
  • 3.18. Stata
• 4. Installing additional software
  • 4.1. Compiling and testing your software on the HPC
  • 4.2. Installing additional Python packages
  • 4.3. Installing additional R packages
  • 4.4. Installing additional Perl packages
  • 4.5. Installing additional Julia packages
  • 4.6. Installing additional packages with conda