System Documentation

USDRCG Wiki Manuals - Here you will find documentation written by us, specifically for our supercomputer. We cover a range of topics, from logging in and navigating to specific software how-to guides.

Software (Note: many of these have USD HPC-specific documentation - check here)

VASP - Chemistry software used for ab initio simulations.

R - A high-level programming language used in stasticial analysis across disciplines.

Geant4 - Physics toolkit used in particle research.

Fortran - A widely used scientific programming language.

Gaussian - Boasting a long list of methods, functionals, and basis sets, this quantum simulation package boasts a user interface.

Python - Python is a widely used and highly versatile high level programming language used in various disciplines.

Bioconda - A channel for the conda package manager specializing in bioinformatics software.

ROOT - Developed by scientists at CERN, ROOT is a data analysis framework that can be integrated with R and Python.

Online Portals

Science Gateway The Unviersity of South Dakota Science Gateway provides a graphical user interface portal for accessing and using HPC resources.

External Resources

Software Carpentry - This site has tutorials for beginners, from shell commands and scripting, to visualization techniques in Python and R.

Linux Journey - This site is in excercise/quiz format and has information in multiple languages on many linux distributions, basic shell usage, advanced shell usage, permissions, processes and more. The site categorizes its information into areas appropriate for users of every skill level.

Unix Grymoire - This site provides simple, yet in-depth, help to take your shell literacy to the next level.

Explain Shell - This site allows you to type (or paste) in shell commands to get an expanation of the components.

Codecademy - This site contains interactive tutorials for many programming languages.

Getting started with the Unix Shell - This will help you understand what the Unix shell is and how it is used. Moving through folders on your computer, finding and editing files, plus basic structure of data manipulation will be covered. Finally, the structure of loops and scripts will be included.

Programming with Python - Python is known for its ability to handle data. This will help you understand how to manipulate data and visualize results.

Programming with R - Statistical methods work great in R. This language can do much more, too. Here, you'll learn how to handle data and make great graphs.

Version Control with Git/GitHub - Keeping track of different versions of files can be a difficult task. Git does it for you. Learn how to set up an account and start using this powerful tool.