Online Tutorials

Linux/Unix and Command Line

Introduction to Linux

Note: You can learn more about most commands you come across by typing "man [command]" into the terminal.

• Practical Introduction to Linux, (Video) *Recommended
• Unix for Beginners
• Interactive command-line bootcamp
• Introduction to Bash

awk (text extraction/parsing)

• Examples of awk command usage
• Full awk tutorial

grep

Grep is useful for searching command line output for a certain phrase or regular expression

• Basic Usage
• In-depth guide

sed

Sed (Stream EDitor) is a useful tool for making substitutions in a text file. The syntax sed uses for substitutions is common in Linux (for example, the same syntax is used in the VIM text editor)

• Basic Usage
• Brief guide to sed
• In-depth guide to sed

SSH (connecting to the clusters)

• Connecting to the Yale clusters
• Transfer files to/from the cluster
• Basics of SSH

Bashrc

• Basics
• Bashrc vs bash_profile

How create and extract a tar or tar.gz archive

The command you are looking for is likely: tar xvf archive.tar , but see the following for details.

• Creating and extracting from a tar file

How to Compile and Link Libraries

• How Programs Work on Linux

Dual Booting Windows and Linux

• Dual Boot Linux Mint and Windows
• Dual Boot Ubuntu and Windows

Python

Intro to Python

• Fantastic resource for anyone interested in Python

Parallel Programming with Python

• Quick Tutorial: Python Multiprocessing
• Parallel Programming with Python
• YCRC tutorial course material

mpi4py

• Documentation for mpi4py
• YCRC mpi4py tutorial
• YCRC mpi4py tutorial video
• YCRC mpi4py example scripts

R

Intro to R

• Brief Intro to R
• Thorough intro to R

foreach

• Using the foreach package, by Steve Weston

foreach + dompi

• Introduction to doMPI

Singularity

Documentation

• Sylabs Docs Page
• Singularity Google Groups

Tutorials

• NIH tutorial
• YCRC container tutorial
• NVIDIA tutorial for using GPUs