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Working With Linux

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Guide to Linux to replace the outdated guide at clusters.engineering.wustl.edu


  1. Getting Started With Linux
    1. Why Linux
    2.  Purpose of this guide
    3. Connecting to the Linux Cluster
    4. Windows Subsystem for Linux
    5. Installing Linux as a VM
    6. Do Not Fear the Command Line
    7. Users and Permissions
  2. Bash Shell Basics
    1. Navigating the Directory
    2. Move edit and create files
    3. Pipes and Redirections
    4. Text Editing
    5. Archiving with tar and zip
    6. Basic Scripting with Bash
    7. LSF Script Example
  3. Workflow Basics (How to Use the Shell Environment)
    1. tmux
    2. Git
    3. processes (ps / kill / top / free )
    4. Space / Storage (df, du)
    5. Getting Help with man and other resources
    6. Moving Data (ftp and scp)
    7. Downloading on the Command Line (wget / curl / lynx)
  4. Users and Permissions
    1. Whoami
    2. Root
    3. Sudo and Su
    4. chmod / chown
    5. useradd / usermod
    6. passwd
    7. Groups
  5. Packages
    1. Installing from Package File
    2. Installing From Source
    3. Flatpak/Appimage/Docker
  6. Filesystem
    1. Root Directory Structure
    2. Filesystem types
  7. Compilers
    1. GCC / CMAKE
    2. python
    3. r
  8. Python on Linux
    1. Virtenv
    2. Dealing with Filesystem
    3. Pip
  9. Cuda
  10. Docker / Singularity
    1. Intro
    2. Installation
    3. Singularity Examples
    4. Singularity and LSF
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