Command Line Kung-Fu

1. Introduction

Read the Documentation

2. SSH

2.1. SSH: Secure SHell

• Protocol for accessing computer resources across a network
• an authentication credential, aka "identity"
• Each key has a "public" and "private" component
• Computers have an SSH fingerprint
• WHY? Makes it easier to connect to remote systems

2.2. SSH Config

Lives in ~/.ssh/config

host bridges
  user gonsie
  hostname bridges2.psc.edu

2.3. Fancy SSH Config

Host *
  ControlMaster auto
  ControlPath ~/.ssh/%r@%h:%p
  ControlPersist 12h
  ForwardX11 yes
  ForwardX11Timeout 12h

2.4. SSH Key Creation

ssh-keygen -t rsa -b 4096

Creates:

id_rsa
id_rsa.pub

2.5. SSH Key Installation

ssh-copy-id bridges

2.6. Files in ~/.ssh/

id_rsa

private key file

id_rsa.pub

public key file, share this one!

config

configuration information

known_hosts

list of saved fingerprints of machines you've connected to

authorized_keys

list of ssh keys that are authorized to connect to this system

3. Shell

3.1. Shell Terminology

Shell

operating system user interface, command-line interface

Prompt

line asking for input

Commands

tools/applications/binaries that you can run

Aliases

typing shortcuts

3.2. Shells

sh

A specification of a shell, not an implementation

bash

Bourne-Again Shell

csh

the C Shell

tcsh

enhanced C shell

zsh

the Z Shell

fish

Friendly Interactive SHell

3.3. Shell Syntax

• variables, loops, string manipulation, wildcards (globs), testing, branching
• line that asks for input, configurable!
• shortcut for typing
• encapsulate complicated (or multiple) shell commands

3.4. Shell dot files

• Vary depending on the shell
• loaded upon login (or shell startup depending)

3.5. Environment Variables

• $USER
• $SHELL
• $PATH and $LD_LIBRARY_PATH
• env command

3.6. .inputrc

"\e[A": history-search-backward
"\e[B": history-search-forward
"\eOA": history-search-backward
"\eOB": history-search-forward
"\C-p": history-search-backward
"\C-n": history-search-forward
set show-all-if-ambiguous on
set completion-ignore-case on

3.7. Install Dot Files

4. Git Basics

4.1. Raise Your Hand

• If you've played a video game with "checkpoints"
• If you've used "Track Changes" (MS Word or Google Docs)
• If you know you have git installed on your system

4.2. VC Through Naming

Open question: Why bother with Version Control?

4.3. Configuring from the Command Line

Software Carpentry: Setting Up Git

$ git config --global user.name "Ada Lovelace"
$ git config --global user.email "ada@lovelace.io"
$ git config --global core.editor "emacs -nw"
$ git config --global init.defaultBranch main

4.4. Help with Config

$ git config --list
$ git config --help
$ cat ~/.gitconfig

4.5. File: ~/.gitconfig

[core]
    editor = emacs -nw
[init]
    defaultBranch = main
[user]
    name = Elsa Gonsiorowski
    email = gonsie@me.com

4.6. Git vs GitHub

• Git Cheatsheet
• GitHub Cheatsheet

5. Git Hands On

5.1. Create a repo

cp -r /jet/home/zjupa/programming_challenge ./
cd programming_challenge
git init
git add *
git commit -m "initial commit"

5.2. Share the repo??

5.3. Clone the Repo

6. Build Systems

6.1. Compiling Code

gcc source.c

gcc source.c -o my_program

gcc source.c util.c -o my_program -g -O2 -lboost -I/opt/boost

6.2. Build Tools

• make
• ~autotools~
• CMake
• Spack or EasyBuild or Conda/pip

6.3. Magical Incantation

./configure # or ccmake
make
make install

7. Other Topics

• resource schedulers / managers
• modules
• moving data: globus, scp, mpifileutils
• editors
• nohup, screen, tmux

8. Credits

Created with Emacs, Org Mode, and RevealJS

(using the Robot Lung theme).