RIS Compute 101

Engineering

Oil and Gas

Diagnostics

Physics: Particle Physics, LIGO

Chemistry/Biology: Molecular Modeling, Drug Discovery

Environmental Science: Weather Forecasting, Climate Modeling

Genomics: Next Generation Sequencing, Variant Analysis

Others?: Big Data Analysis, Qualitative Data able to be Analyzed Quantitatively

A shell is a user interface for interacting with the Operating System (OS) - Either the OS on your personal computer or on the HPC system

OS Examples: Microsoft Windows, Mac OSX, Linux, Android (Mobile)

GUI - Graphical User Interface (Point and Click)

CLI - Command Line Interface (Text Input and Output)

Mac OSX and Linux both have terminals built within their OS and GUI within which you can do CLI

Windows requires software to be installed (recommended software listed below)

• PuTTY - https://www.chiark.greenend.org.uk/~sgtatham/putty/

• MobaXterm - https://mobaxterm.mobatek.net/

Secure Shell (SSH) Protocol

• It was designed as a secure replacement for telnet

• Different software have different implementations of the SSH protocol

• Requires either a username/password combination to authenticate or an SSH key pair

Basic SSH Command (replacing wustlkey with your own WUSTL Key)

ssh username@machine-id
ssh wustlkey@compute1-client-1.ris.wustl.edu

Linux File Tree / Directory Structure

• In the image, you can see the directory structure as it looks in a GUI and as it looks in a CLI.

• There are home and scratch directories for each user.

• You can’t double click to move around inside directories and open files in the CLI as you would a GUI like Mac or Windows

• The directory locations and files need to be expressed as paths

• Imagine we have a file name my-file.txt in the home directory of the above structure, the full path would be:

/home/username/my-file.txt

• ~ is a shortcut that represents the home directory, so the above example can also be expressed as:

~/my-file.txt

Before we get into CLI commands, there is a philosophy around which these commands are based

• Write commands that do one thing and do it well

• Write commands that work together

• Write commands to handle text streams, because that is a universal interface

Commands Within CLI for Dealing with Files and Directories (Folders) (https://ubuntu.com/tutorials/command-line-for-beginners#1-overview)

• These are usually short, in fact many basic commands are only two characters long

• Commands often require arguments and have options

command -o --option argument1 argument2

• Commands usually provide documentation

command -h --help

• Commands also have manual pages that give the most accurate description of a command and it’s options.

• The spacebar is used to page through the manual and ‘q’ is used to quit out of the manual

• They are not easy to read but provides the most complete and accurate information about a command

man command

• pwd - Print Working Directory - this returns the current location in the directory structure that you are in (this is also known as the working directory)

• ls - this command simply lists all the files and directories contained within the directory you are currently in

• ls -lh - this command lists all the files and directories contained within the directory you are currently in with added detail, like owner, permissions, date of latest modification, file size

• mkdir - this command is ‘make directory’ and it makes a directory with the provided name

• cd - this command is ‘change directory’ and it allows you to move between directories

• rm - this command removes a file or files.

This is not like sending items to the trash. This is permanent removal and should be used with care.

• rmdir - this removes a directory, the directory must be empty.

This is permanent removal and should be used with care.

• rm -rf - this is the most dangerous command to use. Do not use this command unless you are experienced and know what you’re doing.

  • the option -r makes the remove recursive meaning it will go into nested directories and remove all files within as well as the directories

  • the option -f forces the removal of files and directories with a prompt, meaning you won’t get asked if you want to delete files

• Running Multiple Commands Simultaneously

  • When a command is executed, the shell doesn’t return to the prompt (user input option) until the command has finished.

  

  • But we often want to run other commands before our first command has finished

  • You can stop a command using ctrl-Z and then have it run in the background with ‘bg’

  

  • Or you can simply start a job in the background by using an ampersand (&) at the end of the command