• Accessing the cluster
  • with Mac OS X
  • with Windows
    • from anywhere!
• Glossary of Common Terms
• Basic commands in linux
  • Starting from where you are (Square One)
  • Manipulating Files/Directories
  • Moving Files and Directories
  • Helpful Utilities
  • Utilities Cont.

Type the command + space bar key on the keyboard to pull up the “Spotlight Search” bar

key presses highlighted

Or press the following highlighted magnifying glass icon in the top right of the screen:

Spotlight icon

The search bar will pop up in the middle of the screen:

Spotlight Search bar

Type “terminal” to search for and highlight the terminal app, then press the enter key.

Terminal Selected

1. After downloading and installing MobaXterm, start the program by clicking on the “MobaXterm_Personal.exe” file.

2. Click on “Start local terminal”

Screen Shot 2020-12-15 at 15.53.54.png

You can log in anywhere! Using the helpful protocol: ssh. SSH is a. Secure SHell program that lets us access a Linux computer across the internet while encrypting the data sent and received.

Whether you’re using Windows or OS X (Mac) you’ll inevitably reach the same step once the terminal is open:

ssh -X YourUsername@cluster.hpcc.ucr.edu

Before we start, we should go over some common vocabulary we use and you should become familiar with. However, for the purpose of this presentation, I will try to make this as easy to understand as possible.

• (binary) executable: another way of referring to a program that has been compiled so it can be used day to day. Windows users might notice their programs end with .exe
• command: input we’re going to type in the shell to perform a specific task
• directory: areas on a hard disk in which files can be stored/organized aka a Folder
• Path: environment variable in linux that tells the shell which directories to search for ready-to-run programs (executables).
• shell: within our circle, a program that lets you control the system using commands via your keyboard. Bash, Zsh are shells.
• variable: a changeable value that stores a certain data type, remembering it for future reference by the system, these are vital to the linux kernal.
  • environment variable: a user will have unique configurations, such as variables that tell the shell where the programs are located

Print Working Directory

• pwd → returns the location (path) of where you have ended up currently

Lis(ting the contents of the current directory)

• ls -a → list all files
• ls -l → list with longer details
• ls -a + ls -l = ls -la → list all files with longer details

Change Directory

• cd → changes your current location to your home directory
• cd .. → changes directory to the one above
• cd ../../ → changes directory to two folders above

Make a new Directory

• mkdir my_directory → makes a new folder called my_directory located in your curmkrent location

Create a new file (touch your fingers on the keyboard)

• touch file → creates an empty file named file
• touch file.txt → creates an empty file named file with the txt extension
• touch PowerAt.Your.FingerTips creates a file named PowerAt.Your with the FingerTips extensions

Remove (a file)

• rm filename → removes filename from where you are currently in the directory

Remove an empty Directory (no files/sub-directories)

• rmdir directory_name/ → removes directory_name/ from where you currently are

Display Contents (of a file to the screen)p

• cat filename → outputs the content of the file
• cat -n filename → outputs the content of the file with line numbers

Copy (file OR directory to somewhere else )

• cp file_source/file.txt destination/ → copies the file named file.txt in the file_source/ folder to the destination/ folder
• cp -r directory_source/ destination/ → copies the folder directory_source/ recursively to the destination/
• cp file_source file_backup → renames the file_source to file_backup in the same directory

Move (file or directory to somewhere else)

• mv old_file_name new_file_name → renames the file old_file_name to new_file_name
• mv file_name path/ → moves file_name to the folder path/

Manual

• man ls → displays the linux manual page for the ls command
• man -k HELP → searches the linux manual page titles and synopses for the word HELP

Find my file in this folder or file

• find . -name '*.txt' → find any files in my current directory with the “.txt” extension in the name of the file
• find . -name 'my_file_name' → find any files in my current directory with the “my_file_name” name
• find some/folder/ -name "*.json" → find any files with any name with the “.json” extension in the some/folder/ path

Word Count (or lines/characters)

• wc file.txt → word/line/character count of the supplied file.txt
• wc -w file.txt → word count of the supplied file.txt
• wc -l file.txt → line count of the supplied file.txt
• wc -c file.txt → character count of the supplied file.txt

Processes

• ps → your processes!
• ps aux → displays processes of all users with all the background processes started at boot time

Which is the correct location of my program (that is executed when you type its name in the terminal) ?

• which python → returns the location (path) of the program

Global Regular Expression Print - Search for a file for lines with your criteria using regular expressions, a powerful/complex method of describing your search material with a string that can use various symbols to indicate patterns

• grep your_search_pattern file_name
• grep "hello" /path/file → searches the word hello in the file named file within the location

less, or more but backwards

• less file.txt → reads the file but with pagination

A helpful graphical table of frequently used commands (on Wikipedia)

echo

• echo "hello" → returns the word hello
• echo $? → returns the exit code of the last command
• echo $PATH → returns the current executable variables within your path (programs you can run)