Command Line Essentials

Introduction to the Command Line
Getting Started with the Command Line
Logging in to an HPC cluster
Transferring files to and from remote systems
1. SCP (Secure Copy)

Introduction to the Command Line

High-performance computing (HPC) systems are controlled through the command line. The command line is a text-based interface that allows users to interact with a computer by typing commands. Unlike graphical user interfaces (GUIs), which rely on icons and windows, the command line provides direct control over the system, making it a powerful tool for managing files, running programs, and automating tasks.

For new users, the command line may seem intimidating at first, but it offers many advantages, especially in HPC. It enables efficient navigation, file manipulation, and job submission on remote systems that lack a traditional desktop environment.

Getting Started with the Command Line

Linux is the operating system commonly used in HPC systems, so it is essential for researchers to become familiar with basic Linux commands. The command line interface (CLI) in Linux offers a powerful way to interact with the system, manage files, and run complex computational tasks. Understanding fundamental commands will help you navigate, manipulate data, and efficiently utilize HPC resources for your research. In this guide, we’ll cover the basics to get you started with the Linux command line.

1. Opening the Terminal

To begin using the command line, you need to open a terminal. You can do this by searching for terminal in your applications menu.

2. Navigating the Command Line

Once your terminal is open, you’ll be able to start typing commands. Here are some essential navigation commands:

pwd (Print Working Directory): Displays your current directory (folder).
```
  pwd 
```
ls (List): Lists the contents of the current directory.
```
  ls
```
ls -a shows hidden files.
ls -l displays detailed file information.
cd <directory> (Change Directory): Changes your working directory to a specified folder.
```
  cd Documents
```
cd .. moves up one level in the directory structure.
cd ~ moves to the home directory.

3. Managing Files and Directories

Here are some common commands to manage files and directories:

mkdir <directory_name>: Creates a new directory.
```
  mkdir my_folder
```
touch <file_name>: Creates a new empty file.
```
  touch myfile.txt
```
rm <file_name>: Deletes a file.
```
  rm myfile.txt
```
cp <source_file> <destination_file>: Copies a file or directory.
```
  cp myfile.txt myfile_backup.txt
```
mv <source> <destination>: Moves or renames a file or directory.
```
  mv myfile.txt new_location/
```
By default, this will move myfile.txt to the new_location folder. It is equivalent to:
```
  mv myfile.txt new_location/myfile.txt
```
rm -r <directory_name> removes a directory and all of its contents.

4. Viewing files

You can use the following commands to view and search the contents of files:

cat <file_name>: Displays the contents of a file.
```
  cat myfile.txt
```
less <file_name>: Opens a file for scrolling.
```
  less myfile.txt
```
head <file_name>: Displays the first 10 lines of a file.
```
  head myfile.txt
```
tail <file_name>: Displays the last 10 lines of a file.
```
  tail myfile.txt
```

6. Editing files

You can edit files using text editors such as vim, nano, or emacs.

nano myfile.txt

7. File permissions

Linux uses file permissions to control who can read, write, or execute files. Use the chmod command to change permissions:

chmod <permissions> <file_name>: Changes the permissions of a file. For example:

chmod +x myscript.sh

This command makes the script file executable.

8. Using `help` and `man` pages

man <command>: Displays the manual for a command.
```
  man ls
```
<command> --help: Provides a brief description and options for a command.
```
  ls --help
```

9. Running programs and processes

You can run a program or script by typing its name:

./<program_name>: Runs an executable in the current directory.

./myscript.sh

Logging in to an HPC cluster

To access an HPC cluster, users typically log in via SSH (Secure Shell):

ssh username@cluster.address

Replace username with your HPC account name and cluster.address with the address of the system’s login node.

Transferring files to and from remote systems

SCP (Secure Copy)

scp <source> <destination>

The scp command is used to securely copy files or directories between a local (your personal computer) and a remote (HPC cluster) host, or between two remote hosts. It uses SSH for data transfer and provides a secure way to transfer files over the network.

Copying a file from local to remote

scp myfile.txt user@remote_host:/path/to/remote/directory/

myfile.txt: The file you want to transfer from your local system.
user@remote_host: Replace user with your username on the remote system, and remote_host with the remote server’s address (it could be an IP address or domain name).
/path/to/remote/directory/: The directory on the remote server where the file will be placed.

Copying a file from remote to local

scp user@remote_host:/path/to/remote/file.txt /path/to/local/directory/

Copying a directory from local to remote

scp -r my_directory/ user@remote_host:/path/to/remote/directory/

The -r flag (stands for recursive) tells scp to copy the entire directory and all its contents.