Why Use HPC?

  • High Performance Computing (HPC) typically involves connecting to very large computing systems elsewhere in the world.
  • These HPC systems can be used to do work that would either be impossible or much slower on smaller systems.
  • The standard method of interacting with such systems is via a command line interface such as Bash.

Connecting to the remote HPC system

  • To connect to a remote HPC system using SSH and a password, run

BASH 

ssh yourUsername@remote.computer.address
  • To connect to a remote HPC system using SSH and an SSH key, run

BASH 

ssh -i ~/.ssh/key_for_remote_computer yourUsername@remote.computer.address

Moving around and looking at things

  • Your current directory is referred to as the working directory.
  • To change directories, use cd.
  • To view files, use ls.
  • You can view help for a command with man command or command --help.
  • Hit Tab to autocomplete whatever you’re currently typing.

Working with files

  • Use nano to create or edit text files from a terminal.
  • Use cat file1 [file2 ...] to print the contents of one or more files to the terminal.
  • Use mv old dir to move a file or directory old to another directory dir.
  • Use mv old new to rename a file or directory old to a new name.
  • Use cp old new to copy a file under a new name or location.
  • Use cp old dir copies a file old into a directory dir.
  • Use rm old to delete (remove) a file.
  • File extensions are entirely arbitrary on UNIX systems.

Wildcards and pipes

  • The * wildcard is used as a placeholder to match any text that follows a pattern.
  • Redirect a command’s output to a file with >.
  • Commands can be chained with |

Scripts, variables, and loops

  • A shell script is just a list of bash commands in a text file.
  • To make a shell script file executable, run chmod +x script.sh.