Linux command line

New on Linux systems

This page contains some tips on how to get started using the PU cluster if you are not too familiar with Linux/ Unix. The information is intended for both users that are new to Stallo and for users that are new to Linux/UNIX-like operating systems. Please consult the rest of the user guide for information that is not covered in this chapter.

For details about the hardware and the operating system of PU, and basic explanation please see the User manual.

ssh
The only way to connect to PU is by using ssh. Check the Logging in for the first time in the user manual documentation to learn more about ssh.

scp
The machines are stand-alone systems. The machines do not (NFS-)mount remote disks. Therefore you must explicitly transfer any files you wish to use to the machine by scp.

Running jobs on the machine

You must execute your jobs by submitting them to the batch system. There is a dedicated section Batch system in our user guide that explain how to use the batch system. The pages explains how to write job scripts, and how to submit, manage, and monitor jobs. It is not allowed to run long or large memory jobs interactively (i.e., directly from the command line).

Common commands

pwd
Provides the full pathname of the directory you are currently in.

cd
Change the current working directory.

ls
List the files and directories which are located in the directory you are currently in.

find
Searches through one or more directory trees of a file system, locates files based on some user-specified criteria and applies a user-specified action on each matched file. e.g.:

find . -name ‘my*’ -type f

The above command searches in the current directory (.) and below it, for files and directories with names starting with my. “-type f” limits the results of the above search to only regular files, therefore excluding directories, special files, pipes, symbolic links, etc. my* is enclosed in single quotes (apostrophes) as otherwise the shell would replace it with the list of files in the current directory starting with “my”.

grep
Find a certain expression in one or more files, e.g:

grep apple fruitlist.txt

mkdir
Create a new directory.

rm
Remove a file. Use with caution.

rmdir
Remove a directory, use with caution.

mv
Move or rename a file or directory.

vi/vim or emacs
Edit text files, see below.

less/ more
View (but do not change) the contents of a text file one screen at a time, or, when combined with other commands (see below) view the result of the command one screen at a time. Useful if a command prints several screens of information on your screen so quickly, that you don’t manage to read the first lines before they are gone.

Called “pipe” or “vertical bar” in English. Group 2 or more commands together, e.g.:

ls -l | grep key | less
This will list files in the current directory (ls), retain only the lines of ls output containing the string “key” (grep), and view the result in a scrolling page (less).

More info on manual pages
If you know the UNIX-command that you would like to use but not the exact syntax, consult the manual pages on the system to get a brief overview. Use ‘man [command]’ for this. For example, to get the right options to display the contents of a directory, use ‘man ls’. To choose the desired options for showing the current status of processes, use ‘man ps’.

Text editing
Popular tools for editing files on Linux/UNIX-based systems are ‘vi’ and ‘emacs’. Unfortunately the commands within both editors are quite cryptic for beginners. It is probably wise to spend some time understanding the basic editing commands before starting to program the machine.

vi/vim
Full-screen editor. Use ‘man vi’ for quick help.
emacs
Comes by default with its own window. Type ‘emacs -nw’ to invoke emacs in the active window. Type ‘Control-h i’ or follow the menu ‘Help->manuals->browse-manuals-with-info’ for help. ‘Control-h t’ gives a tutorial for beginners.

Environment variables
The following variables are automatically available after you log in:

$USER your account name
$HOME your home directory
$PWD your current directory
You can use these variables on the command line or in shell scripts by typing $USER, $HOME, etc. For instance: ‘echo $USER’. A complete listing of the defined variables and their meanings can be obtained by typing ‘printenv ‘.

You can define (and redefine) your own variables by typing:

export VARIABLE=VALUE

Aliases
If you frequently use a command that is long and has for example many options to it, you can put an alias (abbreviation) for it in your ~/.bashrc file. For example, if you normally prefer a long listing of the contents of a directory with the command ‘ls -laF | more’, you can put following line in your ~/.bashrc file:

alias ll=’ls -laF | more’
You must run ‘source ~/.bashrc’ to update your environment and to make the alias effective, or log out and in :-). From then on, the command ‘ll’ is equivalent to ‘ls -laF | more’. Make sure that the chosen abbreviation is not already an existing command, otherwise you may get unexpected (and unwanted) behavior. You can check the existence and location of a program, script, or alias by typing:

which [command]
whereis [command]

~/bin
If you frequently use a self-made or self-installed program or script that you use in many different directories, you can create a directory ~/bin in which you put this program/script. If that directory does not already exist, you can do the following. Suppose your favorite little program is called ‘myscript’ and is in your home ($HOME) directory:

mkdir -p $HOME/bin
cp myscript $HOME/bin
export PATH=$PATH:$HOME/bin
PATH is a colon-separated list of directories that are searched in the order in which they are specified whenever you type a command. The first occurrence of a file (executable) in a directory in this PATH variable that has the same name as the command will be executed (if possible). In the example above, the ‘export’ command adds the ~/bin directory to the PATH variable and any executable program/script you put in the ~/bin directory will be recognized as a command. To add the ~/bin directory permanently to your PATH variable, add the above ‘export’ command to your ~/.bashrc file and update your environment with ‘source ~/.bashrc’.

Make sure that the names of the programs/scripts are not already existing commands, otherwise you may get unexpected (and unwanted) behaviour. You can check the contents of the PATH variable by typing:

printenv PATH
echo $PATH