Unix command line 101

The Hoffman2 Cluster is a Linux-based computing platform. One of the most powerful ways to interact with the Hoffman2 Cluster is via the Unix-command line. You can access the Hoffman2 command line by logging into the system either via a terminal application (see: Connecting-via-SSH) or by opening a remote desktop on Hoffman2 (see: Connecting via NX clients) and opening a terminal window. Any of these methods will open a command-line interpreter or unix shell (or most simply shell). This page presents a review of common tasks you may need to execute or script in your shell.

Navigation

Listing files

To list what files are present in the current directory type at the Hoffman2 command prompt:

ls

to list hidden files or folders:

ls -a

to get extra information on the files or folders in the current working directory use:

ls -la

-l adds a long listing format with a total of nine fields, a typical line of output from ls -la could look, for example, as the following:

-rwxr-xr--   1 joebruin gobruins 3974052 Apr 17 12:53 myexecutable

where: the first character of the first field indicates the file type (-, for a regular file, d for a directory, l, for a link, etc.); the remiaining 9 characters of the first field indicate the file permissions (for example: rwxr-xr-- means that the file can be read, written and executed by its owner, as denoted by the first three fields rwx; read and exectuted by the owner’s group: r-x - if the path to the current directory is also accessible by the group; and read by any other user on the system: r-- - again assuming that the path to the current directory is also accessible by any user on the system)

Note

By default on the Hoffman2 Cluster $HOME directories are accessible only by the owner and therefore no file or folder within them, despite their permissions, can be accessed by any other user.

the second field indicates the number of hard links to the file; the third field indicates the file owner (for example joebruin); the fourth file indicates the file group (gobruins in the example above); the first field indicates the file size - in blocks; the sixth, seventh and eight fields indicate the data and time of last modification; and ninth and last field shows the file name (myexecutable in the example above).

to display the size of the files in units of bytes, MB or GB:

ls -lah

for example:

-rwxr-xr--   1 joebruin gobruins 3.8M Apr 17 12:53 myexecutable

to order the list of files by time (newest on top):

ls -laht

to order the list of files by time oldest on top):

ls -lahtr

Files and directories management

Copying, moving,removing files

To copy a file from a location to another:

cp myfile.txt myfile1.txt

to move a file from a location to another:

mv myfile.txt myfile1.txt

to remove a file:

rm myfile.txt

Changing directory

Upon logging onto the Hoffman2 cluster you land in your $HOME directory which is a space with up to 20 GB of capacity fully backed-up (see: Your-home-directory). To navigate to your temporary storage directory (see: File-system-for-temporary-use) issue:

cd $SCRATCH

to check in which directory you currently are issue:

pwd

user joebruin would get:

/u/scratch/j/joebruin

to move up two directories:

cd ../..

to move back to the `$HOME directory:

cd ~

Creating/removing directories

To create the directory test in your $HOME directory issue:

mkdir $HOME/test

to navigate to this newly created directory issue:

cd $HOME/test

you check the location of this new directory, issue:

pwd

user joebruin would get:

/u/home/j/joebruin/test

To remove an empty directory, issue:

rmdir test

to force removal of a file or a directory:

rm -rf test

Environmental variables

On a unix-like system any string that is preceded by a $ is a variable, which means that the operating system will interpret the string according to what it has been set to. Environmental variables are a set of variables that influences the behavior of the command-line or shell interpreter in use (typically Bash). Example of environmental variables that are set for you are:

$HOME
$SCRATCH
$PATH
$LD_LIBRARY_PATH

to check the content of a variable, for example $HOME, issue:

echo $HOME

the content of your $PATH and $LD_LIBRARAY_PATH influences the kind of executables and libraries that you can access at the command line (without specifying their full path).

Working with files

Unix-like systems have more than one way to display the content of a file, or selecgted snippet of it, on your unix shell. Among some of the most usefule commands are: cut, less, more, head and tail. To see how they work, issue at Hoffman2 command promt, for example:

cut $HOME/.bashrc
less $HOME/.bashrc
more $HOME/.bashrc

to exit from displaying a file with more or less issue:

q

To see just the first few lines of a file:

head $HOME/.bashrc

or, for the first two lines:

head -n 2 $HOME/.bashrc

to see the last few lines of a file:

tail $HOME/.bashrc

or, for the last two lines:

tail -n 2 $HOME/.bashrc

to look at the last few lines of a file that is being written on the fly:

tail -f /u/local/licenses/LOGS/logit.matlab

use:

Control-C (to exit)

Unix-like system have very powerful editors packed with shortcuts that largely simplify the editing task. The learning curve on some of these editors, such as vi, can be pretty steep. However, there are several simpler, if less powerful, alternatives.

Editors that do not require X11 Forwarding

Here are some of the file editors available on the Hoffman2 Cluster presented in order of the complexity of their use, from less to more complex:

nano
emacs
vi

Editors that require X11 Forwarding

Here are some of the file editors available on the Hoffman2 Cluster when X11 Forwarding is enabled (see: Connecting via NX clients) presented in order of the complexity of their use, from less to more complex:

nano
gedit &
emacs &
vi
gvim &

Miscellaneous commands

Most unix commands have manual pages that can be accessed via the man command, for example to learn more about the ls command, issue:

man ls

or:

man vi