New on Linux systems?

Getting started

This page contains some tips on how to get started using the Snowstorm cluster on UiT. The information is intended for both users that are new to Snowstorm 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.

Snowstorm is a Linux Cluster that consists of 100 computational nodes, each with 4 Itanium2 processors (CPUs) and 4/8/16 Gigabyte of memory. You can only connect to the cluster through the interactive node snykov.uit.no (recommended!) or the front-end node snowstorm.uit.no. The nodes are interconnected with Infiniband and Gigabit Ethernet, but a small subset of the nodes also has an SCI interconnect. The computational nodes has both local and common (global) disks. The operating system is CentOS (Linux), a Redhat Enterprise clone. The HW and it's physical set up, is described in more detail in the HW section of this user guide.

ssh. The only way to connect to Snowstorm is by using ssh. Check the ssh section in the User Guide to learn more about ssh.

scp/sftp. 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/sftp.

chsh. You may want to change the shell that you get by default (bash). Use the command 'echo $SHELL' to check your current shell-type and 'chsh' to modify this (if needed). To list all available shells on Snowstorm use the command 'chsh --list-shells'. The C shell 'tcsh', the Korn shell 'ksh', and the Bourne-Again shell 'bash' are popular ones.

Running jobs on the machine. You must execute your jobs by submitting them to the batch system. There is a dedicated section 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).

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. 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 (full path)
PWD  : your current working directory (full path)

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

setenv [VARIABLE] [VALUE]    (csh/tcsh shell
export [VARIABLE]=[VALUE]    (ksh shell)

Aliases (for csh/tcsh users). 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 ~/.cshrc 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 the line

alias ll 'ls -laF | more'

in your ~/.cshrc file. You must run 'source ~/.cshrc' 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 (for csh/tcsh users). 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 'takk' and is in your home ($HOME) directory.

cd $HOME
mkdir bin
cp takk bin/.
setenv 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 'setenv' 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 'setenv' command to your ~/.cshrc file and update your environment with 'source ~/.cshrc'.
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

More advanced usage .....

CVS is a version control system, which allows you to keep old versions of files (usually source code), keep a log of who, when, and why changes occurred, etc. CVS helps to manage releases and to control the concurrent editing of source files among multiple authors. For remote usage you need to set two environment variables (e.g. in your ~/.cshrc file):

setenv CVS_RSH ssh
setenv CVSROOT :ext:[username]@[cvs hostname]:/[cvs rootpath]