Getting started with Linux

By following this wiki, you will login to one of the access nodes of the HPC cluster, learn about the Linux shell and issue a very simple Linux command on the virtaul terminal.

Obtain a user account

Please refer to this guide.

The prompt of the shell

After you login to the access node, the first thing you see is a welcome message together with couple of news messages. Following the messages are few lines of text look similar to the example below:

honlee@mentat001:~
999 $

Every logged-in users is given a shell to interact with the system. The example above is technically called the prompt of the Linux shell. It waits for your commands to the system.

Following the prompt, you will type in commands to run programs.

Note

For the simplicity, we will use the symbol $ to denote the prompt of the shell.

Environment variables

Every Linux shell comes with a set of variables that can affect the way running processes will behave. Those variables are called environment variables. The command to list all environment variables in the current shell is

$ env

Tip

The practical action of running the above command is to type env after the shell prompt, and press the Enter key.

Generally speaking, user needs to set or modify some default environment variables to get a particular program running properly. A very common case is to adjust the PATH variable to allow the system to find the location of the program’s executable when the program is launched by the user. Another example is to extend the LD_LIBRARY_PATH to include the directory where the dynamic libraries needed for running a program can be found.

In the HPC cluster, a set of environment variables has been prepared for the data analysis software supported in the cluster. Loading (or unloading) these variables in a shell is also made easy using the Environment Modules. For average users, it’s not even necessary to load the variables explicitly as a default set of variables corresponding to commonly used neuroimaging software are loaded automatically upon the user login. More details about using software in the HPC cluster is found here).

Knowing who you are in the system

The Linux system is designed to support multiple concurrent users. Every user has an account (i.e. user id) that is the one you used to login to the access node. Every user account is associated with at-least one group in the system. In the HPC cluster at DCCN, the system groups are created in response of the research (i.e. PI) groups. User accounts are associated with groups according to the registration during the check-in procedure.

To know about your user id and the system group you are associated with, simply type id followed by pressing the Enter key to issue the command on the prompt. For example:

$ id
uid=10343(honlee) gid=601(tg) groups=601(tg)

Using online manuals

A linux command comes with options for additional functionalities, the online manual provides a handy way to find the supported options of a command. To access to the online manual of a command, one use the command man followed by the command in question. For example, to get all possible options of the id command, one does

$ man id