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Getting Started#

Logging in#

To get started with the HPC-UGent infrastructure, you need to obtain a VSC account, see HPC manual. Keep in mind that you must keep your private key to yourself!

You can look at your public/private key pair as a lock and a key: you give us the lock (your public key), we put it on the door, and then you can use your key to open the door and get access to the HPC infrastructure. Anyone who has your key can use your VSC account!

Details on connecting to the HPC infrastructure are available in HPC manual connecting section.

Getting help#

To get help:

  1. use the documentation available on the system, through the help, info and man commands (use q to exit). 
    help cd 
info ls 
man cp

  2. use Google

  3. contact hpc@ugent.be in case of problems or questions (even for basic things!)

Errors#

Sometimes when executing a command, an error occurs. Most likely there will be error output or a message explaining you this. Read this carefully and try to act on it. Try googling the error first to find any possible solution, but if you can't come up with something in 15 minutes, don't hesitate to mail hpc@ugent.be

Basic terminal usage#

The basic interface is the so-called shell prompt, typically ending with $ (for bash shells).

You use the shell by executing commands, and hitting <enter>. For example: 

$ echo hello 
hello

You can go to the start or end of the command line using Ctrl-A or Ctrl-E.

To go through previous commands, use <up> and <down>, rather than retyping them.

Command history#

A powerful feature is that you can "search" through your command history, either using the history command, or using Ctrl-R: 

$ history
    1 echo hello

# hit Ctrl-R, type 'echo' 
(reverse-i-search)`echo': echo hello

Stopping commands#

If for any reason you want to stop a command from executing, press Ctrl-C. For example, if a command is taking too long, or you want to rerun it with different arguments.

Variables#

At the prompt we also have access to shell variables, which have both a name and a value.

They can be thought of as placeholders for things we need to remember.

For example, to print the path to your home directory, we can use the shell variable named HOME:

$ echo $HOME 
/user/home/gent/vsc400/vsc40000

This prints the value of this variable.

Defining variables#

There are several variables already defined for you when you start your session, such as $HOME which contains the path to your home directory.

For a full overview of defined environment variables in your current session, you can use the env command. You can sort this output with sort to make it easier to search in:

$ env | sort 
...
HOME=/user/home/gent/vsc400/vsc40000 
...

You can also use the grep command to search for a piece of text. The following command will output all VSC-specific variable names and their values:

$ env | sort | grep VSC

But we can also define our own. this is done with the export command (note: variables are always all-caps as a convention):

$ export MYVARIABLE="value"

It is important you don't include spaces around the = sign. Also note the lack of $ sign in front of the variable name.

If we then do 

$ echo $MYVARIABLE

this will output value. Note that the quotes are not included, they were only used when defining the variable to escape potential spaces in the value.

Changing your prompt using $PS1#

You can change what your prompt looks like by redefining the special-purpose variable $PS1.

For example: to include the current location in your prompt: 

$ export PS1='\w $'
~ $ cd test 
~/test $

Note that ~ is short representation of your home directory.

To make this persistent across session, you can define this custom value for $PS1 in your .profile startup script: 

$ echo 'export PS1="\w $ " ' >> ~/.profile

Using non-defined variables#

One common pitfall is the (accidental) use of non-defined variables. Contrary to what you may expect, this does not result in error messages, but the variable is considered to be empty instead.

This may lead to surprising results, for example: 

$ export WORKDIR=/tmp/test 
$ pwd
/user/home/gent/vsc400/vsc40000 
$ echo $HOME
/user/home/gent/vsc400/vsc40000

To understand what's going on here, see the section on cd below.

The moral here is: be very careful to not use empty variables unintentionally.

Tip for job scripts: use set -e -u to avoid using empty variables accidentally.

The -e option will result in the script getting stopped if any command fails.

The -u option will result in the script getting stopped if empty variables are used. (see https://ss64.com/bash/set.html for a more detailed explanation and more options)

More information can be found at http://www.tldp.org/LDP/abs/html/variables.html.

Restoring your default environment#

If you've made a mess of your environment, you shouldn't waste too much time trying to fix it. Just log out and log in again and you will be given a pristine environment.

Basic system information#

Basic information about the system you are logged into can be obtained in a variety of ways.

We limit ourselves to determining the hostname: 

$ hostname 
gligar01.gligar.os

$ echo $HOSTNAME 
gligar01.gligar.os

And querying some basic information about the Linux kernel: 

$ uname -a 
Linux gligar01.gligar.os 2.6.32-573.8.1.el6.ug.x86_64 #1 SMP Mon Nov 16 15:12:09
    CET 2015 x86_64 x86_64 x86_64 GNU/Linux

Exercises#

  • Print the full path to your home directory
  • Determine the name of the environment variable to your personal scratch directory
  • What's the name of the system you\'re logged into? Is it the same for everyone?
  • Figure out how to print the value of a variable without including a newline
  • How do you get help on using the man command?

Next chapter teaches you on how to navigate.