Welcome Week: Introduction to Linux Linux Practical 1

Linux Practical 1
Introduction

This session is designed to introduce you to the underlying UNIX-based Linux file system and
computing infrastructure used within the School of GeoSciences and similar to many computing
environments worldwide. UNIX-style operating systems are sophisticated and powerful environments
for data analysis and processing, and also power much of the internet and world-wide web.

1. Connecting to Linux in GeoSciences (Windows Labs vs. Remote)

- Connecting to the School’s XRDP service

2. Exploring the Remote Linux Desktop

- Finding files and programs on the remote server via a (semi-)familiar Desktop environment

3. Power Computing: Bash Prompt – The Command Line

- Using the command line interface: universal, quick and powerful.

4. Files and Directories

- Listing, viewing, copying, making. How your workspace is structured.

5. Help!
- How to get it. Is it helpful? Other places to look.

6. File Utilities (Big Data Downloads)

- Useful tools that use the command line - tar, gzip, ftp.

7. Further File Utilities (Zip Files, Automated Download, Web PDFs)

- More useful tools for file-handling and working remotely - zip/unzip, curl, wget, PDFs.

8. Resource Monitoring Utilities

- Finding out how much disk space you have. Finding other users.

9. Searching
- Finding files. Finding files with a specific bit of text in them.

10. Full Applications

- What are available? How do I start them? Transferring machines: ssh

11. Log Out/Off or Close Session?

- Full logout versus leaving a session suspended in memory to return to later (from anywhere!)

This practical will allow you to familiarise yourself with the basics of working with Linux in the School
of GeoSciences. The practical workbook is designed for you to work through during the practical
session in the lab, when there are people around to help. It is NOT a definitive reference! Much
more information is available on the web, including this document which can be found at:

www.geos.ed.ac.uk/~gisteac/wkzero

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Making sense of this Workbook

Throughout this practical workbook any commands you have to type, will be given in bold
courier font, and prompts or responses from the computer will be in plain courier
font, for example:

s1234567@baltic10:~$ pwd
s1234567@baltic10:~$ cd /
s1234567@baltic10:/$ ls –al

 Will indicate tasks to be completed or key learning points

() May be used to indicate useful but optional tasks or related info

Specific questions you can answer will have a letter in the left hand margin – a), b), c) etc.

You can record answers or related notes in the spaces provided (if you choose to print these
notes), or in e.g. a text file or document see the box below on making notes online.

This symbol indicates text of high importance or direct usefulness during the practical.
This symbol indicates further information it would or might be useful to know later.

s1234657 represents your unique student login (matriculation number preceded by an s.)

Note: For staff this may be first initial immediately proceeded by surname up to 8 characters
(e.g. jjohnson, jjohnso1, etc.) and for visitors with an initial vnfsurna (e.g. v1jjohns).

~ (known as tilde) represents your home directory. In the command prompt above note that
this will change to reflect whichever directory you are currently working in.

Note that Linux is case sensitive - all commands must be typed exactly as they are shown
on this sheet or they will not work!

How to make notes/record answers during practicals in an online age

While you may print out the practical notes and annotate them, or use the spaces
provided to answer any questions, you may wish to work efficiently wholly on-screen. You
can arrange multiple windows side by side (2x2 or even up to 4x4) by holding down the
Windows key, then using the cursor keys to arrange the windows. This often also works
for/on remote systems so you may first need to click Restore Down on the remote
window blue bar to be able to move it this way. Note: Use the lower horizontal scrollbar
on the remote Linux system to access the whole desktop, or Maximise as required. If
you need to you can also drag window sides to resize in other configurations (e.g. 3x3).

Better however is to make notes in a text file directly on the remote Linux desktop and
arrange your program windows side by side entirely within Linux – very effective for
working! You can use LibreOffice Writer from Applications ► Office (and can save in
Word .docx format if preferred) or use another text program. Save to Home or Home ►
Documents to save within your GeoSciences home directory space (M: under Windows).

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There follows a set of attainment targets listed below. Make sure you can do everything in the list.
Many students will be using Linux throughout the year. It is therefore enormously important that you
speak to one of the demonstrators if you are confused or have been unable to complete the tasks.

Targets for this Session

You should be able to:

 Connect to the Geosciences XRDP service from a Windows lab PC or remote location
 Know where to find information regarding connecting off-campus/via other platforms
 Locate your Linux home directory
 Change directories
 Create directories
 View simple text files; use simple file viewers (pagers)
 Know how to find quick help on commands/programs
 Download and retrieve data via FTP or similar mechanisms
 Monitor disk space used, and find out about other users on the system
 Search for (and through) files; simple pattern matching
 Start full Linux applications and understand about different types of application
 Connect to different machines using ssh
 Log out of a Linux session and out of XRDP

And you should know:

 How your directory system is structured and the notation used

 Where to go for help on Linux (real people and the web!)
 Why you would use Linux
 When to switch off

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1 Connecting to Linux in GeoSciences (Windows Labs vs. Remote)

XRDP: The School’s Remote Linux Desktop Service

 The main School-supported mechanism for connecting to GeoSciences Linux systems is by

using the School’s XRDP service. The connection method used is much the same across
multiple operating systems/computing platforms and whether working on-site or remotely.

() The XRDP service offers a full user-friendly graphical environment with command line
options, and allows you to simply disconnect without logging out in order to leave complex
software running, with the ability to later resume working exactly as before logging out.

() The officially supported connection method on or off campus is made using Windows’
Remote Desktop Connection client which provides a remote view of the Linux server in the
form of a virtual desktop. This allows us to work directly (or natively) on a Linux server as if
sat directly at the machine, as we would a lab PC. For the full and latest instructions, and
further options including connecting Apple Macs and Linux machines to GeoSciences
servers, and low bandwidth options, see the information at:
https://blogs.ed.ac.uk/geosciences-it-help/linux-servers/
https://blogs.ed.ac.uk/geosciences-it-help/remote-desktop/

 We will assume you are connecting from a Windows PC. When using a lab PC (or other PC
already within the GeoSciences network) you can of course skip step1 (VPN/eduroam wifi).
The following assume you are using Windows’ Remote Desktop Connection client.

1. If you are off-campus you must connect to the University’s VPN first. (Note: If you
are on-campus and connected to eduroam wifi no VPN connection is required!)
2. Open the Remote Desktop Connection client (you can type this in the search bar).
3. Click on Show Options to expand the drop-down to the bottom of the window
4. Click on the General tab. Specify the Computer: name as xrdp.geos.ed.ac.uk.
5. Enter your uun username only (e.g. s1234567) without any @ed.ac.uk part.
6. Now click Connect.
7. Click Yes to any certificate popup message (you’re already safely within the network!)
8. Finally, ensure your username is again uun only (no @ed.ac.uk part) then enter the
usual EASE password at the Linux (XRDP) prompt and click OK. You should now
be logged into a virtual Linux desktop. If the screen goes blank due to a screen-saver
or Linux lock-screen simply nudge or click the mouse to wake the machine up.

Connecting from home; connecting from various operating systems (e.g. Mac)
Apple Mac users can obtain the Windows’ Remote Desktop Connection client from the
Mac App Store. Linux users can use built-in or similar RDP functionality e.g. Remmina in
much the same way. (Alternative RDP clients can also be used on Windows e.g.
MobaXTerm which also permits simple SSH and SFTP connections should VPN
connections be problematic.)

Following the relevant instructions below connect now to the XRDP service (we’ve
outlined the steps for connecting from Windows in this document directly below).
https://blogs.ed.ac.uk/geosciences-it-help/remote-desktop/windows-to-xrdp/
https://blogs.ed.ac.uk/geosciences-it-help/remote-desktop/macos-to-xrdp/
https://blogs.ed.ac.uk/geosciences-it-help/remote-desktop/linux-to-xrdp/

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Problems? Remote Desktop stuck? Use RDP alternative OR text-only SSH

This can sometimes happen with large classes all accessing the system at once, and can
happen to any system! If the RDP (Remote Desktop) service temporarily reaches full
capacity you may need to wait a little while, or you can start a new basic SSH command
line session rather than have to wait.

Basic SSH functionality is built-into Macs, and also DOS (Windows’ cmd command
prompt – type cmd into the search box at the bottom of Windows’ screen), though
Windows PCs are better served by e.g. MobaXterm. Moba also contains all of: SSH
(command line)+X Server for graphics, simple graphical Secure FTP for file transfer (good
in case of any VPN/drive mapping issues) and an alternative RDP client!

Off-campus? VPN or use ssh.geos gateway first

Off-campus you will need to either start a VPN connection before connecting to
xrdp.geos.ed.ac.uk, *or* you can make an initial connection without VPN requirement to
ssh.geos.ed.ac.uk, then once connected you can simply hop onto a full compute server
by typing ssh xrdp. You can then proceed without further delay!

Note: You can use ssh –X if you need to run programs that use a graphical display
rather than simply running at the command line. This may also be set in config settings.

More on SSH Clients (for interacting with a server):

Simple SSH clients can be useful if internet bandwidth or allowances are extremely limited
when working remotely. Using a program called an X Server (ssh –X) allows graphical
programs to be launched as required but via a command line connection.

MobaXterm used this way includes all of a command line terminal, an X server for
graphical display, and additionally a conventional Windows-like file browser making it a
powerful alternative to the remote desktop client. MobaXTerm also offers an SSH-based
Secure FTP (SFTP) client which allows you to connect to a Linux/UNIX server and
browse files and folders with a file manager. Critically however it allows you to open and
edit files using Windows’ programs but, unlike other mechanisms – e.g. samba, it will edit
files as if working natively on the remote Linux machine, respecting file ownership/access
permissions and other settings. Very useful for development work!

MobaXterm can also work as a replacement Remote Desktop client (use RDP rather than
SSH) instead of Windows’ own client, however it is easier to stick with the officially
supported/more flexible Windows’ Remote Desktop Connection for this purpose.

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2 Exploring the Remote Linux Desktop

The MATE Desktop Environment

Shown above is the current Ubuntu Linux based MATE environment provided upon logging
into the GeoSciences XRDP service. This consists of a virtual desktop (actually four
workspaces, i.e. screens, are available as usual with such systems – and comparable to
modern smartphones), plus some shortcut icons and a system of menus to the top-left of the
screen. A clock is shown to the top-right which expands to a calendar once clicked.

 Note a number of useful features. Like all computer operating systems files are organised in
sets of folders, or in Linux terms directories. In a Linux system each user has a default
folder – their home directory.

 On the desktop is a shortcut icon to your home directory. Clicking on this opens the Caja file
manager at (or first located in) your own home directory.

 You can see the entire network by clicking on File System. Note that some directories are
not visible by default and need to be accessed via the command line or a search bar first
(use Ctrl+L – i.e. hold Ctrl and press L – to specify a file location to browse) – most
commonly these are the directories on the GeoSciences web server (those in /web)!

 A great number of programs and tools can be found from the menus. The top-left
Applications menu is particularly useful. The right-hand System menu is the one for
logging out. Beside the menus are a selection of icons including one for the open-source
Firefox web browser, and another shortcut to the Caja file manager – shown as a filing
cabinet. The most useful icon for us though is the middle black box one! Therefore left-click
now on this Terminal icon (or go to Accessories ► System Tools ► MATE Terminal).

() Colours: We will make extensive use of the command line during this session. Historically
terminal windows tend to bave a black background with white text which may be good for
easing eye strain however regular breaks are recommended with computers. A white
background may be better for displaying on a projector screen. You can control colours
within the terminal window should you wish from Edit ► Profile Prefefences ► Colours.

 We will now look at using the command line interface to demonstrate the power of Linux.
Many of you will make use of the most common of these commands to manage your work
during taught classes or research. If you have not got a Terminal window to appear, or are
not happy at this point – please ask for help!

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3 Power Computing: Bash Prompt – The Command Line

The Bash (Shell) Prompt

 When you open up a Terminal window you should see a largely blank window apart from a
semi-cryptic bit of text known as the bash prompt. The command line is known in Linux
terminology as a shell (sh for short) and for historical reasons the default shell commonly
used is called bash*. The prompt shown awaits your command(s), which you should type
“at” (i.e. just after) it. The prompt here also gives some helpful information to help you.

s1234567@server:~$

 The prompt consists of your username (your uun), shown at (@) the host or server name
(i.e. the name of the server you are logged into). Currently xrdp is as an alias for the server
baltic10 however it could easily be any School server such as the compute server stream.)

 Far more usefully, the tilde (~) tells you that you are currently located in your home directory
(just as with the file manager earlier). This directory also has a full form address (or path)
which we will ask you to note in the next section in order to bolster your Linux knowledge!

() Note: For School postgraduate students, this home directory, or homedir, is normally the
same space that also appears in Windows as M: (In Windows this Linux network location is
mapped to the Windows M: drive using a software technology known as Samba.)

() Note: If your prompt contains a server name other than baltic10 then you can type ssh
xrdp to ensure you are on a suitable server. E.g. the address ssh.geos.ed.ac.uk points
to a very basic ssh gateway server from which you will need to then connect to a full server.

Space – the frontier between ALL commands! Use spaces!

A key point before we proceed is that computers (despite recent advances in so-called
Machine Learning) are really rather dumb and thus all commands and any other
parameters (known as arguments or flags) must be specified separated by spaces so
that the computer has a chance to identify where one command or argument ends and
the next begins. In these, and other exercises, if it looks like a space then it probably is
one and should be typed as such! Note: This is different from e.g. web browsers which
simply render text as instructed using special mark-up ‘tags’ and which otherwise ignore
spaces (“whitespace”)! When working at any command line however you need spaces!

*bash? Why?
In case you are curious, there have been various shells over the years, but the most
common is a variant of the Bourne shell called the Bourne Again Shell (or bash for short!).

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4 Files and Directories

Listing Files and Directories

a) One of the most useful commands in Linux is pwd - print working directory. It tells you
where you are in the directory structure, and the full path to that location. On School
systems the prompt already does this for you however it is worth knowing this command.
Note: In Linux/UNNIX (and in fact in DOS, i.e. anywhere outside of Windows Explorer!)
folders are known as directories. A directory is actually a file; a list of groups of other files.

To use the pwd command simply type it as is at the bash prompt and press Return or
Enter: This command takes no following arguments (further control information or
parameters) and therefore no spaces are required here.

s1234567@baltic10:~$ pwd

What is the address of (path to) your home directory? (Either note this here, or in a text file).

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

Be aware that drive letters such as M: (or P:, G:, U: etc.) are a Windows-only feature and
that when using Linux you will need to reference your home directory as /home/s1234567.

Fortunately the Linux desktop environment provides convenient shortcuts to your home
directory and each time you start a Terminal session you are logged ‘into’ (i.e. located
within) your home directory to start with automatically.

b) You will also need to know what files and directories there are within your home directory.
The command for this is ls (i.e. list). Try it now. Are there any files in your home directory?

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

 ls is a command which can optionally take a following argument (separated from the
command by a space). Normally this is a folder path to list the contents of, and the output
from it can be changed further by the use of extra control flags extra argument(s) in such
cases. Conventionally flags are specified first. For examples of these we shall explore the
wkzero directory held on our main shared teaching resource, netdata.

/geos/netdata/wkzero

 Look at the example below and try it yourself. Notice it takes a single argument (the path to
a directory location) and so a single space is required between the command (ls) and
argument (/geos/netdata/wkzero).

 s1234567@baltic10:~$ ls /geos/netdata/wkzero
demodir if.txt jabberwock.txt nation_data.txt protocols xyzpoints.txt

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 Now let’s try a more advanced version with two spaces required; either side of the –al flags.

 s1234567@baltic10:~$ ls -al /geos/netdata/wkzero

total 68
drwxr-xr-x 3 omacdona netdata 4096 Sep 14 2010 .
drwxrwsr-x 54 omacdona netdata 4096 May 29 17:10 ..
drwxr-xr-x 3 omacdona netdata 4096 Sep 7 2011 demodir
-rwxr-xr-x 1 omacdona netdata 1734 Sep 7 2011 if.txt
-rwxr-xr-x 1 omacdona netdata 1353 Sep 7 2011 jabberwock.txt
-rwxr-xr-x 1 omacdona netdata 8296 Sep 7 2011 nation_data.txt
drwxrwxr-x 2 omacdona netdata 4096 Sep 12 2016 protocols
-rwxr-xr-x 1 omacdona netdata 34965 Sep 7 2011 xyzpoints.txt

 The first version used ls with an argument only (the address of or path to a directory), the
command means "list the files that are in the directory /geos/netdata/wkzero".

 The second version uses both an argument and flags. The flags are -a and -l (you can
stick flags together as above -al). ls -a means show all the files, including hidden ones
(hidden filenames in Linux start with a . character). ls -l means give longer (more)
information on each file (or l for long-form perhaps).

 In the example above you should note the two extra entries . and .. . A single .
means "the current directory" in this case /geos/netdata/wkzero. A double ..
means the directory above this one – "the parent directory" or in this case /geos/netdata.
We will come back to this notation later on…

 So ls -al /geos/netdata/wkzero means "show all the files in the directory

/geos/netdata/wkzero and give a long description of them".

In the long description you can see the read and write permissions of the files, what type of
file (file or directory) they are, who owns them, how big they are etc. For example:

drwxrwxr-x 3 omacdona netdata 2 Dec 1 0 2 020 de m od ir

10
11
12
13
14
15
16
17
18
19
20
21
22
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24
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63
1
2
3
4
5
6
7
8
9

 The explanation for this follows:

Column 1: the d in this column shows that this file is a directory – normal files have a -
symbol here.
Columns 2-10 show the permissions set up for this file – see the full explanation below
Column 13 shows the number of links to the file (you need not worry about this)
Columns 15-22 record the user name of the owner of this file – omacdona
Columns 24-30 record the Linux group (of users) to which the file belongs – netdata
Columns 34-37 show the size of this file in bytes or characters
Columns 39-50 show the date and, if recent, the time this file was last modified
Columns 52-57 show the name of this file – wkzero

Columns 2, 3, and 4 and 5, 6, and 7 respectively show that the file owner and the Linux
group both have permission to read, write/delete, and execute (run commands on) this file.
Columns 8, 9, and 10 show that all other users only have permission to read and execute
for this file. They cannot alter it or delete it. We commonly talk of “world read” but in reality
this only extends to other users already securely logged in to the system – not like a website!

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c) Using the commands above, find out if there are any files in
/geos/netdata/wkzero/demodir and if there are, note their name, owner, and size – or
at the very least, note the command used to find this information. Once again you can use
the space below to record these if using printed notes, or put your answers in a text file.

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

Simple Viewing of Files

d) Viewing simple text files is easy – you can use one of these 3 pager commands (and
others!):

more filename displays filename one page at a time

head filename displays the first few lines of filename
tail filename displays the last few lines of filename

You should have found a file called if.txt in /geos/netdata/wkzero/. What are the
first few lines? Or if you are in a hurry, just tell us who the author of the file is!

(Hint: A filename is itself just a path to some data so when referencing files outwith the
current folder (as we are doing here) the full path – including filename – should be specified
and passed to the command as its argument – e.g. if entering a command to act on a file it
would take the form below (we’ll shortly show you an invaluable shortcut to save typing!):
my_chosen_command /top-folder/sub-folder1/sub-folder2/…/myfile.txt.)

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

As well as more there is actually also a similar command less which is usually set as the
default text viewing (pager) program on the version of Linux used within the School! It
works mostly the same way but requires you to press q to quit once you are finished
reading. This prevents you scrolling to the end of the file and having the text viewer
program close automatically as can happen with more.

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Linux/UNIX Filesystem Structure (Example)

 /

geos home web

netdata s1234567 gisteac

wkzero my_wkzero* public_html

 The above diagram shows a simplified extract of the GeoSciences Linux filesystem. At the
top (of the inverted tree structure) is the home directory of the root (or super) user – this is
the administrator or filesystem owner. Following along the branches from this ‘root’ are
various folders and subfolders, or directories in a non-graphical command line context.

 You should recognise the shared directory/folder netdata as part of this with one of its
subdirs/subfolders wkzero shown which you used earlier. The other my_wkzero* folder
marked with an asterisk (*) is meant to signify one lying within your own home directory – we
haven’t actually created this yet but in fact will get you to create this next!

() Note: The user gisteac (note there is no ‘h’!) is a very useful user to remember for those
taking GIS/EO courses in GeoSciences. In particular, shown here are gisteac’s web folders
at /web/gisteac/public_html which contain much useful info relating to geospatial
computing. Any publicly accessible info stored here can be reached over the web as per the
URL given at the very top of this practical, i.e. at www.geos.ed.ac.uk/~gisteac. Note the
special use of the tilde character (~) here to signify the main (home) web directory of a user.

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Creating and Changing Directories; Deleting Files or Directories

 Managing directories and files is an important aspect of working with Linux (or indeed any
operating system). You only have a limited amount of disk space yet putting all your files
together in one directory is only going to lead to large amounts of wasted time searching for
previous work! Making a directory is easy – use the command mkdir. For example:

 s1234567@baltic10:~$ mkdir my_wkzero

will create a new directory called my_wkzero – Note: it will create this in your current
directory, if your prompt matches the form above. Logically we could call this wkzero to
ensure that any replicated file paths match exactly, however for today we will try to make
things ultra-clear! Remember the need for spaces to separate commands and arguments.

e) Using mkdir create some other new directories to put your work in. How about webpages
and papers for starters? Once you have made these new directories, check they exist
using ls. Can you record how below – what is the specific variant of ls needed?

……………………………………………………………………………………………………………

 Having other directories is only useful if we can move to them. To change directory use cd.

 s1234567@baltic10:~$ cd my_wkzero
 s1234567@baltic10:~/my_wkzero$ pwd
/home/s1234567/my_wkzero
 s1234567@baltic10:~/my_wkzero$ cd ..
 s1234567@baltic10:~$ pwd
/home/s1234567

 Remember the .. notation from before? Here it is used (i.e. in the command) to change to
the parent directory of the directory that you are currently in (i.e. to move to one level above).

 Note: Also notice how the prompt reflects the current directory and changes from ~ to
my_wkzero and then back again in the above example. Keep an eye on this prompt
changing and use this feature during the practical to ensure that you are issuing
commands from within the correct folder! I.e. your prompt should always match the
one given in the worksheets at each stage. Ubuntu seems to have rather full prompts!

f) Now use the cd command to change back into your my_wkzero directory and add two
more new subdirectories there (i.e. create these within my_wkzero!) called data and docs.
You can use ls to check everything is OK. Note the cd and mkdir commands used below.

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

! If a command fails, first check you are in YOUR my_wkzero folder and not our reference
version wkzero on read-only netdata! (I.e. You should have your username in the path, and
not netdata!) Use pwd to check, or cd ~/my_wkzero to go to the right place!

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Note: You can create directories in your Linux home directory from within Windows using
Windows’ File Explorer. Your home directory usually appears in Windows, mapped to M:\
for GeoSciences postgraduates, or perhaps to another letter (usually T:) for
undergraduates as required; useful knowledge for anyone demonstrating on UG courses.

When using Windows to access Linux network drives – be careful! Windows lets you put
spaces in your directory names. Linux is happy enough with this, but it can make moving
around in directories within Linux more awkward since you may need to enclose the
directory names in quote marks " ". You may also find some software will object to paths
with spaces in their names; much better to use an underscore _ or hyphen - instead.

 To delete a file in Linux you use the rm command. For a directory you use the rmdir
command. Be very careful when using rm! Once a file is gone, it is gone forever! It is
much better to always use rm with the -i flag. This means that Linux will ask you to
confirm the deletion of a file or directory. Much safer… Remember that with network drives,
(e.g. Windows’ M: drive), the same rules apply – it will not go to the Recycle Bin, it will be
gone forever! It may be best to simply mark files for deletion in Linux later (see links box!).

 Use rmdir to delete one of your new directories and mkdir to recreate it.

Symbolic Links; Group Projects/Shared Files – Beware…

Be careful if using Linux links (known more fully as symbolic links or symlinks) which will
appear simply as folders under Windows. If you are collaborating with several colleagues
you should always use rm or, better still, unlink to remove any unwanted links so as not
to accidentally delete any linked files or sub-folders which you have write access to!
Deleting symlinks directly from Windows could be rather risky to say the least!! Links can
be shown in cyan (light blue) when listed in a Terminal window. The long form of the ls
command ls –l will also reveal these, shown linkname -> linked_destination.

Sneaky (useful!) tips:

1) Using the up arrow button on the keyboard will scroll through the commands you have
typed before so you can re-use them… You can also use cursor (arrow) keys for editing.

2) In a similar vein, the Terminal offers a copy and paste facility even across operating
systems (i.e. between Linux and Windows and vice versa). Either go to the Edit menu
and Copy and Paste as required (or Shift+Ctrl+C for copy and Shift+Ctrl+V to
paste, note: Shift key only required in a Linux Terminal. Note: Some clients are even
more rapid allowing you to simply highlight text to copy, and right-click to paste. If you
highlight past the end of a line a ‘newline’ is also included and any text (e.g. commands)
submitted to the computer with one click! For Ctrl on Macs, use Cmd.

3) If you are typing a file or path name, you can use auto-completion with the Tab key
usually shown on the keyboard itself as ->|. Don’t spend ages typing!!! Instead, hit Tab!

4) You can use a handy version of rm to delete any files and folders safely and in one
operation. Use rm –ir (or rm –iR). The recursive –r flag allows deletion within folders.

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Copying and Moving Files and Directories

 You can copy files and directories not only within your own working area (i.e. in your home
directory, or any directories below that in the hierarchy) but also from other users' directories
so long as you have the correct permissions.

 To copy a file or directory, use the command cp. For example, once again check you are in
YOUR my_wkzero directory – check the prompt!, then type both of the following commands:
(Remember: when we say type, also use the tab auto-complete function to ease the pain!!)

 s1234567@baltic10:~/my_wkzero$ cp /geos/netdata/wkzero/if.txt .
[NOTE THE SINGLE DOT AT THE END, SEPARATED BY A SPACE!!]

 s1234567@baltic10:~/my_wkzero$ cp /geos/netdata/wkzero/if.txt 2nd_if.txt

g) But what do they do? What has happened? Use ls to list all the files in your directory and
find out. So what does each command above do? Be sure and ask if not clear!

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

 Copying a whole directory is very similar – you just add a flag -R (or –r) which stands for
recurse the directory i.e. look at all the files within the directory and copy them as well,
keeping the directory structure the same as that of the original. As an example, try the
following (again use tab auto-complete to save typing:

 s1234567@baltic10:~/my_wkzero$ cp -R /geos/netdata/wkzero geos_wkz_copy

h) Then use ls again. What has happened? Again, ask if not sure before moving on!

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

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 Moving and renaming a file or directory are the same thing in Linux and the command used
is mv. If you rename a directory then the path (or address) of all the files within that
directory will move as well. Try the example below:

 s1234567@baltic10:~/my_wkzero$ ls geos_wkz_copy/
demodir if.txt jabberwock.txt nation_data.txt protocols xyzpoints.txt
 s1234567@baltic10:~/my_wkzero$ mv geos_wkz_copy/ not_wanted_now

 You have now moved (renamed in this case) the directory so the following command fails:

 s1234567@baltic10:~/my_wkzero$ ls geos_wkz_copy/
geos_wkz_copy/: No such file or directory

 You can also move groups of files around within your directory structure. Having renamed
geos_wkz_copy we should move the files out of it to somewhere more logical: So:

 s1234567@baltic10:~/my_wkzero$ mv not_wanted_now/*.txt docs/

 s1234567@baltic10:~/my_wkzero$ ls docs/
if.txt jabberwock.txt nation_data.txt xyzpoints.txt

 The * character is a wildcard symbol that means "all characters".

() Note: The final / is often not required, it simply indicates clearly that we are referencing a
directory. Therefore the following will work just as well:

 s1234567@baltic10:~/my_wkzero$ ls docs
if.txt jabberwock.txt nation_data.txt xyzpoints.txt

 To keep your home directory (and thus M:) tidy and well-organised you should move from
yesterday your PCInduction folder IF (AND ONLY IF) YOU CREATED IT!! (it should be in
your uppermost top-level home directory if you created it). Logically, you should move this
into your my_wkzero folder. This covers the important learning point of good data and
folder management and also serves to give you more command line Linux practice. We can
do this as follows:

 s1234567@baltic10:~/my_wkzero$ mv ../PCInduction PCInduction

 If you did not create this folder yesterday, no need to worry but you will get an error message
to say the folder does not exist. Note: We could also have issued any of these alternatives:

s1234567@baltic10:~/my_wkzero$ mv ../PCInduction .
s1234567@baltic10:~/my_wkzero$ mv ~/PCInduction PCInduction
s1234567@baltic10:~/my_wkzero$ mv ~/PCInduction .

 The tilde character (~) is a short-hand reference for your own home directory. Thus we can
more usefully write this command as:

 s1234567@baltic10:~/my_wkzero$ mv ~/PCInduction ~/my_wkzero/PCInduction

! Note: This last command can thus be issued from anywhere within the directory structure!

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5 Help!

 Help in Linux can be a little unfriendly until you get used to it! There are lots of sites on the
web that will be clearer and easier to follow for beginners. You should, however, know how
to get help for specific commands, and once you get used to the syntax and structure of the
pages, the help system might even start to grow on you…

 Help is accessed with the man (short for manual) command and the help pages are exactly
that – digital pages of instructions. The structure is man <command> where <command> is
the name of the command you want help with. Angle brackets <>: are often used in notes
either for specific keypresses/buttons, or to show a user-specified and thus variable textual
instruction. (Optional parameters are often shown further enclosed in square [] brackets).

 For now try:

 s1234567@baltic10:~/my_wkzero$ man man

 Press Space, Enter, or the cursor (arrow) keys, to scroll through the content of the manual
pages, and q to quit or exit. This should give you a better idea of how to use help! Notice
that the help system uses the default text viewer, less, described earlier.

Another useful feature of man involves the -k flag. This allows you to specify a keyword,
which man will look for in the help pages. Try:

 s1234567@baltic10:~/my_wkzero$ man -k transfer

i) This will return quite a lot of possible commands – lurking in the list is one we will use next –
ftp. What does the man page for this say it is for?

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

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6 File Utilities (Big Data Downloads)

FTP (File Transfer Program/Protocol)

 FTP is a long-standing way of transferring files from a remote computer/site – either a

standalone PC, workstation, or server, to your machine. The following example uses a
demonstration FTP site set up for this practical. Due to the simple open nature of FTP many
sites will now require Secure FTP (sometimes known as SFTP) or will provide a more
involved (registration probably required), but more modern, web interface. FTP is still a
useful fundamental tool to learn though, and still used by many data providers in some form.

 Type the following (when asked for a user name type anonymous and in line with
‘anonymous ftp’ convention, enter your email address when asked for your password):

 s1234567@baltic10:~/my_wkzero$ cd data
 s1234567@baltic10:~/my_wkzero/data$ ftp
 ftp> open ftp.ed.ac.uk
Connected to ftp1.is.ed.ac.uk.
220-University of Edinburgh Anonymous FTP server
===========================================================================

When requested for a username enter 'ftp' or 'anonymous'. If you have

problems, try using a dash (-) as the first character of your password.
If you still have problems or wish to make a comment then send email to
[email protected].

All transfers are logged.

220 FTP Server
 Name (ftp.ed.ac.uk:s1234567): anonymous

 You should get a response like this:

331 Anonymous login ok, send your complete email address as your password
 Password: [email protected]
230-This service is managed by Information Services. It holds information
which may be useful to system managers and space is provided for
individuals and groups upon request. Upload facilities are also
available. Anyone can make use of this service.
.
.
.
230 Anonymous access granted, restrictions apply
Remote system type is UNIX.
Using binary mode to transfer files.

 You are now connected to the Edinburgh FTP server – ftp.geos.ed.ac.uk - and have
limited rights to list and download files. Remember that you are now a user of the FTP
application; it has its own set of commands (though they are very similar to Linux
commands).

 Type the following commands:

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 ftp> ls
229 Entering Extended Passive Mode (||||54135|)
150 Opening ASCII mode data connection for file list
drwx-wx-wx 2 root root 4096 Sep 7 02:00 edupload
drwx-wx-wx 2 root root 8192 Sep 6 12:22 incoming
lrwxrwxrwx 1 root root 8 Nov 24 2020 INSTRUCTIONS-FOR-USING-
THIS-SERVICE -> .message
drwxr-xr-x 35 root root 4096 May 20 2020 pub
226 Transfer complete
 ftp> cd pub/geos
250 CWD command successful
 ftp> ls
229 Entering Extended Passive Mode (||||54275|)
150 Opening ASCII mode data connection for file list
drwxr-xr-x 2 309643 root 30 Sep 10 2008 wkzero
226 Transfer complete
 ftp> cd wkzero
250 CWD command successful
 ftp> ls
229 Entering Extended Passive Mode (||||54353|)
150 Opening ASCII mode data connection for file list
-r--r--r-- 1 root daemon 365 Sep 10 2008 jefferson.tar.gz
226 Transfer complete

 The commands you have typed above ONLY apply to the remote system – you are still
located in the same directory on your local Linux server. The command sequence
above shows you some of the files you can download. Often you will first have to set the
transfer type. You are going to download the file jefferson.tar.gz which is a
compressed binary file. So just to be sure type:

 ftp> type binary

200 Type set to I

 Then, use the get command to begin transfer (since this is a file path you can use tab here):

 ftp> get jefferson.tar.gz

local: jefferson.tar.gz remote: jefferson.tar.gz
229 Entering Extended Passive Mode (|||54290|)
150 Opening BINARY mode data connection for jefferson.tar.gz (365 bytes)
100% |**********************************| 365 7.91 MiB/s 00:00 ETA
226 Transfer complete
365 bytes received in 00:00 (717.19 KiB/s)

 Then, to log off from FTP and close the network connection:

 ftp> bye
221 Goodbye.

 You should now have your own copy of the file jefferson.tar.gz transferred from the
FTP Server running the Edinburgh FTP Service. While modern day FTP servers will often
allow you to obtain files via a web browser, the next part is key knowledge for Linux users.

() FTP problems?

If you have FTP issues you can obtain jefferson.tar.gz from the wkzero web pages. Save
this file with Firefox, available in XRDP. It will save to e.g. /home/s1234567/Downloads
but you can then use the file manager Caja simply right-click and copy/paste, or use
Ctrl+C and Ctrl+V. Alternatively you could practice using the mv or cp commands! Or,
simply download remotely in Windows as normal (e.g. saving to M:\my_wkzero\data).

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GZIP (GunZip)

 So you've got a file that looks like it might have some data in it. But what kind of a file is it?
And how do you get at the data? As is often the case for Linux data files, this ‘file’ is actually
a collection of files specially encoded as one to save space and then compressed further to
save disk space (e.g. when dealing with high-res images or large datasets). Unpacking this
is thus a two stage process that will introduce you to two more useful Linux utilities.

 First make sure the file jefferson.tar.gz (mv if necessary) is in your

my_wkzero/data/ as it should be. Note: You can launch applications (e.g. ftp) from any
chosen destination directory, in this case we used the data directory, to make life easier
once finished with FTP. Make sure you are in the data directory now.

 The file jefferson.tar.gz has been compressed using the GunZip utility. This allows
you to compress files so that they take up less disk space (and transfer faster across FTP).
To look at the data, we first have to reverse this compression, using the command gzip:

 s1234567@baltic10:~/my_wkzero/data$ ls -l
total 1
-rw-rw-r-- 1 s1234567 s1234567 365 Sep 11 12:00 jefferson.tar.gz
 s1234567@baltic10:~/my_wkzero/data$ gzip -d jefferson.tar.gz
 s1234567@baltic10:~/my_wkzero/data$ ls -l
total 10
-rw-rw-r-- 1 s1234567 s1234567 10240 Sep 11 12:00 jefferson.tar

 Note what has happened. The -d flag told GunZip to decompress the file, so it loses its
extension and gets bigger. You can see which flags to use to compress files by typing gzip
-h (h for help).

 Now you have uncompressed the file, but it is still archived – it is one file that contains
many other files. You thus need another utility to get the archived contents out again.

TAR (Archiving Tool)

 To get the files back out from their archived form, you need to use the tar command. The
instructions below are a very simple example of using tar to extract files, you can do
much much more with it than this!

 To extract the files, type the following:

 s1234567@baltic10:~/my_wkzero/data$ tar -xvf jefferson.tar

jefferson.txt

 Ok in this case there is only one file but usually you will have many files – e.g. datasets,
images, etc. (The name tar originally stood for tape archive/archiving, involving many files.)

 The flags:
-x Extract files from the archive.
-v Verbose- provide feedback to the user.
-f The file to extract from will be specified by the user and is the next argument.

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7 Further File Utilities (Zip Files, Automated Download, Web PDFs )

Working with Windows .zip files; Minimising Upload/Download

 While the UNIX gz format is common in the scientific and computer programming worlds,
often there is a need or preference for the, possibly more common, Windows zip format. On
the School Linux servers there are therefore tools to work with files in this format. Try:

 s1234567@baltic10:~/my_wkzero/data$ zip jefferson.zip jefferson.txt

 This would compress jefferson.txt to become jefferson.zip. Note: The command

requires the output zipped file to be specified first!

() You could also compress a whole folder of files in the same way, or specify a set of files to
zip into one compressed file. This makes it much easier to distribute multiple files intended
for use by Windows users without having to download all the files to your local Windows PC,
zip up and re-upload the compressed zip file to a web server. You can simply do the work
on the server and move the result directly to the School web server all in Linux. This is
handy if working with limited internet where only a command line Terminal connection is
available, or perhaps if broadband allowances or speeds are low and files are big in size.

 Now let’s decompress the zipped file to a new copy of the file in a new folder jefferson2.

 s1234567@baltic10:~/my_wkzero/data$ unzip jefferson.zip –d jefferson2

 Alternatively you can leave out the folder specification and will be asked whether you wish to
overwrite any existing files. You can find more information by simply running zip with no
arguments specified (this is commonly the case with Linux/UNIX commands).

Remote/Automated File and Web Page Retrieval (e.g. via WWW)

 Instead of obtaining files or datasets from special file-servers via FTP, you may have to
retrieve files via the more conventional world-wide web (WWW) and save them to your
GeoSciences home directory. If you wish to automate downloads or are working with very
limited internet connectivity then you can use special Linux command line tools to allow the
GeoSciences server to download these files for you. You can then issue other commands
via Linux to perform processing or analysis on these and obtain results leaving your
broadband allowance or internet bandwidth unaffected, or to automate the entire process.

Introducing curl and wget

 The curl and wget commands can be used to retrieve files from any web URL, e.g. with
curl, [Note: Type these all on one line, use the up arrow to edit the (second) command.]:

 s1234567@baltic10:~/my_wkzero/data$ curl
https://www.geos.ed.ac.uk/~gisteac/wkzero/protocols.txt -o protocols.txt

 s1234567@baltic10:~/my_wkzero/data$ curl
https://www.geos.ed.ac.uk/~gisteac/wkzero/protocols.html -o protocols.html

() If you omit everything from the output –o flag onwards the file contents will just be displayed.

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 The wget command functions in a similar way. Each command has both advantages and
disadvantages over the other, but wget also offers a useful recursive facility where it is
possible to download not only a web page, but other pages or links contained within it, e.g,
[Note: Again, type this all on one continuous line]:

 s1234567@baltic10:~/my_wkzero/data$ wget
http://www.geos.ed.ac.uk/~gisteac/wkzero/protocols_all.html -r

 Notice the –r at the end of the line. Use ls and more to see what you get from the above
commands! Do you really get a directory called www.geos.ed.ac.uk? Try ls and check!

() Note: It is also possible to use these commands non-interactively in pre-written script files to
automate file retrieval across the web (via HTTP/S), or by FTP as we used earlier, or in fact
by a number of other data transfer protocols including Secure FTP (SFTP). This also means
you can set a large download going and log out (we’ll see more on this later). The ability to
automate such tasks is a major strength of these tools and of sophisticated operating
systems such as Linux or UNIX. Windows does offer some such sophisticated tools but is
still catching up in many respects and arguably does not cater so well for multiple users
(despite its everyday prevalence!)

() Be careful to use wget (and curl) responsibly. You may not be able to use all functions of
the command without having first been given the appropriate access to a website! Also, if
you try to bulk save people’s websites en masse too often they may well complain!

Working with PDFs remotely (For WWW -based PDF distribution )

There are an unlimited number of tools that you may wish to use to analyse large datasets
downloaded to your GeoSciences home directory, or that you might wish to run on the
School servers. As a slight change however let’s look at a useful tool for working with PDF
files, a very common method of distributing information over the web either for local
colleagues (saving clogging email inboxes) or for distribution of information world-wide.

 While saving or printing to PDFs is now common place, often you may require to join
multiple PDFs together into one document, or to separate a single PDF into multiple files.
E.g. you may wish to stitch together pages scanned individually on a School or University
multi-function scanner-copier machine, or perhaps scan a selection of documents in one go
then split into separate documents later.

 You perform such tasks with pdfunite and pdfseparate. Here is an example of using
pdfunite to merge a set of PDF files, from netdata, into a single PDF in your current
directory:

 s1234567@baltic10:~/my_wkzero/data$ pdfunite
/geos/netdata/wkzero/protocols/*.pdf protocols.pdf

() Don’t worry if you don’t fully understand this just now – do ask though!! – the point is to know
you can do it and to have a document (this one!) of where to find the tools. You can review
the output of this from a file manager window and/or by running a PDF reader.

() Sample joined output (and then the result of this re-split by pdfseparate) can be seen at
/geos/netdata/wkzero/protocols/joined_then_separated. You can use the
Caja file manager and a suitable PDF reader to view these.

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8 Resource Monitoring Utilities

 Despite the ability to download large datasets automatically, you only have a limited amount
of disk space on the Linux system. You can keep a close eye on how much disk space you
are using with the command du. Some examples follow but see man du for fuller details.

 s1234567@baltic10:~/my_wkzero/data$ du -sk

will give you the total amount in kilobytes of disk space used in the current directory which
should still be data unless you have changed this yourself! (Running this command in your
home directory will tell you your total disk usage.)

 Replacing the k with an h will give you a more human-readable form:

 s1234567@baltic10:~/my_wkzero/data$ du –sh

 Alternatively you can use SI units (where 1 Kb = 1000 bytes instead of 1024 bytes). This
may help better manage data volumes as you will appear to have more MBs or GBs etc!!

 s1234567@baltic10:~/my_wkzero/data$ du –s --si

 Note that this uses a secondary (sub) flag signified by a double-hyphen.

 Finally, running the following command in your home directory will give you a breakdown of
the total space used by each file and directory located there, hence type:

 s1234567@baltic10:~/my_wkzero/data$ cd ~
 s1234567@baltic10:~$ du -sh *

 Alternatively you can achieve the same effect (all your files and folders) but from anywhere
in the filesystem as follows:

 s1234567@baltic10:~$ du -sh ~/*

j) Using du, you can find out how much storage space you are using and note it here:

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

 As well as checking disk space, you may wish to know about available computer memory or
running processes. Commands such as top (listing the top resource-consuming tasks or
applications) and ps (for controlling running processes, i.e. programs) are used for such
tasks. We’ll look at these in detail in the advanced session that follows.

() Miscellaneous Admin Commands

If you are tasked with managing a system it may also be useful to know who is logged in! In
a privacy-concerned “GDPR” age however, any further details will be securely held in a
proper system well away from the average user (sysadmin access only!). You can however
use a related command if you forget who you are – whoami. Finally, hostname is also
useful on occasions when the command prompt changes upon running another application.

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9 Searching

k) You can search for all sorts of things in Linux – usually it will be files or bits of text. The
commands you would normally use are grep and find. But what do the commands do?
Time for you to do some work. Use man to find out what grep and find actually do…

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

l) Found out? Try these commands - what do they do?

s1234567@baltic10:~$ find /geos/netdata/wkzero -name "*.txt"

s1234567@baltic10:~$ grep -n 'stan' /geos/netdata/wkzero/nation_data.txt

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

……………………………………………………………………………………………………………

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10 Full Applications

 The way you interact with Linux/UNIX applications can vary. Some will operate simply at the
command line in one go, sometimes interactively, others may take over the Terminal window
with a text-based menu or screen system, others still may offer full-blown graphical
capabilities. While you can open multiple Terminal windows easily, it is still worth knowing
the fundamental principles should you ever have reason to work with a single standalone
Terminal program, a small screen display or have reason to control programs in more detail.

Textual: Command Line or Screen based

 When you start a full application from the command line, control and response is
transferred from shell to application. You have already used one such application – ftp.
Remember how the command prompt changed from s1234567@baltic10...$ to ftp> ?
Another program that may once have been of use in extremely low bandwidth field-research
environments is the email program Alpine. This is an entirely textual email client! The
important point to note with all these is that once you are running the application, the
commands will be specific to that application. As a quick example, do the following:

 s1234567@baltic10:~$ alpine

m) Note how this time the command prompt format then changes significantly to that of a
different type of program. How would you describe this?

……………………………………………………………………………………………………………

 Type e to exit the initial greeting if shown, then type q and then y to quit.

 Another program that uses the same whole-window/screen format is the editor nano which
is used as a basic default editor by some applications, such as the School Oracle databases.

Graphical: Graphical User Interface (GUI) based

n) GUI based applications are very different. Here, the application usually opens a new
window for itself, and your interaction with the application is through that window, not
the command line. For example:

s1234567@baltic10:~$ xcalc

will start up xcalc in a new window. Your interaction with xcalc is now through the GUI,
not the command line. Move the window if necessary so that you can see the Terminal
window. What has happened to the command line? We will come back to this later…

……………………………………………………………………………………………………………

 Now with a rich full-featured environment such as xrdp you can simply open a second
Terminal window should you require to issue commands whilst xcalc runs, however we can
only keep opening a new Terminal for so long, so it’s useful to be able to understand how
applications work in Linux and how we can control running programs – more on this later!

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SSH: Connecting to programs running on specific s ervers

 You may require access to other Linux machines e.g. if they have different software or
greater processing power. This is common when using Linux/UNIX workstations. You can
achieve this by connecting with the ssh (secure shell) command from a Terminal window.

 Other School servers exist which you may wish to connect to at some point, e.g. stream.

 s1234567@baltic10:~$ ssh stream

() You may be asked for your username and password, or just your password, each time you
make another ssh connection from an existing session. From time to time you may receive
warning messages about network addresses or host keys etc. in relation to the new ssh
connection. Since you are already safely within the network such warnings can often be
safely read once and then disregarded however if unsure you can always ask IT by
sending an email to [email protected].

 Each time you log in, you are connected to that machine via a brand new connection, just
the same as when you first open a terminal window on a PC. You will thus once again start
in your home directory each time you make a new connection. To close the connection to
the remote machine use exit: Control will pass back to your original machine (or ssh
window) and so on if you have multiple logins ‘on the go’ at one time.

 1234567@stream:~$ exit

11 Log Out/Off or Close Session?

? Logout… (completely!)
You can close and logout an individual Terminal session by typing exit as above. This is
recommended as it will close the session ‘cleanly’ – i.e. without any unclosed programs or
files. It is always best to clean up after yourself. To close the whole graphical XRDP
session and all programs you can go to the System menu and select Log Out. You will be
asked to confirm. This also avoids leaving Terminal windows open for long periods (e.g.
days or weeks) during which time configuration files may be changed resulting in
unpredictable or unexpected results in a Terminal window. Alternatively…

? Close – Disconnect (temporarily!)

You can also go to the top of the screen and wait for the blue Remote Desktop drop-down
bar to appear and click Close (X). The major strength of XRDP and closing this way is that
when you login later any open programs should remain running. (Note: There is also a tool
called screen which can be used to keep programs open when running at a command line
only using an SSH client such as if having to connect to a more powerful server as
described above. See: https://blogs.ed.ac.uk/geosciences-it-help/linux-servers/)

 That’s all for this jam-packed practical. You can use this document for guidance during the
coming months, and certainly during your dissertation!

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