C2110 UNIX and programming Lesson 4 / Module 1 -1C2110
UNIX and programming
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
PS / 2020 Distance form of teaching: Rev1
Lesson 4 / Module 1
C2110 UNIX and programming Lesson 4 / Module 1 -2Desktop
Environment
➢ GNOME
➢ Standard Applications
➢ Command Line
➢ Scientific and Technical Applications
C2110 UNIX and programming Lesson 4 / Module 1 -3GNOME
- Standard Applications
Search
Main menu
Firefox firefox Web browser
LibreOffice libreoffice Text editor (Writer), spreadsheet (Calc)
presentation (Impress)
Gimp gimp raster graphics editor
Inkscape inkscape vector graphics editor
Okular okular PDF document viewer
the name of the command that starts the application on the command line
C2110 UNIX and programming Lesson 4 / Module 1 -4Customize
Quick Access
C2110 UNIX and programming Lesson 4 / Module 1 -5Exercise
1
1. Create a remote VNC session on a WOLF cluster (see separate presentation).
Start the VNC server with the option --fullgui.
2. Run the program Gimp using the GNOME menu. In the program, draw a house
with only one stroke. Fill the resulting triangles with different colors.
3. Run the program Inkscape. Draw the flag of the Czech Republic in the
program. Try to estimate the fundamental difference between the programs
Inkscape and Gimp.
4. Run the program LibreOffice. Display the sine function in the range 0 to 360˚ in
the spreadsheet.
C2110 UNIX and programming Lesson 4 / Module 1 -6-
Terminals
The command line is accessible directly from text terminals. In the X11 graphical
environment, it is necessary to run a suitable application emulating a text terminal:
➢ gnome-terminal (Terminal)
➢ console (console)
➢ xterm (XTerm)
xterm
console
simple, standard on all
UNIX systems
The default directory is: /home/username
simple, yet highly configurable
gnome terminal
C2110 UNIX and programming Lesson 4 / Module 1 -7Command
Line
[kulhanek@wolf ~]$
username
computer name
current directory (~ means home directory /home/username)
Prompt - type of user / prompt ($ regular user, # super user, other possible %, >)
place for command
The command is executed by pressing a key Enter.
Copying text: Do not use Ctrl + C! To copy text from the terminal, just highlight the text,
press the mouse wheel to paste it (mouse middle button).
Autocomplete: by pressing the Tab key the command line interpreter tries to complete the
spelled word. Command names, paths and file names are added (if one press does not
cause anything, there are more options for completion, repeated press will display them).
History: Use the up and down arrow keys to scroll through the list of commands you have
already entered. Command from history can be reused or modified and the modified one
used. The history is also accessible by command history.
C2110 UNIX and programming Lesson 4 / Module 1 -8File
Manager
!!!! do not use !!!!
Hard training, easy battle.
During exercises, unless stated otherwise,
use only the command line.
Graphical interfaces are usually not available in supercomputer centers.
OK
File managers:
GNOME: nautilus
KDE: dolphin
C2110 UNIX and programming Lesson 4 / Module 1 -9Scientific
and Technical Applications
Overview of available applications:
$ module
$ module versions vmd
Overview of available module versions:
Module activation:
$ module add vmd
Launch the application from the module vmd
$ vmd
Scientific and technical applications, which are installed in several versions (application
version, compilation type, parallel version), are available in the form modules. Before
using the application, the relevant module must be activated.
$ module add vmd: 1.9.0
the version number is
separated from the module
name by a colon
activates the default version
of the module
is entered on the command line, text is typed without $ sign
module and application names do not have to be the same
$ module help vmd
Module documentation:
C2110 UNIX and programming Lesson 4 / Module 1 -10Exercise
2
1. Open a terminal in the GNOME GUI on a WOLF cluster. Try gnome-terminal (Terminal),
konsole (Konsole), xterm (Xterm). Choose one for further work.
2. Run the Inkscape program from the terminal. Type "inkscape“ into the terminal and
press Enter.
3. What happens if you type "Inkscape“?
4. View all available modules.
5. What is the module vmd for?
6. With program vmd, open the file struktura.pdb (L2.M4.C2.U1).
7. What is the module Nemesis for?
8. Activate module "Nemesis“ and run the program nemesis.
9. In the program, model an acetic acid molecule and optimize its geometry.
C2110 UNIX and programming Lesson 4 / Module 1 -11Exercise
3
1. Open a new terminal in the GNOME GUI on the WOLF cluster.
1. Print the contents of the variable PATH (echo $PATH).
2. Print directories in PATH on individual lines.
3. Is application Nemesis available in the terminal (type, which)?
4. Add a module Nemesis.
5. Write the contents of the variable PATH.
6. In which directory is the application Nemesis located?