C2110 UNIX and programming 2nd lesson -1C2110
UNIX and programming
Petr Kulhánek, Jakub Štěpán
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
CZ.1.07/2.2.00/15.0233
3.lekce
C2110 UNIX and programming 2nd lesson -2-
Contents
 Scientific-technical applications
• Module
 Remote file transfer
• scp, wget
 Remote graphical applications
• Display export
 Virtualization
• What is virtualization, typical usage, hypervisor overview
• MS Windows in VirtualBox, instalation of Ubuntu OS
 MS Windows as client
• Putty, WinSCP
• Text file transfer
C2110 UNIX and programming 2nd lesson -3-
Scientific-technical
applications
 module
C2110 UNIX and programming 2nd lesson -4Scientific
– technical applications
Available modules list:
$ module
$ module versions vmd
Available versions of module:
Module activation:
$ module add vmd
Running application from module vmd
$ vmd
Scientific-technical applications are installed in multiple versions (application version,
compilation type, parallel version), these are available through module system. Before
running application, particular module has to be activated.
$ module add vmd:1.9.0
Module version is separated
by colon
Activates default version
C2110 UNIX and programming 2nd lesson -5-
Exercise
1. List all applications accessible in module system.
2. Which versions are accessible for module vmd and nemesis.
3. Activate module vmd version 1.9.0 and run program vmd.
4. Activate module nemesis in default version and run program nemesis.
C2110 UNIX and programming 2nd lesson -6Remote
file transfer
 scp
 wget
C2110 UNIX and programming 2nd lesson -7Remote
copy
$ scp [-r] source destination
Usage examples:
Syntax:
[] – maybe omitted
Source and destination can be file or directory. In case of directory copy option –r
(recursive) has to be used.
Remote source or destination is identified by machine hostname separated by colon.
[user@]hostname:[path/]file
$ scp pokus.txt wolf01.wolf.inet:/scratch/kulhanek
$ scp wolf01.wolf.inet:/scratch/kulhanek/pokus.txt .
For remote copy there is command scp.
C2110 UNIX and programming 2nd lesson -8Web
file download
For file download from web command wget can be used. Remote machines has to provide
files using protocol ftp, http or https.
$ wget [-O output_name] url
url (uniform resource locator)
www file identification
Usage examples:
$ wget http://www.rcsb.org/pdb/files/1SS9.pdb
PDB structure code
Upper case O
C2110 UNIX and programming 2nd lesson -9Remote
graphical applications
 Display export
C2110 UNIX and programming 2nd lesson -10Running
remote GUI application
Graphical applications can be run directly in X11 environment (graphical terminal) or with
display export to remote desktop X11 environment.
Direct run Display export
wolf01
Application
wolf01
Application
wolf01
wolf02
C2110 UNIX and programming 2nd lesson -11Display
export
Application
wolf01
wolf02
Command ssh sets all necessities
for display export automatically if
option -X (uppercase X) is used.
[wolf01] $ ssh -X wolf02
[wolf02] $ ./my_application
Option -x (lowercase x) disables export.
Display export can be done also manually, by setting variable DISPLAY and correct calls of commands
xhost and xauth.
C2110 UNIX and programming 2nd lesson -12-
Exercise
1. Log to machine of your colleague using command ssh. Check your login
mutually (command w or who).
2. Create subdirectory pdb in directory /scratch/your_login
3. Download structure 1SS9 from PDB database using command wget and
save it as test.pdb.
4. Open structure in program vmd. Check, that your application runs on
remote machine (ps -e). Check that application of your colleague runs on
your machine (ps –u his_login).
5. Create subdirectory structures in directory /scratch/your_login
6. Copy file 1SS9.pdb to your machine using command scp to directory
/scratch/your_login/structures
7. Open structure in program vmd on your machine. Compare program
qualitatively response (speed) for remote and local running.
Work in pairs.
C2110 UNIX and programming 2nd lesson -13-
Virtualization
 What is virtualization?
 Typical usage
 Hypervisor overview
 MS Windows in VirtualBox
 Ubuntu OS installation
C2110 UNIX and programming 2nd lesson -14Virtualization
– Hypervisor
Hardware
Host OS
Hypervisor
OS
1
OS
2
OS
3
Virtualization are procedures and techniques, that enables to approach computer
hardware in different way, then they physically exist. Virtualization can be done on
different levels, from whole computer (virtual machine), to particular hardware devices
(virtual processors, memory etc.) or only software environment (virtualization of operating
system).
source: www.wikipedia.org
Hypervisor – virtual machine manager
Host OS (in virtual machine)
C2110 UNIX and programming 2nd lesson -15Virtualization
advantages
• On one physical machine, there may run multiple virtual machines (each with different
operating system).
• Physical hardware performance can be used more efficiently (lower costs).
• Easier backup. Virtual machine state maybe saved as snapshots, these can be used to
restore original state.
• Teleport. Virtual machines can be transferred in between two physical machines with
minimal stop time. Appropriate for hardware updates.
• Easier testing of OS.
C2110 UNIX and programming 2nd lesson -16Virtualization
tools overview
VirtualBox www.virtualbox.org
supported host OS: MS Windows, Mac OS X, Linux
Licence: freeware + proprietary extension for non-commerce usage
KVM Linux kernel part
Supported host OS: Linux
Support programs: virt-manager, qemu
Licence: freeware
VMWare http://www.vmware.com/
Supported host OS: MS Windows, Linux
Licence: commerce
C2110 UNIX and programming 2nd lesson -17MS
Windows on WOLF cluster
Running MS Windows XP in virtual machine (hypervisor VirtualBox)
$ /win/win
C2110 UNIX and programming 2nd lesson -18Virtual
machine control
Full screen on / off switch
Host = (right Ctrl key)
(MS Windows and Linuxem)
How to input Ctrl+Alt+Del
C2110 UNIX and programming 2nd lesson -19Virtual
machine switch off
Correct switch off way
Wrong switch off
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Exercise
1. Run virtual machine with MS Windows XP (command /win/win).
2. Open Internet Explorer in virtual machine and find keyword Hypervisor in
Wikipedia.
3. On host OS monitor hypervisor using command top.
4. Pause virtual machine.
5. Resume virtual machine.
6. Finish virtual machine.
C2110 UNIX and programming 2nd lesson -21Ubuntu
12.04 LTS installation
Install program VirtualBox (http://www.virtualbox.org).
Download installation image of OS Ubuntu as iso format:
http://www.ubuntu.com/
Ubuntu 12.04 LTS (Ubuntu Desktop)
Create virtual machine in VirtualBoxu manager:
Choose OS Linux and Ubuntu version.
Other settings can be left on default values.
First virtual machine run:
First run prompts for install media input. We attach iso image as installation
media (icon on right and select downloaded iso image)
System install
Then follow installation wizard hints.
Homework.
C2110 UNIX and programming 2nd lesson -22MS
Windows as client
 Putty
 WinSCP
 Text file transfer
C2110 UNIX and programming 2nd lesson -23MS
Windows as client – overview
Login to Linuxu from MS Windows (text terminal)
 putty www.chiark.greenend.org.uk/~sgtatham/putty
 ssh from Cygwin environment; www.cygwin.com
File transfer between Linuxem and MS Windows
 WinSCP www.winscp.com, twin-panel file manager
 scp from Cygwin environment;
Display export from Linuxu to MS Windows (X11 server)
 cygwin www.cygwin.com
 Xming http://sourceforge.net/projects/xming/
Login from Linuxu to MS Windows (remote desktop)
 rdesktop
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Putty
Putty http://www.chiark.greenend.org.uk/~sgtatham/putty/
Implementation of SSH (Secure Shell) for Windows, Putty enables remote
connection to SSH servers (machines supporting ssh protocol and login –
unix/linux type).
C2110 UNIX and programming 2nd lesson -25Putty
– settings
wolf.ncbr.muni.cz
Remote machine address Backspace key interpretation.
C2110 UNIX and programming 2nd lesson -26Putty
– settings II
Unix compatible mouse select / paste
system.
Non-proportional font
(all symbols have same width)
C2110 UNIX and programming 2nd lesson -27-
WinSCP
WinSCP http://winscp.net/eng/docs/lang:cs
Program for file transfer between MS Windows and computers supporting SFTP
or SCP protocols (unix and linux type).
Local machine
Remote machine
C2110 UNIX and programming 2nd lesson -28Text
files MS Win  Linux
Text files created in MS Windows and Linuxem are not totally compatible, Each
OS uses different coding of line end.
Linux: \n (line feed 0x0A)
MS Windows: \r+\n (carriage return 0x0D, line feed 0x0A)
For file conversion one can use programs d2u and u2d (on cluster WOLF).
1) Activation of cats module
$ module add cats
2) Conversion MS Windows => Linux
$ d2u file.com
3) Conversion Linux => MS Windows
$ u2d file.log
C2110 UNIX and programming 2nd lesson -29-
Exercise
1. Run virtual machine with MS Windows XP (/win/win).
2. Run application Putty.
3. Using terminal Putty log on machine wolf.ncbr.muni.cz.
4. Monitor who has logged on wolf.ncbr.muni.cz.
5. In terminal Putty try running application vmd. Why does it fail to run?
6. Run application WinSCP.
7. Download file 1SS9.pdb to virtual machine. Open file in program Notepad.
Is content shown correctly?
8. Correct line end coding in file 1SS9.pdb and open file again in virtual
machine program Notepad.