C2115 Practical introduction to supercomputiong Lesson 4 -1-
C2115
Practical introduction to
supercomputing
Lesson 4
Petr Kulhánek
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
Revision 1
C2115 Practical introduction to supercomputiong Lesson 4 -2Ubuntu
18.04
(code name: bionic)
http://www.ubuntu.com/
➢ Installation of Ubuntu Server
VirtualBox, access via ssh, installation of applications
C2115 Practical introduction to supercomputiong Lesson 4 -3Virtualization
- Hypervisor
HardwareHardware
Host OS
Hypervisor
OS
1
OS
2
OS
3
Virtualization are procedures and techniques that access to available resources in a
different way than they physically exist. Virtualization can be done at different levels, from
the whole computer (so-called. virtual machine), to its individual hardware components
(e.g., virtual processors, virtual memory, etc.), or only the software environment
(virtualization of operating system).
source: www.wikipedia.org
Hypervisor - virtual machine administrator
Guest OS (in a virtual machine)
VirtualBox
www.virtualbox.org
Supported host OS:
MS Windows, Mac OS X, Linux
License: freeware + proprietary extension for noncommercial
use
C2115 Practical introduction to supercomputiong Lesson 4 -4PLEASE
CAREFULLY READ FOLLOWING
INSTRUCTIONS
C2115 Practical introduction to supercomputiong Lesson 4 -5Exercise
1
Install Ubuntu Server 18.04 in a virtual environment VirtualBox.
1. Download the installation image (ISO) for Ubuntu Server 18.04.5 LTS (64 bit version).
Download the installation image to your scratch directory (/scratch/login_name)
[storage path can be changed in Firefox settings].
2. Settings VirtualBox (File -> Preferences)
1. Default Machine Folder: change to a subdirectory (of your choice) in your scratch
directory (/scratch/login_on me)
3. Creating a virtual machine
1. Machine name at your discretion, Linux, Ubuntu 64 bit, leave other settings at
default values.
2. Verify that a virtual disk has been created for you in your scratch directory
(Settings: Storage, select a virtual disk from the list, verify the path specified in the
"Location")
C2115 Practical introduction to supercomputiong Lesson 4 -6Exercise
1, continued
4. Virtual machine settings
1. Network -> Attached to: NAT
2. Network -> Advanced -> Port Forwarding
1. Host Port: 2222
2. Guest Port: 22
3. Leave the rest unchanged
5. Start the virtual machine
1. Choose installation media, choose installation ISO image.
2. When installing follow the instructions on the next page.
C2115 Practical introduction to supercomputiong Lesson 4 -7Brief
installation instructions
1. territory - Czech Republic (in Others -> Europe)
2. English keyboard (US) - do not use autodetection
3. machine name - any name (letters only, no accents)
4. Creating a user:
1. username - any
2. login name - SAME* as on the WOLF cluster
3. password - preferably the same as on a WOLF cluster (not a condition), do not use
the numeric part of the keyboard to enter the password
5. do not encrypt your home directory
6. use the entire disk without LVM
7. install OpenSSH server (selection is indicated by the key Space), if you forget to choose,
it is possible to install later using:
8. Grub install to MBR (Master Boot Record) equipment /dev/sda
Note: graphical interface can be installed via ubuntu-desktop package (we don’t do it, it's
time consuming and increases memory requirements of the virtual machine)
$ sudo apt-get install openssh-server
* otherwise you will greatly complicate your life
C2115 Practical introduction to supercomputiong Lesson 4 -8Virtual
Network
ssh remote term. # 2
(console)
ssh remote term. # 3
(console)
port 2222
ssh server
port 22
VirtualBox
NAT
Host machine (wolfXX)
Screen
local terminal # 1
Ubuntu server
virtual machine
(ubuntu)
ID: ubuntu
ID: wolfXX
port
forwarding
ssh remote term. #4
(console)
the virtual machine can access
the external network via NAT
the virtual machine cannot
be accessed directly from
the external network
ssh server
port 22
ssh remote term. #1
(console)
C2115 Practical introduction to supercomputiong Lesson 4 -9Exercise
2
1. Log in to the running instance of the virtual machine through the graphical interface of
the virtualization environment.
2. Log in to the running instance of the virtual machine using the program ssh from the
host computer. Open several independent sessions.
3. Using command w (or who) list the current sessions on the virtual machine.
4. Log in to the running instance of your virtual machine using the program ssh from node
wolf01.
ssh -p 2222 server_login@wolfXX
or
ssh -p 2222 server_login@localhost
version with "localhost“ must be
started from the machine on which
your virtual machine is running
part "server_login@ “ will be used if
you created an account with a
different login name during
installation ("server_login“ will be
replaced by your login name in the
virtual machine)
C2115 Practical introduction to supercomputiong Lesson 4 -10Exercise
3
1. Install the program mc : $ sudo apt-get install mc
2. What is the program mc for?
3. Shut down the server: $ sudo poweroff
4. Turn on the server.
5. Create snapshot of the virtual machine (Machine->Take Snasphot ...)
6. Log in interactively as superuser ($ sudo su -)
7. What is NAT?
8. Install the package "pi“. What is it used for?
install a package (application) named mc
Package overview:
https://packages.ubuntu.com/