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
2nd lesson
C2110 UNIX and programming 2nd lesson -2-
Contents
 Unix in cube
• File system, paths
• Submitting commands
• Basic commands
• File system browsing
• Copying, moving, deleting
 Remote login
• ssh
• Encryption
• Recursive login
C2110 UNIX and programming 2nd lesson -3Unix
in cube
 File system, paths
 Submitting commands
 Basic commands
 File system browsing
 Copying, moving, deleting
C2110 UNIX and programming 2nd lesson -4File
system structure
UNIX uses hierarchical directory file system consisting of directories and files. All
directories and files are located in the only root rirectory (/).
/
home
bin
ivo
root directory
filetest.txt
directory
Subdirectory of directory home
Home directory:
● User data and settings.
● Common path: /home/user_name
C2110 UNIX and programming 2nd lesson -5Comparison
with MS Windows fs
Property Linux (ext2/ext3/ext4) MS Windows
(FAT32,NTFS)
Disk
partitions
Hidden
Disk partitions are connected as
directories.
C:, D:, etc.
Optionally connectable as
directory (ntfs).
Names Case sensitive. Case insensitive.
Name
separator
Slash Back slash
Access
permissions
Yes
POSIX
Yes (only NTFS)
ACL
Devices
(hardware)
As special files. No.
C2110 UNIX and programming 2nd lesson -6PATH
File and directory identifier
/
home
bin
user
test.txt
absolute path to file
/home/user/test.txt
Path to directory or file can be defined as absolut or relative. File and directory names are
separated by slash /.
relative path to file
user/test.txt
C2110 UNIX and programming 2nd lesson -7Path
types
Absolute path has to be specified to root or home directory. Thus it starts either by slash /
or tilde ~.
Relative path is specified to current / work directory. (Absolute path of current directory
can be obtained by command pwd.)
/home/kulhanek/Documents/home_work.txt
../alois/Documents
Use of tilda:
~ home directory of current user
~user_name home directory of user with name user_name
Special directory names:
. (dot) current / work directory
.. (two dots) parent (higher) directory
C2110 UNIX and programming 2nd lesson -8Path
examples
Absolute paths:
/home/kulhanek/Documents
/home/kulhanek/Documents/domaci_ukol.txt
~/Documents → /home/kulhanek/Documents
~alois/Documents → /home/alois/Documents
Relative paths:
Documents/domaci_ukol.txt
../alois/Documents
./muj_script
C2110 UNIX and programming 2nd lesson -9WOLF
cluster file system
wolf01
/scratch
wolf02
/scratch
wolf03
/scratch
wolf04
/scratch
/home
........
Shared contents on all WOLF cluster nodes.
Data has backup. Capacity is restricted by
quota per-user to maximum 1,5GB.
Different contents on all nodes.
Data on volume /scratch has no backup and can
be deleted anytime.
Per-user capacity is not restricted.
C2110 UNIX and programming 2nd lesson -10Command
line
[kulhanek@wolf ~]$
User name
Machine name
Current directory (~ is home directory /home/login)
Prompt – user type ($ regular user, # super user, other prompts %, >)
commands
Command is given by key Enter.
Text copy: Do not use Ctrl+C! Mouse text select automatically adds text to clipboard, press
mouse wheel to paste on cursor place.
Auto complete: Tab key makes command line interpreter to try complete started word.
Completed can be command names, paths, file names (if one click does not complete
word, there is more possibilities to complete, another click shows list of them).
History: by arrow keys (up, down) list of recently used commands can be searched. Any
command can be re-used or edited and used. Full list of recorded commands can be printed
by command history.
C2110 UNIX and programming 2nd lesson -11Commands
help, cmd searching
Manual pages (When I do not know what to do?):
man prints manual page of command
$ man [section_number] topic
Sections:
 Section 1 user commands
 Section 2 system calls
 Section 3 library functions
 Section 4 special files
 Section 5 file formats
Name of command, function, theme, chapter
Section name is needed if there is same name in multiple sections.
 Section 6 games
 Section 7 conventions and miscellany
 Section 8 administration and privileged commands
 Section L math library functions
 Section N tcl functions
$ man 1 printf
$ man 3 printf
Manual page of command printf
Manual page of C language function printf()
C2110 UNIX and programming 2nd lesson -12Commands
help, cmd searching
Browsing in manual pages text:
● Movement in text by lines (up, down arrows, keys j and k)
● Movement in text by pages (PgDn and PgUp or keys f and b)
● Searching ( /search_pattern , key n for next occurrence, N for previous)
● Manual pages close (key q)
On-line manual pages in HTML:
http://linux.die.net/man/
Useful commands:
whatis prints short command description (manual page header)
apropos search for commands containing pattern in manual page
info command info pages (similar to manual pages)
C2110 UNIX and programming 2nd lesson -13Running
commands, applications
Commands and system applications
User scripts and commands
$ ls -l
$ cp file.txt file1.txt
$ ./muj_script
$ ~/bin/my_application
Running application on background
$ gimp &
Redirect standard output
$ kwrite &> /dev/null
Command name or application name
Command or script name with full
path (absolute or relative)
Behind command, arguments and redirections by
& (ampersand) command is run on background.
command Command arguments (modifies command behavior,
input information for processing)
Redirection of standard output is done behind
command, arguments.
C2110 UNIX and programming 2nd lesson -14Basic
commands
File system:
• pwd prints path to current / working directory
• cd change current / working directory
• ls prints list of contents of current / working directory
• mkdir create directory
• cp copy directory or file
• mv move directory or file
• rm remove directory or file
Investicative commands:
• hostname prints machine name
• whoami prints name of logged user
• id prints ID info of user
• w prints who is logged and his running command
• ps prints running processes
C2110 UNIX and programming 2nd lesson -15Create
directory
• Create directory
$ mkdir dir_name
• Create directory substructure
$ mkdir -p dir_name1/dir_name2/dir_name3
C2110 UNIX and programming 2nd lesson -16-
Copy
• To copy files and directories use command cp
$ cp file1 file2
Creates copy of file vytvoří kopii file "file1" s názvem "file2"
$ cp file1 file2 file3 directory1/
Copy files “file1 ", “file2", “file3" to directory “directory1"
$ cp -r directory1 directory2
Creates copy of directory “directory1" with new name “directory2"; if directory
“directory2" already exists, creates copy of directory “directory1" as subdirectory
of directory “directory2"
$ cp -r file1 directory2 file3 directory1/
Copy files “file1", “file3" and directory “directory2" to directory “directory1"
C2110 UNIX and programming 2nd lesson -17-
Move
• To move files and directories use command mv
$ mv file1 file2
Rename file "file1" to "file2"
$ mv file1 file2 file3 directory1/
Move files "file1", "file2", "file3" to directory "directory1"
$ mv directory1 directory2
Rename directory "directory1" to "directory2"; if directory "directory2" exists,
then move directory "directory1" to directory "directory2"
$ mv file1 directory2 file3 directory1/
Move files "file1", "file3" and directory "directory2" to directory "directory1"
C2110 UNIX and programming 2nd lesson -18-
Mazání
• K mazání slouží příkaz rm
$ rm file1
Removes file "file1"
$ rm -r directory1
Removes directory "directory1"
C2110 UNIX and programming 2nd lesson -19-
Exercise
Try to use shortcuts:
• Auto complete (key TAB)
• Text copy (select by mouse / insert by wheel)
• history
1. Download study materials from IS to directory ~/Downloads.
2. Create subdirectory pokus in directory /scratch/your_login .
3. Create directory studmat in your home directory.
4. To directory studmat copy study materials from directory ~/Downloads .
5. Open presentation (Lesson 02) in okular software, run okular so that it does
not print any standard output information on terminal.
6. Copy presentation to directory /scratch/your_login/pokus .
7. Rename presentation to new name pokus.pdf in directory
/scratch/your_login/pokus .
8. Open presentation pokus.pdf in okular software, run program on
background.
9. Remove presentation in directory ~/Downloads .
C2110 UNIX and programming 2nd lesson -20Remote
login
 ssh
 Encryption
 Recursive login
C2110 UNIX and programming 2nd lesson -21Remote
login
There is number of protocols / commands for remote login (rsh, XDMCP, etc.),
most used and most secure is protocol / command ssh (secure shell).
$ ssh [user@]hostname [command]
Syntax:
User name;
If name is not given, curent user
name is used
Machine name
[] - optional
Logout:
Remote interactive login is closed by
command exit.
Examples:
$ ssh wolf.wolf.inet
$ ssh wolf01.wolf.inet w
Command to be submitted to
remote machine, if omitted
command line on remote machine
is activated
C2110 UNIX and programming 2nd lesson -22First
remote login
[kulhanek@wolf01 ~]$ ssh wolf02
The authenticity of host 'wolf02 (10.251.28.102)' can't be established.
ECDSA key fingerprint is 1f:9d:f3:d3:1d:24:28:12:56:30:99:ef:2d:68:d2:cf.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'wolf02,10.251.28.102' (ECDSA) to the list of known hosts.
[kulhanek@wolf02 ~]$
On first remote login user has to confirm authenticity of remote machine.
In secure network remote machine fingerprint can be accepted without
verification.
In the Internet it is better to verify fingerprint by independent way (receive
fingerprint from remote machine admin by mail).
C2110 UNIX and programming 2nd lesson -23Asymmetric
encryption
key I key IIPair of encryption keys
Message Encrypted message
Decryption to original message by key used
for encryption is not feasible.
Message Encrypted message
Message Encrypted message
C2110 UNIX and programming 2nd lesson -24Asymmetric
encryption, use I
Public key Private key
Sender Receiver
Secure message transfer:
1. Obtain receiver public key.
2. Encrypt message with receiver public key.
3. Message transfer over unsecure network.
4. Receiver decrypts original message by his private key.
Unsecure network
Anybody who knows receiver private key can decrypt original message!
Pair of encryption keys
Message Encrypted message
C2110 UNIX and programming 2nd lesson -25Asymmetric
encryption, use II
Public key Private key
Sender Receiver
Authentication of public message sender:
1. Encryption of message by sender private key
2. Receiver obtains encrypted message and sender public key.
3. Receiver decrypts message by sender public key.
Unsecure network
Public message Encrypted
message
Pair of encryption keys
Anybody who steels sender private key, can pretend to his identity!
C2110 UNIX and programming 2nd lesson -26-
Exercise
1. Log on to remote machine wolf01.wolf.inet
2. Print all connected users by command w.
3. Logout from machine wolf01.wolf.inet.
4. Print all users logged on wolf01.wolf.inet without interactive login to
node.
C2110 UNIX and programming 2nd lesson -27Remote
login
wolf
wolf03 wolf04 wolf05wolf02wolf01
wolf06 wolf07 wolf08 wolf23
Command ssh can be used for recursive remote login.
ssh wolf06ssh wolf
ssh wolf02
Each new remote login level increases overhead costs, thus we use the most direct
possible remote login
ssh wolf02
C2110 UNIX and programming 2nd lesson -28Remote
login
University network
wolf.ncbr.muni.cz
Local network
wolf.wolf.inet
wolf
wolf03 wolf04 wolf05wolf02wolf01
wolf06 wolf07 wolf08 wolf23
Domain not accessible directly
wolf.inet
skirit.ics.muni.cz
Recursive remote login is necessary for access of computers in private networks.
ssh wolf08.wolf.inet
ssh wolf.ncbr.muni.cz
ssh wolf07
C2110 UNIX and programming 2nd lesson -29Remote
login
University network
wolf.ncbr.muni.cz
Local network
wolf.wolf.inet
wolf
wolf03 wolf04 wolf05wolf02wolf01
wolf06 wolf07 wolf08 wolf23
Domain not accessible directly
wolf.inet
skirit.ics.muni.cz
ssh skirit.ics.muni.cz
Remote login from local private networks to machines located in public network
can be done directly.
C2110 UNIX and programming 2nd lesson -30Remote
login without password
wolf
wolf03 wolf04 wolf05wolf02wolf01
wolf06 wolf07 wolf08 wolf23
First login with password
Login to other WOLF cluster nodes
without password
Using authorized public key.
There are also different techniques with similar extent:
system Kerberos (http://web.mit.edu/Kerberos/)
C2110 UNIX and programming 2nd lesson -31Remote
login without password
[kulhanek@wolf01 ~]$ cd .ssh
[kulhanek@wolf01 .ssh]$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (/home/kulhanek/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/kulhanek/.ssh/id_rsa.
Your public key has been saved in /home/kulhanek/.ssh/id_rsa.pub.
The key fingerprint is:
e9:07:0b:fc:17:23:b3:c5:1a:8a:0c:1a:98:8f:fe:28 kulhanek@wolf01.wolf.inet
No input!
2. Paste your public key to list of authorized keys:
[kulhanek@wolf01 .ssh]$ cat id_rsa.pub >> authorized_keys
Advantages:
 No need to input password each time
 More secure usage of ssh and scp
commands in scripts.
 Faster work
Disadvantages:
 In case of loosing one account, all
nodes with authorized keys can be
accesed.
Description: man ssh
1. Create private and public key pair:
C2110 UNIX and programming 2nd lesson -32-
Exercise
1. Activate remote login without password in WOLF cluster.
2. Verify that remote connection works. Connetc to node wolf01.
3. Try recursive remote login within WOLF cluster.
4. Monitor who is logged on your machine.