C2110 UNIX and programming Lesson 2 / Module 3 -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
Lesson 2 / Module 3
PS / 2020 Distance form of teaching: Rev2
C2110 UNIX and programming Lesson 2 / Module 3 -2File
System
➢ Structure
➢ Differences from MS Windows
➢ Relative and Absolute paths
➢ Wildcards
➢ Basic Commands
C2110 UNIX and programming Lesson 2 / Module 3 -3File
System Structure
UNIX uses hierarchical directory file system composed of directories (folders) and files. All
directories and files are located in a single root directory (/).
/
home
bin
ivo
root directory
filetest.txt
directory
subdirectory of the directory home
Home directory:
● directory used for data and user settings
● usually in the path /home/username
C2110 UNIX and programming Lesson 2 / Module 3 -4Comparison
with MS Windows
Property Linux (ext2/ext3/ext4) MS Windows
(FAT32, NTFS)
Disk
Partitions
No
Disk partitions are mounted as
directories.
C:, D:, etc.
However, it is also
possible to mount them
as directories (ntfs).
Names Case sensitive Not case sensitive
Separation
of names
Slash Back slash
Access
rights
Yes
POSIX
Yes (only NTFS)
ACL
Equipment
(hardware)
As special files. No
C2110 UNIX and programming Lesson 2 / Module 3 -5File
System on the WOLF Cluster
wolf01
/scratch
wolf02
/scratch
wolf03
/scratch
wolf04
/scratch
/home
........
Shared content on all nodes of the WOLF cluster.
Data are backed up. Backups are available in
form of snapshots in the directory
/backup/<date>/WOLF/wolf.ncbr.muni.cz/home
Capacity per user is limited by quota 1.5 GB.
Different content on each node.
Data on volume /scratch up are not backed up
and can be deleted at any time without prior
notice.
Capacity is not limited by quota per user.
C2110 UNIX and programming Lesson 2 / Module 3 -6Identification
of directories and files
/
home
bin
user
test.txt
/home/user/test.txt - absolute path identifying file test.txt
with respect to the root directory
Path to a directory or file may be written as absolute or relative. Directory and file names
are separated by slash /.
user/test.txt - relative path identifying the file
test.txt with respect to the current directory (in
this case it is the directory /home)
C2110 UNIX and programming Lesson 2 / Module 3 -7Types
of Paths
The absolute path it is always listed relative to the root or home directory. So it has to start
with either a slash / or tilde ~.
Relative path is the path listed to the current/working directory. (The absolute path of the
working directory can be obtained with the command pwd.)
/home /kulhanek/Documents/domaci_ukol.txt
../alois/Documents
Using the tilde:
~ home directory of the logged in user
~username the home directory of user username
Special directory names:
. (dot) current directory
.. (two dots) parent directory
Paths in the file system (regardless of OS) can be relative or absolute. The meaning of
relative paths depends on the current working directory, while the meaning of absolute
paths is independent of the current working directory.
C2110 UNIX and programming Lesson 2 / Module 3 -8Paths
vs postal addresses
A very close parallel to paths are, for example, postal addresses:
Czech Republic
Globe
Brno Zlín
Kopretinová
Kopretinová
5
6
5
6
Relative address:
Absolute address:
Kopretinová 5
/Globe/Czech Republic/Brno/Kopretinová 5
C2110 UNIX and programming Lesson 2 / Module 3 -9Use
of relative and absolute paths
In everyday work, both types are often used, even in parallel.
experiment1 experiment2 experiment3 experiment4
analysis script
Database of
PDB structures
absolute paths
relative paths
C2110 UNIX and programming Lesson 2 / Module 3 -10Use
of relative and absolute paths
In everyday work, both types are often used, even in parallel.
experiment1 experiment2 experiment3 experiment4
analysis script
Database of
PDB structures
absolute paths
relative paths
C2110 UNIX and programming Lesson 2 / Module 3 -11Wildcards
in File Names
Wildcards (special characters) in file or directory names:
* - anything in the name (without hidden files)
? - one character in the name
[] - range (one character) in the name, e.g., [ajk], [a,j,k], [a-j]
Expansion of wildcards is performed by shell (command line access environment) before
starting the command itself. Expansion can be prevented by enclosing the name in
quotation marks or by using a backslash before the special character. In this case, the
expansion can be performed by a running command (e.g., find).
Entered command: $ cp *.pdf Documents/
Added command: $ cp 01.pdf 02.pdf Documents/
Example:
The current directory contains files 01.pdf and 02.pdf
expansion
running the
command
C2110 UNIX and programming Lesson 2 / Module 3 -12Special
Characters in File Names
Special characters can be used concurrently in both directory and file names:
Examples:
$ cp ~/task[1,4,5]/*.pdf Documents/
copies all pdf documents from subdirectories ukol1, ukol4 and ukol5 in the home
directory to a subdirectory Documents
Examples:
$ cp *.pdf Documents/
copies all pdf documents from the current directory to the subdirectory Documents
$ rm *
deletes all files in the current directory (except directories and hidden files and
directories)
$ mv A? Tmp/
moves files with a name beginning with a letter "A" and containing two characters
into the directory "Tmp"
C2110 UNIX and programming Lesson 2 / Module 3 -13Basic
Commands
File system (basic commands):
cd changes the current working directory
pwd lists the path to the current working directory
ls lists the contents of the directory
mkdir creates a directory
rmdir deletes directory (must be empty)
cp copies a file or directory
mv moves a file or directory
rm deletes a file or directory
find searches for files or directories
"Golden Trinity"- I need to know how to get there (cd). where I am, if I do not know it
(pwd) and what is there (ls)
Useful tips:
$ cd the command without the specified argument sets the home directory as
the working directory
It is recommended to have at least two terminals opened in the source and destination
directories, to use automatic completion (TAB), and to check the contents of directories
before and after the operation.
C2110 UNIX and programming Lesson 2 / Module 3 -14Access
Rights - Prelude
$ ls –l
drwxrwxr-x 3 kulhanek lcc 4096 2008-10-13 09:57 bin/
drwx------ 2 kulhanek lcc 4096 2008-10-13 09:58 Desktop/
-rw-rw-r-- 1 kulhanek lcc 5858 2008-10-17 11:58 distance.cpp
file or directory name/owner (user)
and user group (group)
size (B)
time of last change
access right
Access rights determine what operations a user can perform on files or directories in the file
system.
Access rights:
r ability to read the file to list the contents of the directory
w ability to change file change directory content (create or delete a file or directory)
x ability to run the file ability to enter the directory
Each file or directory has a designated owner and user group. Access rights are listed
separately for file owner (u), user group (g) and other users (o).
a
t
G O
type: file (-) or directory (d)
C2110 UNIX and programming Lesson 2 / Module 3 -15Creating
Directories
• Creating a directory
$ mkdir direktory_name
• Creating a nested directories
$ mkdir -p name_dir1/name_dir2/name_dir3
option -p (parents) causes parent directories to be created if
they do not exist
C2110 UNIX and programming Lesson 2 / Module 3 -16-
Copying
• Command cp is used to copy
$ cp file1 file2
creates a copy of file "file1" named "file2"
$ cp file1 file2 file3 directory1/
copies files "file1", "file2", "file3" into the directory "directory1"
$ cp -r directory1 directory2
creates a copy of directory "directory1" named "directory2"; if directory
"directory2" already exists, creates a copy of directory "directory1" as a
subdirectory of directory "directory2"
$ cp -r file1 directory2 file3 directory1/
copies files "file1", "file3" and directory "directory2" to directory "directory1"
Option -r (recursive) must be used to copy the contents of directories.
C2110 UNIX and programming Lesson 2 / Module 3 -17-
Moving
• Command mv is used to move or rename
$ mv file1 file2
renames file "file1" to "file2"
$ mv file1 file2 file3 directory1/
moves files "file1", "file2", "file3" to directory "directory1"
$ mv directory1 directory2
renames directory "directory1" to "directory2"; if directory "directory2" already
exists, moves directory "directory1" to directory "directory2"
$ mv file1 directory2 file3 directory1 /
moves the files "file1", "file3" and the directory "directory2" to the directory
"directory1"
C2110 UNIX and programming Lesson 2 / Module 3 -18-
Removing
• Command rm is uded to remove
$ rm file1
deletes file "file1"
$ rm -r directory1
deletes directory "directory1"
rm -rf .*
recursion (r) and without query (f - force)
.* -> .. (removing even upwards)
C2110 UNIX and programming Lesson 2 / Module 3 -19Searching
for Files
You can use the command find to search for files.
$ find [where] what
if not specified, it is searched in
the current directory
Search query (what) is composed of subqueries that can be joined by logical operators.
Frequently used queries:
-name pattern finds all files that have a name pattern
pattern may contain special characters: *,?, []
(when using special characters we state pattern in quotes)
-type C finds all files of type C (file, directory, etc., for list of types see
man find)
Logical operators:
-and left and right queries are met simultaneously
-or left or right query is met
search is recursive (default)
C2110 UNIX and programming Lesson 2 / Module 3 -20File
Search - Examples
$ find /home/ -name '*.txt'
$ find ~kulhanek –Name '*.txt' –or –name '*.hpp'
$ find –name 'D*' –and –type d
in directory /home/, finds all files that end with .txt
in directory /home/kulhanek, finds all files that have a end with .txt or .hpp
in the current directory, finds all subdirectories whose names begin with the letter D
C2110 UNIX and programming Lesson 2 / Module 3 -21Hidden
Files and Directories
Names of hidden files or directories start with a dot. They are normally not displayed, but
they can be listed using the command ls -a. Special characters *, ? and [] do not include
hidden files in the normal context.
Hidden files contain system configuration, and if you
don't know what you're doing, don't delete or change
them.
C2110 UNIX and programming Lesson 2 / Module 3 -22Command
Line Query Format
Default settings:
$ PS1="[\u@\h \W]$ "
Adjusted settings:
$ PS1="[\u@\h \w]$ "
You can change the appearance of the command line query. The system
variable used for this is PS1 (man bash). If the current format does not
suit you (it displays the name of the last directory from the current path),
you can change the look as follows:
uppercase and lowercase letter w
The change will only take effect in the terminal where it was made. The settings can be
made permanent by inserting the command at the end of hidden file ~/.bashrc on a
separate line. Use a text editor (gedit or kwrite) to change the contents of the file. The
change in settings will be reflected in the newly opened terminals.
The adjusted setting will display whole path to the working directory.
C2110 UNIX and programming Lesson 2 / Module 3 -23Exercise
1
1. Log in to the wolf02.ncbr.muni.cz workstation.
2. Create directories in the home directory: Documents/C2110
3. Copy the lectures into the C2110 directory in pdf format from directory:
/home/kulhanek/Documents/C2110/Presentations
4. Create a directory studmat in your home directory
5. Copy the presentation C2110-CZ-L02.pdf from your directory Documents/C2110 to the
directory studmat and name it presentation.pdf
6. Create a directory /scratch/username/test
7. Copy file prezentace.pdf to directory /scratch/username/test
8. In the directory /scratch/username/test, rename the presentation to lesson2.pdf
9. Log in to the wolf03.ncbr.muni.cz workstation
10. Is the lekce2.pdf file present in the directory /scratch/username/test? Discuss the
observation.
11. Delete directories /scratch/username/test and ~/studmat
Try to learn to use:
• multiple terminals
• auto complete (TAB key)
• simplified copying: mark with the left button / insert with the middle mouse button
• command line history
username - your username
C2110 UNIX and programming Lesson 2 / Module 3 -24-
Homework
➢ Practicing Commands
C2110 UNIX and programming Lesson 2 / Module 3 -25-
Homework
1. Log in to the WOLF cluster workstation.
2. Create a directory in your home directory Data
3. Copy the contents of the directory /home/kulhanek/Documents/C2110/Lesson02
including subdirectories to the directory Data
4. Find all files with the extension .cpp which are located in the directory Data (write the
file names on the screen)
5. Create a directory Headers in the directory /scratch/username
6. Copy all files from the directory
/home/kulhanek/Documents/C2110/Lesson02/dev/src that have an ending .h to the
directory Headers
7. Move all files from the directory
/home/kulhanek/Documents/C2110/Lesson02/dev/src that have an ending .cpp to
the the directory Headers. What really happened and why?
8. What is the size in B and kB of file
/home/kulhanek/Documents/C2110/Lesson02/dev/src/GraphicsSetup.cpp
9. In the directory Headers delete all files with the extension .h and containing the word
Graphics at the beginning of the file name
10. Delete the directory Headers