Introduction to Computational Quantum Chemistry
Lesson 02: Introduction to LINUX
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 1
The Wolf Cluster
scientific software administrator: RNDr.Petr Kulhánek,PhD.
https://einfra.ncbr.muni.cz/whitezone/root/index.php?lang
=en&action=ncbr&show=wolf
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 2
History of Linux
started with UNIX, that was developed in 1970s
UNIX lead to two distributions developed by UCBerkeley
(BSD) and AT&T (System 5) which started the “UNIX
Wars" in the 80s
then GNU (GNU not UNIX) and Minix enters the scene
GNU tools allows to build a ’free’ version of UNIX without
relying on both BSD and AT&T files
from GNU and Minix, arise the Linux Kernel, publicly
announced in 1991 by Linus Torvalds, since then many
distributions developed:
Ubuntu, Debian, Fedora,...
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 3
Systems of User
Superuser
administrative privileges
can edit system files
User
cannot edit system files
only selected items are editable/accessible
belongs to certain groups with respective rights
(hardware/software access...)
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 4
Filesystem
no “Windows-like” discs
everything mounted under “/” (root) directory
slash sign is used as separator between directories
important paths:
/home/username/ or “~”: Quota 1.5 GB, backed-up
/scratch/username/: No quota, NOT backed-up
/media/filesystem/: USB sticks, DVD discs...
everything is either file or process
arbitrary suffixes for files
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 5
Directories and Filenames
General advices aka “Good-To-Follow” rules:
case-sensitive system
do NOT use spaces in filenames (use underscore or dash)
good characters:
alphanumerics
_ . − +
forbidden characters:
any kind of diacritics
quotation marks
brackets
# % ? ! , * ˆ & @ / ~...
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 6
The Linux Terminal
found in Applications → Accessories → Terminal
shell interpreter translating written commands into actions
Cygwin, PuTTY: Terminal emulators for Windows
machines
Pros:
fast and effective way of work
directly visible output from operation
error tracking
no GUI needed
Cons:
need of memorizing commands
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 7
Work in Terminal
use ArrowUp and ArrowDown for searching the command
history
use Tabulator for word completion
Copy/Paste from terminal using mouse (CTRL+c/CTRL+v
does NOT work here)
Will terminate current command!
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 8
Linux Survival Commands
Command Action
pwd print working directory
ls list files in directory
cd wolf change current working directory to “wolf”
cp source target copy source file to target file
cp -r source target copy source directory recursively into target
mv source target move source file to target file
mkdir wolf create “wolf” directory
rmdir wolf removea “wolf” directory (only if empty)
rm wolf removea “wolf” file
rm -r wolf removea “wolf” directory recursively
cat wolf print content of a “foo” file into terminal
grep wolf file print only line containing “foo” keyword in “file”
top see currently running processes
a removing means deleting from the disc. NOT moving into trash.
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 9
Linux Survival Commands II
Command Action
head -n number wolf print first “number” rows of “wolf” file
tail -n number wolf print last “number” rows of “wolf” file
echo wolf prints “wolf” into terminal
printf similar to echo but handles formatted text
chmod switch wolf changes rights of “wolf” file according to switc
quota prints current quota of user and disc usage
ssh user@host remote access to host machine
exit logout from the terminal
who prints all users logged into machine
passwd change current pasword
kill PID kill the process with number “PID”
ps print all current processes running in terminal
module accessing the scientific software
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 10
Wild Characters
Notation Matches
* any string of characters including empty string
? any single character
[jklm.] single character j, k, l, m or a dot
[a-m] single character from range a to m
[2-9] single number from range of 2 to 9
example:
$ ls a*[0-2].??[df] this command will print all files which:
start with “a”
then they have any string of characters
then there is either 0, 1, or 2
followed by a dot
then any two characters
last character is either “d” or “f”
all conditions must be satisfied
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 11
Listing and Killing Processes
once command is run, it obtains a unique process ID (PID)
$ top # displays currently running jobs in real time
$ kill PID # kills process with a given PID
$ kill -9 PID # kills process (signal cannot be blocked)
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 12
Text Editors
a text editor only edits plain text, such programs can be
used to manipulate such as configuration files,
documentation files and programming language source
codes.
programmed to highlight keywords of many
languages/source codes
with graphical interface:
gedit, kate, kwrite, gvim
without graphical interface (editing in terminal):
vi / vim
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 13
The VI Editor
fast and effective way to edit files in remote machine
3 modes:
Command mode
Edit mode
Visual mode
enter command mode via ESC key
enter edit mode via Insert or “i” key
visual mode for editing blocks of text:
http://vimdoc.sourceforge.net/htmldoc/visual.html#Visual
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 14
The VI Editor, Commands
Command Action
:w save document
:w filename save document as “filename”
:q quit document
:q! quit without saving
:wq save and quit
:u undo
i / insert enter edit mode
R enter replace mode
gg go to the beginning of the document
G go to the end of the document
dd delete current line
25D delete next 25 lines
dG delete all lines starting from cursor
/keyword search for keyword
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 15
The VI Editor, Tutorial
Writing a plain text file:
$ vi test.dat open ‘test.dat’ file for editing
i / insert enter editing mode
Write some text
:w write text to file
gg go to first line
2D delete two lines
:u undo last change
:wq write and quit
$ rm test.dat remove file
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 16
Remote Access
accessing remote machine via ethernet or internet
ssh command:
$ ssh [username@]hostmachine
username does not have to be specified if same as current
login
if X applications should be exportable, use “-X” switch
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 17
Remote Access, Example
access the wolf node next to yours with X server export
enabled
find out who is logged in there
exit from this computer
help: here
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 18
Passwordless Authentication Within Cluster
no password required for access the host machine
should be used with great care only on local networks
procedure:
$ cd .ssh
$ ssh-keygen
<enter>
<enter>
$ cat id_rsa.pub » authorized_keys
try to remotely access the same machine
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 19
Copying Files between Machines
$ scp source target
source and/or target can be on remote machine:
user@wolf12:~$ scp text.dat wolf13:/scratch/user/
user@wolf12:~$ scp -r wolf13:/scratch/user/ directory/
$ mc
midnight commander - same as in Windows/Mac machines
“graphical interface”
$ gftp
“real” graphical interface
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 20
Absolute vs. Relative Paths
Absolute path:
total path from the root directory
/scratch/user/test
~/Documents/
Relative path:
./ # current directory
../ # parent directory
../../../data/test/
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 21
Access Permissions
each file has permissions for Owner, Group and Others
drwxrwxrwx
d – directory
r – read
w – write
x – execute
- – permission not granted
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 22
Change Permissions
$ chmod switch file
examples of switches:
u+x user can execute file
go+w group members and others can write to file
a-r remove right to read for all users
o-rwx remove right to read, write and execute to others
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 23
ACTIVITY
create in your home folder directory folder01
copy current pdf presentation and *.tex from address
wolf01:/share/ivavik/instructor_username/teaching to
your newly created directory, try to open it from terminal
using evince, make it readable for all users
using vi editor create a plain text file called prop.txt and
insert inside complete info about the pdf file based on ls
output
please store all subsequent working commands in this
prop.txt file (use another terminal window for easier
copying)
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 24
ACTIVITY
study the manual info about pdfjam tool for manipulating
pdf files and generate a new pdf file containing first 4 slides
in landscape orientation (pres4.pdf)
run simple command in terminal and inspect its function:
for (( i=1; i<30; i++ )); do head -n$i 01.tex | tail -1 > $i.tex;
done
remove all .tex files whose index ends 0 or 5
create folder your_username a move there .tex files and
prop.txt with inserted commands for the entire excercise
copy recursively the folder your_username to
wolf01:/share/ivavik/instructor_username/teaching
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 25
Introduction to Computational Quantum Chemistry
END
(Prepared by Radek Marek Research Group)
Lesson 02 - Introduction to LINUX 26