1. Practice #0: Introduction
Yong-Hyun Kim
NST551

2. How to Access Linux Cluster
This approach is for Windows users.
Download programs Xshell and Xmanager through the following website:
Install both programs.
Run Xshell and then click 파일/등록정보/터널링
5. 다음 그림과 같이,
X11 포워딩 부분에서 Xmanager로
연결 check !

3. How to Access Linux Cluster
6. Use the ssh command with your designated account ID
cluster’s address
7. Input your account’s password.
8. Upon successful login, you will see the welcoming message.

4. Basic Linux Commands
1. List the files & folders in current directory: ls
2. Edit text file: vi [ filename ]
3. Make new folder: mkdir [ name of folder ]
After using the mkdir command,
the folder “example” is made.
4. Change directory: cd [ directory ]
After using the cd command, you are inside “example” folder.
Note: to change to the parent(상위) directory of current directory: cd ..

5. Basic Linux Commands 5. Copy a file or directory:
For file: cp [ filename ] [ target directory ]
For directory: cp -r [ dirname ] [ target directory ]
After using cp command,
“ atom_table.dat” is copied to example
6. Rename a file or directory:
For file: mv [ filename] [ new filename ]
For directory: mv [ dirname ] [ new dirname ]
7. Move file or folder: mv [ filename/dirname ] [ target directory ]
8. Remove a file or directory:
For file : rm [ filename ]
For empty directory: rmdir [ dirname ]
For directory and its content: rmdir –rf [ dirname ]

6. VIM: Command vs. Insert Mode
ESC
Command
Insert i
insert before cursor position a
insert after cursor position o
insert below current line I
insert at the beginning of line A
insert at the end of line O
insert above current line

7. VIM: Basic Movement Move Jump Scroll 2 h one char left gg to fist line
Ctrl+b
one page up j
one line down G
to last line
Ctrl+f
one page down k
one char right 5G
to 5th line
Ctrl+y
one line up l
one line up
Ctrl+e
one line down ^
to first char of line $
to last char of line

8. VIM: Basic Editing delete delete x one char dd one line X backspace
five lines
(number)d(c.c.) d$
to end of line
combined command dG
to end of file $
to last char of line
copy & paste
copy G
to last line
()y()
yank = copy yy
one line p
paste after
5yy
five lines P
paste before u
undo
Ctrl+r
redo
save & exit
Escape to command mode first ! :w
save :q
quit
:q!
quit w/o saving :x
save and quit

9. PBS: Submission Script
run.sh
Put this script in the same directory as your VASP input files!

10. PBS: Submit and Delete Job
1. Submit job: qsub run.sh
2. Check job status: qstat
Available status: queue (Q), running (R), complete (C) or exit (E)
Only display your job: qstat -u [ your_ID ], ex: qstat -u nst551
Output of qstat
3. Delete job: qdel [ job_ID ], ex: qdel 58240
4. Check for available computing resources: pestat

11. General Guidelines for PBS Jobs
Output of pestat
Do not run job interactively unless the calculation can finish within few minutes. It will cause lag in others’ login sessions
In total, 32 nodes are available for class members
There is no specific scheduling scheme, i.e. first in first out.
Job will run on 1, 2 or 4 nodes for at most 48 hours.
Frequently check your jobs to make sure that the calculations are going for the right direction.

12. * Software VASP VASP ? Running VASP
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
Running VASP
To submit job(to use VSAP), five input files have to be exist in the same directory.
Input
Output
POSCAR
: Initial atomic position
Total energy
Force
Electronic structure .
KPOINT
: K-point sampling parameters
POTCAR
: Pseudo potential
INCAR
: Input parameters for calculation
run.sh
: Submitting job