Practice 0 Introduction YongHyun Kim NST 551 How

Practice #0: Introduction Yong-Hyun Kim NST 551

How to Access Linux Cluster 1. This approach is for Windows users. 2. Download programs Xshell and Xmanager through the following website: http: //www. netsarang. co. kr/download/software. html 3. Install both programs. 4. Run Xshell and then click 파일/등록정보/터널링 5. 다음 그림과 같이, X 11 포워딩 부분에서 Xmanager로 연결 check !

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.

ID and Password Initial password is your student ID 201***** After you login using initial password, you can change password using command yppassd

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. .

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 ]

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

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

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

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

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 nst 551 Output of qstat 3. Delete job: qdel [ job_ID ], ex: qdel 58240 4. Check for available computing resources: pestat

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

* Software VASP • 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. https: //www. vasp. at/ • Running VASP To submit job(to use VSAP), five input files have to be exist in the same directory. Output Input POSCAR : Initial atomic position KPOINT : K-point sampling parameters POTCAR : Pseudo potential INCAR : Input parameters for calculation run. sh : Submitting job • • • Total energy Force Electronic structure. . .