Getting started

User acess

Go to www.metacenter.no > User Login (Passwords) > 1. Request a user account > HPC

Fill in the form and choose the appropriate project. It is recommended to use your UiO username.

The project manager can give you access to the VASP license through the VASP portal and thereafter informing sigma2@uninett.no to give your user the necessary group affiliations (xvasp and vasp5).

Project	Manager	Group	Resources
NN4604K	Jonathan M. Polfus	Electrochemistry	Saga
NN9136K	Lasse Vines	LENS	Saga
NN9180K	Clas Persson	Structure Physics	Saga

Login

ssh

ssh can be used to login using a terminal app on UNIX, macOS or Windows Subsystem for Linux

ssh [username]@saga.sigma2.no

Hostnames and usernames can be defined by creating or editing the file ~/.ssh/config .

This can be done using the text editor vim

vim ~/.ssh/config

Press i to insert text

Host saga
   HostName = saga.sigma2.no
   user [username]

Press escape to exit insert mode, and then :wq to 'write' and 'quit'.

Login is then simplified

ssh saga

Copy files from cluster to current folder (.)

scp saga:[path]/[filename] .

Copy files to the home directory on the cluster

scp [filename] saga:

PuTTY and WinSCP

PuTTY is an ssh client for Windows that can be downloaded from www.putty.org.

WinSCP is an scp client for Windows that can be downloaded from winscp.net.

Working in UNIX

Basic commands

Use TAB to autocomplete commands, paths and filenames.

Use man [command] to view the manual for any command.

Navigating the filesystem

Command	Description
ls	List files and directories in current directory
mkdir [directoryname]	Make a directory
cd [directoryname]	Change path to another directory
pwd	Display current path
cd ..	Change path to parent directory
cp [path]/[filename] .	Copy file to current directory
cp [filename] [directoryname]	Copy file to another directory
mv [filename] [path]	Move file to another directory
mv [filename] [newfilename]	Change the name of a file
cp -r [directory] [path]	Copy directory to new location
rm [filename]	Delete file
rm -r [directoryname]	Delete directory and its contents

Reading text files

Command	Description
less	View text file. Shift-F to view live updates to file
head	Display top 10 lines of text file. Options: -n [count] to specify number of lines
tail	Display bottom 10 lines of text file. Options: -n [count] to specify number of lines
grep [pattern]	Display each line in text file containing text specific text/symbol pattern
cat	Concatenate text files sequentially. Use > [filename] to write to file.

Filesystem on Saga

Home directory

/cluster/home/[username]

Project folder

/cluster/projects/[project number]

• NN4604K: create a subfolder [username] to store your files

Check disk usage

dusage

Find and remove files in current folder and subfolders

find . -name "[filename]" -exec rm {} \;

Jobscript

/cluster/projects/nn4604k/jobfile

sbatch jobfile

Aliases and settings

Define shortcuts by adding aliases to ~/.bash_profile

alias l='ls -l'
alias la='ls -l -a'
alias ..='cd ..'
alias nn='cd /cluster/projects/[project number]'
alias q='squeue -u [username]'

Changes will take effect on next login or manually with source ~/.bash_profile

vim can be configured in ~/.vimrc . Turn on line numbers

set number