Getting started

User access

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 to the cluster with a terminal app on UNIX, macOS or Windows Subsystem for Linux

ssh [username]@saga.sigma2.no

Hostnames and usernames can be saved 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

Learn to use TAB to autocomplete commands, paths and filenames.

Learn to 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 the output to a file.

Filesystem on Saga

Home directory: mainly for personal files, scripts etc. due to limited storage space

/cluster/home/[username]

Project folder: running jobs and store large output files

/cluster/projects/[project number]

• NN4604K: create a subfolder [username]

Check disk usage and storage quota for home directory and project folder

dusage

Find and remove files matching [filename] in current folder and subfolders

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

Jobscript

Saga has 40 cores per node www.sigma2.no/systems

#SBATCH --job-name=[jobname]
#SBATCH --account=[project number]
#SBATCH --time=hh:mm:ss
#SBATCH --mem-per-cpu=4600M
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40

Copy files to temporary job folder

cp [filenames] $SCRATCH

Copy files from job folder when job completes. Savefile will also copy files if the job crashes.

savefile [filenames] 

The working folder can be accessed while a job is running /cluster/work/jobs/[slurm-id]

/cluster/projects/nn4604k/jobfile

Submit job to queue sbatch jobfile

View the queue squeue -u [username]

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 to easily jump to a specific line using  :[line number]

set number