Difference between revisions of "Getting started"

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<code> ssh [username]@saga.sigma2.no </code>
 
<code> ssh [username]@saga.sigma2.no </code>
  
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Hostnames and usernames can be saved by creating or editing the file <code> ~/.ssh/config </code>.
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Hostnames and usernames can be saved by creating or editing the config file using for instance the vim text editor
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This can be done using the text editor vim
 
  
 
<code> vim ~/.ssh/config </code>
 
<code> vim ~/.ssh/config </code>
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==Working in UNIX==
 
==Working in UNIX==
 
===Basic commands===
 
===Basic commands===
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Learn to use TAB to autocomplete commands, paths and filenames.
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Learn to use the TAB key to autocomplete commands, paths and filenames.
  
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Learn to use <code> man [command] </code> to view the manual for any command.
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Learn to view the manual for any command: <code> man [command] </code>  
  
 
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|-
 
|-
 
|<code> less </code>
 
|<code> less </code>
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|View text file. <code> Shift-F </code> to view live updates to file
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|View text file. View live updates to end of file: <code> Shift-F </code>
 
|-
 
|-
 
|<code> head </code>
 
|<code> head </code>
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|Display top 10 lines of text file. Options: <code> -n [count] </code> to specify number of lines
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|Display top 10 lines of text file. Specify number of lines: <code> -n [count] </code>
 
|-
 
|-
 
|<code> tail </code>
 
|<code> tail </code>
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|Display bottom 10 lines of text file. Options: <code> -n [count] </code> to specify number of lines
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|Display bottom 10 lines of text file. Specify number of lines: <code> -n [count] </code>
 
|-
 
|-
 
|<code> grep [pattern] </code>
 
|<code> grep [pattern] </code>
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|Display each line in text file containing text specific text/symbol pattern
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|Display each line in text file containing text specific text/symbol pattern.
 
|-
 
|-
 
|<code> cat </code>
 
|<code> cat </code>
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|Concatenate text files sequentially. Use <code> > [filename] </code> to write the output to a file.
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|Concatenate text files sequentially. Write the output to a file: <code> > [filename] </code>
 
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|}
  

Revision as of 17:26, 26 September 2021

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 and scp

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 config file using for instance the vim text editor

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 the TAB key to autocomplete commands, paths and filenames.

Learn to view the manual for any command: man [command]

Navigating the filesystem
Command Description
ls List files and directories in current directory
mkdir [directoryname] Make a directory
cd [directoryname] Change current 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 and its contents to new location
rm [filename] Delete file
rm -r [directoryname] Delete directory and its contents
Path and filename designation
Symbol Description
. Current directory
.. Parent directory
~ Home directory
/ Root directory
* Any text pattern
 ? Any symbol
Reading text files
Command Description
less View text file. View live updates to end of file: Shift-F
head Display top 10 lines of text file. Specify number of lines: -n [count]
tail Display bottom 10 lines of text file. Specify number of lines: -n [count]
grep [pattern] Display each line in text file containing text specific text/symbol pattern.
cat Concatenate text files sequentially. Write the output to a file: > [filename]

Filesystem on Saga

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

/cluster/home/[username]

Project folder: Run jobs and store output files in a subfolder called your username

/cluster/projects/[project number]/[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]'

You can also add commands such as automatically changing directory to the project folder upon login.

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

Bash scripting

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