Difference between revisions of "Getting started"
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==Login== | ==Login== | ||
===ssh=== | ===ssh=== | ||
| − | ssh can be used to login | + | ssh can be used to login to the cluster with a terminal app on UNIX, macOS or Windows Subsystem for Linux |
<code> ssh [username]@saga.sigma2.no </code> | <code> ssh [username]@saga.sigma2.no </code> | ||
| − | Hostnames and usernames can be | + | Hostnames and usernames can be saved by creating or editing the file <code> ~/.ssh/config </code>. |
This can be done using the text editor vim | This can be done using the text editor vim | ||
| Line 67: | Line 67: | ||
==Working in UNIX== | ==Working in UNIX== | ||
===Basic commands=== | ===Basic commands=== | ||
| − | + | Learn to use TAB to autocomplete commands, paths and filenames. | |
| − | + | Learn to use <code> man [command] </code> to view the manual for any command. | |
{| class="wikitable" | {| class="wikitable" | ||
| Line 131: | Line 131: | ||
|- | |- | ||
|<code> cat </code> | |<code> cat </code> | ||
| − | |Concatenate text files sequentially. Use <code>> [filename] </code> to write to file. | + | |Concatenate text files sequentially. Use <code> > [filename] </code> to write the output to a file. |
|} | |} | ||
===Filesystem on Saga=== | ===Filesystem on Saga=== | ||
| − | Home directory: personal files | + | Home directory: mainly for personal files, scripts etc. due to limited storage space |
<code> /cluster/home/[username] </code> | <code> /cluster/home/[username] </code> | ||
| − | Project folder: | + | Project folder: running jobs and store large output files |
<code> /cluster/projects/[project number] </code> | <code> /cluster/projects/[project number] </code> | ||
| Line 149: | Line 149: | ||
<code> dusage </code> | <code> dusage </code> | ||
| − | Find and remove files in current folder and subfolders | + | Find and remove files matching [filename] in current folder and subfolders |
<code> find . -name "[filename]" -exec rm {} \; </code> | <code> find . -name "[filename]" -exec rm {} \; </code> | ||
===Jobscript=== | ===Jobscript=== | ||
| − | + | Saga has 40 cores per node [https://www.sigma2.no/systems www.sigma2.no/systems] | |
#SBATCH --job-name=[jobname] | #SBATCH --job-name=[jobname] | ||
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savefile [filenames] | savefile [filenames] | ||
| − | The | + | The working folder can be accessed while a job is running |
<code> /cluster/work/jobs/[slurm-id] </code> | <code> /cluster/work/jobs/[slurm-id] </code> | ||
<code> /cluster/projects/nn4604k/jobfile </code> | <code> /cluster/projects/nn4604k/jobfile </code> | ||
| − | |||
Submit job to queue | Submit job to queue | ||
| Line 193: | Line 192: | ||
| − | vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers to | + | vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers to easily jump to a specific line using <code> :[line number] </code> |
set number | set number | ||
===Bash scripting=== | ===Bash scripting=== | ||
Revision as of 16:58, 26 September 2021
Contents
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.
| 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 |
| 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
