Difference between revisions of "Getting started"
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− | ==User | + | ==User access== |
Go to [https://www.metacenter.no www.metacenter.no] > User Login (Passwords) > 1. Request a user account > HPC | Go to [https://www.metacenter.no www.metacenter.no] > User Login (Passwords) > 1. Request a user account > HPC | ||
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===Filesystem on Saga=== | ===Filesystem on Saga=== | ||
− | Home directory | + | Home directory: personal files and scripts due to limited storage space |
<code> /cluster/home/[username] </code> | <code> /cluster/home/[username] </code> | ||
− | Project folder | + | Project folder: run jobs and store large output files |
<code> /cluster/projects/[project number] </code> | <code> /cluster/projects/[project number] </code> | ||
− | *NN4604K: create a subfolder [username] | + | *NN4604K: create a subfolder [username] |
− | Check disk usage | + | Check disk usage and storage quota for home directory and project folder |
<code> dusage </code> | <code> dusage </code> | ||
Line 154: | Line 154: | ||
===Jobscript=== | ===Jobscript=== | ||
+ | |||
+ | |||
+ | #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 job folder can be accessed while the job is running | ||
+ | <code> /cluster/work/jobs/[slurm-id] </code> | ||
+ | |||
<code> /cluster/projects/nn4604k/jobfile </code> | <code> /cluster/projects/nn4604k/jobfile </code> | ||
+ | |||
+ | Submit job to queue | ||
<code> sbatch jobfile </code> | <code> sbatch jobfile </code> | ||
+ | |||
+ | View the queue | ||
+ | <code> squeue -u [username] </code> | ||
===Aliases and settings === | ===Aliases and settings === | ||
Line 167: | Line 190: | ||
alias q='squeue -u [username]' | alias q='squeue -u [username]' | ||
− | Changes will take effect on next login or manually with <code> source ~/.bash_profile </code> | + | Changes will take effect on next login or manually with <code> source ~/.bash_profile </code>. |
+ | |||
− | vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers | + | vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers to |
set number | set number | ||
===Bash scripting=== | ===Bash scripting=== |
Revision as of 23:19, 25 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 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.
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 to file.
|
Filesystem on Saga
Home directory: personal files and scripts due to limited storage space
/cluster/home/[username]
Project folder: run 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 in current folder and subfolders
find . -name "[filename]" -exec rm {} \;
Jobscript
#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 job folder can be accessed while the 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
set number