Navigating in Sigma2's HPC server

Basic bash commands

Communication between you and the HPC server is usually done through an interface named a bash and no Graphical User Interface (GUI) is provided

Here is how the bash looks like

[bencretois@login-5.SAGA ~]$

Communicating with a bash requires learning a particular programming language, bash scripting. Below we provide a list of selected commands that will allow you to navigate in HPC server:

Change directory

Command:

  • cd + path to the directory

Output:

[bencretois@login-5.SAGA ~]$ cd deepexperiments/
[bencretois@login-5.SAGA ~/deepexperiments]$

Get to the previous directory

Command:

  • cd .. -> get to the previous directory

Output:

[bencretois@login-5.SAGA ~/deepexperiments]$ cd ..
[bencretois@login-5.SAGA ~]$

List the content of a directory

Command:

  • ls + name of a directory - Note that ls by default list the files of your current directory

Output:

[bencretois@login-5.SAGA ~/deepexperiments]$ ls

bash_cheatsheet.md   Dockerfile             list_ignore.txt  poetry.lock     runs            sync.sh
bayesianfy.ipynb     docker_run_jupyter.sh  models           pyproject.toml  scripts         utils
deepexperiments.sif  jobs

get the path of your current directory

Command:

  • pwd

Output:

[bencretois@login-5.SAGA ~]$ pwd
/cluster/home/bencretois

Create a new folder

Command:

  • mkdir + name of the folder you want to create

Output:

[bencretois@login-5.SAGA ~]$ mkdir new_folder
[bencretois@login-5.SAGA ~]$ ls
deepexperiments new_folder

Learning more bash commands

Bash command* are very well documented on Internet and if you wish to learn more you can begin here.

Bash commands specific to Sigma2's HPC

There are also some useful commands specific to your Sigma2 account:

List your projects

Command:

projects -> list your projects

Output:

[bencretois@login-5.SAGA ~]$ projects
nn5019k

Look at used space and allocated quota for your projects

Command:

dusage -> . Note that space used is what you are currently using and quota is the limit.

Output:

[bencretois@login-5.SAGA ~]$ dusage

dusage v0.1.4
                          path    backup    space used     quota    files      quota
------------------------------  --------  ------------  --------  -------  ---------
                      /cluster        no       5.6 GiB         -   38 819          -
      /cluster/home/bencretois       yes       4.6 GiB  20.0 GiB    1 311    100 000
/cluster/work/users/bencretois        no       0.0 KiB         -        0          -
     /cluster/projects/nn5019k       yes     938.2 MiB   1.0 TiB   37 508  1 000 000