Log in and other preparations

Goal

The goal of this optional sessions is to make sure that you have fulledfilled the
- Prerequisites
- Preparations of environment to follow this course:
  you can log in
  
  you have have a folder to work in
  
  you can start a text editor
We will also download exercise snippets and solutions that you can work with. Use the tarball with exercises

Learning outcomes

Be able to login, where you are

Cluster-specific approaches

The course is a cooperation between UPPMAX (Rackham, Snowy, Bianca), HPC2N (Kebnekaise), and LUNARC (Cosmos) and will focus on the compute systems at all these centres, as well as select resources at NSC (Tetralith) and PDC (Dardel).
Although there are differences we will only have few separate sessions.
Most participants will use NSC’s or Dardel’s systems for the course, as Rackham, Kebnekaise and Cosmos are only for local (UU, UmU, IRF, MIUN, SLU, LTU, LU) users.
The general information given in the course will be true for all/most HPC centres in Sweden.
- The examples will often have specific information, like module names and versions, which may vary. What you learn here should help you to make any changes needed for the other centres.
- When present, links to the Julia/R/Matlab documentation at other NAISS centres are given in the corresponding session.

Note

You were invited to be part of the course project.
If you already have research projects in any of the clusters you can use them. The CPU-hours required during the course will be low!

Tip

If you have user account and research project on Kebnekaise, follow the HPC2N track below.
If you have user account and research project on Cosmos, follow the LUNARC track below.
If you have user account and course/research project on Rackham, follow the UPPMAX track below.
If you have user account and course/research project on Tetralith, follow the NSC track below.
If you have user account and course/research project on Dardel, follow the PDC track below.

To be done before

Follow the steps in the emailed instructions.
First time you need to use a terminal to set password
When password is set you can begin to use ThinLinc as well.

Step 1: Log in!

For beginners: use the bold login method.

HPC cluster	Login method [*]	Documentation	Video
COSMOS	SSH client	here	here
COSMOS	Local ThinLinc client	here	here
Dardel	SSH client	here	here
Dardel	Local ThinLinc client	here	here
Kebnekaise	SSH client	here	here
Kebnekaise	Local ThinLinc client	here	here
Kebnekaise	Remote desktop website	here	here
Rackham	SSH client	here	here
Rackham	Local ThinLinc client	here	here
Rackham	Remote desktop website	here	here
Tetralith	SSH client	here	here
Tetralith	Local ThinLinc client	here. Scroll down to ThinLinc	here

What are the differences between these login methods?

These are the ways to access your HPC cluster and some of their features:

How to access your HPC cluster	Features	How it looks like
Remote desktop via a website	Familiar remote desktop, clumsy, clunky, no need to install software, not available at all centers
Remote desktop via a local ThinLinc client	Familiar remote desktop, clumsy, need to install ThinLinc
Console environment using an SSH client	A console environment, powerful, need to install an SSH client

Use Thinlinc or terminal?

It is up to you!
Graphics come easier with Thinlinc
For this course, when having many windows open, it may sometimes be better to run in terminal, for screen space issues.

Warning

When logging in to UPPMAX the first time in ThinLinc, choose XFCE desktop.
On HPC2N, you will use the MATE desktop as default.
Whe logging in to LUNARC the first time in ThinLinc, choose GNOME Classis Desktop.
On NSC you will use XFCE desktop as default.

Warning

When you login to Cosmos, whether through ThinLinc or regular SSH client, you need 2FA
- https://lunarc-documentation.readthedocs.io/en/latest/getting_started/login_howto/
- https://lunarc-documentation.readthedocs.io/en/latest/getting_started/authenticator_howto/

Warning

When you login to Tetralith, whether through ThinLinc or regular SSH client, you need 2FA
- https://www.nsc.liu.se/support/2fa/

Please log in to the cluster that you are using.

Log in to Rackham!

Terminal: ssh -X <user>@rackham.uppmax.uu.se

ThinLinc app: <user>@rackham-gui.uppmax.uu.se

ThinLinc in web browser: https://rackham-gui.uppmax.uu.se

Kebnekaise through terminal: <user>@kebnekaise.hpc2n.umu.se
Kebnekaise through ThinLinc, use: <user>@kebnekaise-tl.hpc2n.umu.se

Cosmos through terminal: <user>@cosmos.lunarc.lu.se
Cosmos through ThinLinc, use: <user>@cosmos-dt.lunarc.lu.se

Tetralith through terminal or Thinlinc: <user>@tetralith.nsc.liu.se

Dardel through terminal: <user>@dardel.pdc.kth.se
Dardel through ThinLinc: <user>@dardel-vnc.pdc.kth.se
- Warning! Only 30 Dardel users at a time can use ThinLinc. Do not count on it being available.

Keypoints

When you log in from your local computer you will always arrive at a login node with limited resources.
- You reach the calculations nodes from within the login node (See Submitting jobs section)
You reach UPPMAX/HPC2N/LUNARC/NSC clusters either using a terminal client or Thinlinc
Graphics are included in Thinlinc and from terminal if you have enabled X11.
Which client to use?
- Graphics and easy to use
- ThinLinc
Best integrated systems
- Visual Studio Code has several extensions (remote, SCP, programming IDE:s)
- Windows: MobaXterm is somewhat easier to use.

Step 2: Make a work directory

Directory names OK?

If not already: create a working directory where you can code along.

We recommend creating it under the course project storage directory

Example. If your username is “mrspock” and you are at UPPMAX, then we recommend you create this folder:
```
$ mkdir /proj/hpc-python-uppmax/mrspock/
```

Create a working directory where you can code along.
- Example. If your username is bbrydsoe and you are at HPC2N, then we recommend you create this folder:
```
$ mkdir /proj/nobackup/hpc-python-spring/bbrydsoe/
```

Create a working directory in your home space where you can code along.
- Example. Create this folder:
```
$ mkdir $HOME/hpc-python
```

Create a working directory where you can code along.
- Example. If your username is jlpicard and you are at NSC, then we recommend you create this folder:
```
$ mkdir /proj/hpc-python-spring-naiss/users/jlpicard
```

Create a working directory where you can code along.
- Example. If your username is sevenof9 and you are at PDC, then we recommend you create this folder:
```
$ mkdir /cfs/klemming/projects/supr/hpc-python-spring-naiss/sevenof9/
```

Test an editor

Learn how to use an text editor at Use a text editor.

Download and extract the tarball with exercises

Learn how to download and extract the tarball with exercises at Use the tarball with exercises.