Prepare the environment

Goal

The goal of this page to make sure you can follow the course.

These are the things you need to follow the course:

• you can log in to at least one HPC cluster, in at least one way

• you can start a text editor

These are discussed in detail below

Note

• There will be an opportunity to get help with log in every morning of the workshop at 9:00.

• You are also welcome to join the On-boarding at 13:00 the day before the ordinary program starts.

Log in to one of the HPC systems covered in this course

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.

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/

See also

• Log in to Rackham

• Log in to Kebnekaise

• Log in to Cosmos

• Log in to Tetralith

  • Log in to Tetralith with graphical applications (scroll down for ThinLinc)

These are the ways to access your HPC cluster and how that looks like:

How to access your HPC cluster	How it looks like
Remote desktop via a website
Remote desktop via a local ThinLinc client
Console environment using an SSH client

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

How to access your HPC cluster	Features
Remote desktop via a website	Familiar remote desktop
	Clumsy and clunky
	Slow on UPPMAX
	No need to install software
	Works on HPC2N and UPPMAX
	Needs 2FA for UPPMAX
Remote desktop via a local ThinLinc client	Familiar remote desktop
	Clumsy
	Need to install ThinLinc
	Works on all centers
	Needs 2FA for UPPMAX
Console environment using an SSH client	A console environment may be unfamiliar
	Great to use
	Need to install an SSH client
	Works on all centers

Here is an overview of where to find the documentation and a video showing the procedure:

HPC Center	Method	Documentation	Video
HPC2N	SSH	here	here
HPC2N	Local ThinLinc client	here	here
HPC2N	Remote desktop website	here	here
LUNARC	SSH	here	here
LUNARC	Local ThinLinc client	here	here
NSC	SSH	here
NSC	Local ThinLinc client	here . Scroll down to ThinLinc
UPPMAX	SSH	here	here
UPPMAX	Local ThinLinc client	here	here
UPPMAX	Remote desktop website	here	here

Need help? Contact support:

HPC Center	How to contact support
HPC2N	Contact HPC2N support
LUNARC	Contact LUNARC support
UPPMAX	Contact UPPMAX support
NSC	Contact NSC support

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.

Text editors on the Clusters

• Nano

• gedit

• mobaxterm built-in

See also

• http://docs.uppmax.uu.se/software/text_editors/

• https://docs.hpc2n.umu.se/tutorials/linuxguide/#editors

Hint

• There are many ways to edit your scripts.

• If you are rather new.

  • Graphical: $ gedit <script> &

    • (& is for letting you use the terminal while editor window is open)

    • Requires ThinLinc or ssh -Y ... or ssh -X

  • Terminal: $ nano <script>

• Otherwise you would know what to do!

• ⚠️ The teachers may use their common editor, like vi/vim

  • If you get stuck, press: <esc> and then :q !

Demo

• Let’s make a script with the name example.py

$ nano example.py

• Insert the following text

# This program prints Hello, world!
print('Hello, world!')

• Save and exit. In nano: <ctrl>+O, <ctrl>+X

You can run a python script in the shell like this:

$ python example.py
# or
$ python3 example.py

Prepare the course environment

Prepare your environment now!

• Please log in to Rackham, Kebnekaise, Cosmos or other cluster that you are using.

• For graphics, ThinLinc may be the best option.

  • The ThinLinc app.

• Rackham has access for regular SSH, through a regular ThinLinc client and a through a web browser interface with ThinLinc:

  • SSH: rackham.uppmax.uu.se

  • ThinLinc client: rackham-gui.uppmax.uu.se

  • Web browser interface: https://rackham-gui.uppmax.uu.se

  • ThinLinc user guide at UPPMAX

    • 2FA may be needed, which can be handled by logging in with regular SSH, doing 2FA, logging out again, then there is a grace period of some minutes for you to login to ThinLinc. More here:

• Kebnekaise has access for regular SSH, ThinLinc clients, and through a web browser interface with ThinLinc:

  • SSH: kebnekaise.hpc2n.umu.se

  • ThinLinc client: kebnekaise-tl.hpc2n.umu.se

  • From webbrowser: https://kebnekaise-tl.hpc2n.umu.se:300/

• Cosmos:

  • SSH: cosmos.lunarc.lu.se

  • ThinLinc: cosmos-dt.lunarc.lu.se

    • 2FA required! For more info, go here:

Project

• The course project on UPPMAX (Rackham) is: naiss2024-22-1442

• The course project on HPC2N (Kebnekaise) is: hpc2n2024-142

• The course project on LUNARC (Cosmos) is: `` ``

UPPMAXHPC2NLUNARC

• Rackham: ssh <user>@rackham.uppmax.uu.se

• Rackham through ThinLinc,

  • use the App with

    • address: rackham-gui.uppmax.uu.se NB: leave out the https://www.!

    • user: <username-at-uppmax> NB: leave out the https://www.!

  • or go to <https://rackham-gui.uppmax.uu.se>

    • here, you’ll need two factor authentication.

• 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 to create a user folder in the project folder of the course and step into that:

  • cd /proj/hpc-python-fall

  • mkdir mrspock

  • cd mrspock