Pre-requirements

Technical on local computer

• We recommend that you set up both:

  • a terminal on you computer that can handle X11 graphics AND

  • install the “Remote Access Desktop application” ThinLinc, see below.

Basic terminal clients

If you are in a hurry or get problems in the installation procedure you can do most of the work from these first steps.

MacWindows

• Use terminal (e.g. from Launchpad) or iTerm2

Mac built-in terminal

• iTerm2 goodies:

  • You can save hosts for later.

  • Drag and drop scp

Add X11 graphics to terminal

MacWindows

• Download and install XQuartz or other X11 server for Mac OS

  • https://www.xquartz.org

• Start terminal (e.g. from Launchpad) or iTerm2

X11-forwarding from the command line (generally)

• Graphics can be sent through the SSH connection you’re using to connect

  • Use primarily ssh -X <…> and secondary ssh -Y <…>

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

  • https://docs.hpc2n.umu.se/documentation/access/#ssh__x11__forwarding

  • https://www.nsc.liu.se/support/graphics/

• The X servers that enables graphics are needed, as mentioned above!

  • When starting a graphical program, a new window will open, but your terminal will be “locked”.

  • Run using “&” at the end to run it as a background process e.g. “xeyes &” or “gedit &”

• Alternatively, use <ctrl>-z to put a graphical window to sleep and type “bg” to make this process work in the background.

ThinLinc

• Rackham, Kebnekaise, Bianca, Cosmos, and Tetralith all offer graphical login.

• This gives you a desktop environment, as if you were working on your own computer!

• Install ThinLinc client

  • https://www.cendio.com/thinlinc/download

• Login to ThinLinc desktop application by providing the following

RackhamKebnekaiseCosmosTetralith

• server: rackham-gui.uppmax.uu.se

• username

• password

Try to log in

• 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

• Using ThinLinc to log in to Rackham may require 2FA

  • https://www.uppmax.uu.se/support/user-guides/setting-up-two-factor-authentication/

• 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.

• Test it!

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)

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 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

Coding

• Basic knowledge of Python.

• We won’t test your skills though.

• Rather you will learn to understand the ecosystems and navigations for using Python on a HPC cluster.

See below for links to useful material if you need a refresher before the course.

• More important is how to work in Linux and especially Bash

Linux

• some familiarity with the LINUX command line (recordings from HPC2N:s Linux intro and UPPMAX Intro course),

  • Short introduction

  • Linux “cheat sheet”

  • UPPMAX

    • Linux

    • Basic commands

    • Whole intro course material

    • UPPMAX software library

  • HPC2N

    • HPC2N Linux tutorial

    • HPC2N’s Linux intro course material (including link to recordings)

    • HPC2N’s YouTube channel video playlist on Linux

Material for improving your programming skills

First level

The Carpentries teaches basic lab skills for research computing.

• Software carpentry courses/material

Second level

Code Refinery develops and maintains training material on software best practices for researchers that already write code.

• Their material addresses all academic disciplines and tries to be as programming language-independent as possible.

• Code refinery lessons

Third level

ENCCS (EuroCC National Competence Centre Sweden) is a national centre that supports industry, public administration and academia accessing and using European supercomputers. They give higher-level training of programming and specific software.

• ENCCS training material

Understanding clusters

The HPC centers UPPMAX, HPC2N, LUNARC, and NSC

Four HPC centers

• There are many similarities:

  • Login vs. calculation/compute nodes

  • Environmental module system with software hidden until loaded with module load

  • Slurm batch job and scheduling system

  • pip install procedure

• … and small differences:

  • commands to load Python, Python packages

  • sometimes different versions of Python, etc.

  • slightly different flags to Slurm

• … and some bigger differences:

  • UPPMAX has three different clusters

    • Rackham for general purpose computing on CPUs only

    • Snowy available for local projects and suits long jobs (< 1 month) and has GPUs

    • Bianca for sensitive data and has GPUs

• HPC2N has Kebnekaise with GPUs

• LUNARC has Cosmos with GPUs (and Cosmos-SENS)

• NSC has several clusters

  • BerzeLiUs (AI/ML, NAISS)

  • Tetralith (NAISS)

  • Sigma (LiU local)

  • Freja (R&D, located at SMHI)

  • Nebula (MET Norway R&D)

  • Stratus (weather forecasts, located at NSC)

  • Cirrus (weather forecasts, located at SMHI)

  • We will be using Tetralith, which also has GPUs

• Conda is recommended only for UPPMAX/LUNARC/NSC users

Warning

• At HPC2N, UPPMAX, LUNARC, and NSC we call the applications available via the module system modules.

• https://www.uppmax.uu.se/resources/software/module-system/

• https://docs.hpc2n.umu.se/documentation/modules/

• https://lunarc-documentation.readthedocs.io/en/latest/manual/manual_modules/

• https://www.nsc.liu.se/software/modules/

To distinguish these modules from the python modules that work as libraries we refer to the later ones as packages.

What is a cluster?

• Login nodes and calculations/computation nodes

• A network of computers, each computer working as a node.

• Each node contains several processor cores and RAM and a local disk called scratch.

• The user logs in to login nodes via Internet through ssh or Thinlinc.

  • Here the file management and lighter data analysis can be performed.

• The calculation nodes have to be used for intense computing.

Common features

• Intel (and for HPC2N/LUNARC, also AMD) CPUs

• Linux kernel

• Bash shell

Overview of the UPPMAX systems

Overview of the HPC2N system

Overview of the LUNARC system

Overview of the NSC systems