Login

Questions

• How to reach UPPMAX clusters?

• Where do I arrive when I log in? Login or calculation node?

• What clients should/could I use for my work at UPPMAX?

• How can I enable graphics?

Objectives

• We’ll go through platform specific (Mac/Linux/Windows) ways to log in to UPPMAX

• See different clients

• Enable graphics

• Try yourself!

Note

If you lack a user account, visit the Getting started page

The login

Login procedure

Which login procedure is best for You, depends on:

• Your background

• Your OS environment,

• Your planned interaction with your local computer

• Your planned use of graphics on the cluster

Login procedure

If you plan to:

• do day-to-day work where terminal shell is sufficient

  • Mac: Terminal, iTerm2

  • Linux: Terminal

  • Windows: Putty, Windows Powershell or even command prompt (CMD)

• interact with you local computer

  • Mac/Linux: you can always work in a local shell (mutiple terminal windows open)

    • (S)FTP browser: Filezilla, Cyberduck

  • Windows

    • (S)FTP browser: WinSCP

    • MobaXterm has built-in SFTP browser

    • you may benefit from having a Windows Subsystem for Linux, WSL(2)

• do day-to-day work with some graphical applications (X forwarding)

  • Mac: Terminal, iTerm2 + XQuartz

  • Linux: Terminal

  • Windows: MobaXterm

• integrate you cluster work with code development

  • All OS: Example Visual Studio Code

• use sophistic graphical interfaces like RStudio and MATLAB etcetera

  • ThinLinc application

• use Bianca

  • ThinLinc from web

General understanding

• When logging in to UPPMAX from your local computer you will arrive to your home folder at the login node.

• This means that only light analysis and and calculations should be made here.

• You will see this in the prompt after “@” as the clustername and a low number. For instance:

     [<user>@rackham3 linux_tutorial]$
  

• You will later learn how to reach the calculation nodes. Then the prompt states the node number with a single letter, like “r” for Rackham. For instance:

     [<user>@r484 linux_tutorial]
  

Terminals

MacWindows

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

$ ssh <username>@rackham.uppmax.uu.se

• “< >” prompts you to set the keyword specific for you or your needs. In the example above, this is basically your username.

• iTerm2 goodies:

  • You can save hosts for later.

  • Drag and drop scp

Terminal with X11 server and light graphics

MacWindows

• Download XQuartz or other X11 server for Mac OS

  • https://www.xquartz.org/

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

$ ssh -Y <username>@rackham.uppmax.uu.se

• -X Enables X11 forwarding.

• -Y Enables trusted X11 forwarding

X11-forwarding from the command line (generally)

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

  • Use primarily ssh -Y <...> or secondary ssh -X <...>

• 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 e.g. gedit to sleep and type “bg” to make last process in background.

Login to Rackham, using your terminal

• First try:

$ ssh -Y <username>@rackham.uppmax.uu.se

• If you receive errors or warnings, instead try:

$ ssh <username>@rackham.uppmax.uu.se

• If you do have X11 installed:

$ xeyes &

Graphical file manager

• This is good if you want to move many files between host and local and cannot use wildcards.

MacWindows

• For copying of files with sftp (secure file transfer protocol) between your client computer (where you are) and the cluster Filezilla can be the choice.

• Filezilla

• Cyberduck

Problems with installations?

Putty/Terminal without X11 is sufficient first days of the course!

Linux on your computer

Local Linux environment

• You may sometimes benefit from having a local Linux environment.

• Examples:

  • Mimic cluster environment to work with your local files and data as on the Cluster

  • get used to Linux (!)

• Mac is UNIX and very Linux-like

• Windows requires WSL (Windows subsystem for Linux)

For windows users who wants to get started with WSL (not covered here)

• Install WSL (Windows Subsystem for Linux)

  • https://docs.microsoft.com/en-us/windows/wsl/install-win10 (Links to an external site.)

  • Don’t forget to update to wsl2

• Install a distribution or a ssh (secure shell) program

  • Distribution such as ubuntu or

  • (recommended) a ssh program such as MobaXTerm

  • https://mobaxterm.mobatek.net/ (Links to an external site.)

    • sftp frame makes it easy to move, upload and download files.

• You may want to check this webpage as well!

  • https://hackmd.io/@pmitev/Linux4WinUsers (Links to an external site.)

Visual Studio Code (not covered in course)

• Intergrate you cluster work with code development

• SSH-remote from VS Code

• Remote development using Visual Studio Code on Alvis cluster

  • Similar to Rackham. Just change login details!

ThinLinc (all platforms!)

• Both Rackham and Bianca offer graphical login.

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

• On web:

  • https://rackham-gui.uppmax.uu.se

  • https://bianca.uppmax.uu.se

    • requires 2-factor authentication

• Or use the client (only for Rackham)

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

Try Thinlinc from web

• Try the web version now if you don’t already have the software installed!

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 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.