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Log in to Rackham

Here we describe how to log in to Rackham

Objectives

  • We'll go through platform specific (Mac/Linux/Windows) ways to log in to UPPMAX
  • See different clients
  • Enable graphics

Warning

If you lack a user account, visit the UPPMAX page on user accounts

General understanding

  • When logging in to UPPMAX from your local computer you will arrive to your home folder at the login node of an UPPMAX cluster.
  • 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 ~]$
  • 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 ~]

Quick start log in!

  • Below you find how to log in
  • Further down we present other procedures to reach Rackham, depending on your planned work.

Log in with a terminal, omitting support for graphics

  • Start terminal (e.g. from Launchpad) or iTerm2 to run ssh
$ 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
  • Start a terminal (see below) to run ssh:
$ 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.

Terminal

  • The ssh (secure shell) client putty

    • You can save hosts for later.
    • No graphics.

  • Windows Powershell terminal can also work

  • Windows command prompt can also work

  • Git bash

Working on Rackham

  • Now we present alternatives to work on Rackham

Alternative ways to log in and work

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

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

  • use sophistic graphical interfaces like RStudio and MATLAB etcetera

    • ThinLinc application

Terminals (see above)

Terminal with X11 server and light graphics

How do I know XQuartz has been installed?

As far as we know: you cannot check this directly: you will have to find out by running an application of Rackham that uses this. See below :-)

  • Start terminal (e.g. from Launchpad) or iTerm2 to run ssh:
$ ssh -X [username]@rackham.uppmax.uu.se

where [username] is your UPPMAX username and -X enables X forwarding. For example, if your UPPMAX username is sven, this wold be ssh -X sven@rackham.uppmax.uu.se

How do I know XQuartz has been installed?

See SSH X forwarding.

Spoiler: use xeyes

  • Download and install ONE of the X-servers below (to enable graphics)

  • or...

  • Install a ssh (secure shell) program with built-in X11 and sftp file manager

    • MobaXterm
    • sftp frame makes it easy to move, upload and download files.
    • ... though downloading from remote host to local is usually easier.
    • tabs for several sessions
$ ssh -X <username>@rackham.uppmax.uu.se

Caption

  • Or even better, create and save a SSH session, as shown in image below.
    • This allows you to use MobaXterm as a file manager and to use the built-in graphical texteditor.
    • You can rename the session in the Bookmark settings tab.

Caption

X-forwarding from the command line (generally)

X forwarding allows graphics to be sent through the SSH client connection you’re using to connect

  • Use 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.
Test log in to Rackham, using your terminal
  • First try:
$ ssh -X <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 &

Remote desktop

Rackham's remote desktop environment

You can also login to Rackham's remote desktop environment. This gives you a desktop environment, as if you were working on your own computer!

You can do so:

Remote desktop via the web

Go to https://rackham-gui.uppmax.uu.se.

Remote desktop via a ThinLinc client

Use the ThinLinc client from https://www.cendio.com/thinlinc/download

  • Set the server name to rackham-gui.uppmax.uu.se. NB: leave out the https://www.!

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)

Visual Studio Code (not covered here)

How to use Visual Studio Code/Codium on Rackham in detail?

See a detailed guide how to use Visual Studio Code/Codium on Rackham here

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.