Connection guides¶

This guide will show you how to connect to Kebnekaise’s login nodes, with specifics dependent on the operating system you are using.

Login nodes¶

Since Kebnekaise is a heterogenous system, the different architectures often have different software (versions). In order to see what is available, and to compile for the correct architecture, there are a few login nodes available.

In addition, there are different login nodes for regular SSH and for access through ThinLinc.

Kebnekaise main SSH login node

kebnekaise.hpc2n.umu.se

Kebnekaise ThinLinc login node

kebnekaise-tl.hpc2n.umu.se

Kebnekaise AMD Zen3 login node

kebnekaise-amd.hpc2n.umu.se

Kebnekaise ThinLinc AMD Zen3 login node

kebnekaise-amd-tl.hpc2n.umu.se

ThinLinc can be used as a stand-alone client and through a web browser. See below for details.

ThinLinc¶

ThinLinc is a cross-platform remote desktop server developed by Cendio AB. You can access Kebnekaise through ThinLinc.

ThinLinc is especially useful when you need to use software with a graphical interface, like INTEL VTune or MATLAB. Look at our MATLAB page for information about running MATLAB.

ThinLinc can be used as a standalone application and also through a browser with the Web Access desktop.

ThinLinc standalone client¶

The full capabilities of ThinLinc can be obtained with the standalone version. Here, you need to follow the next steps for installing ThinLinc.

Download and Install instructions

Download the ThinLinc client from https://www.cendio.com/thinlinc/downloadto your own workstation/laptop and install it.

Login to cluster login node¶

• Start the ThinLinc client (ThinLinc client, tlclient depending on your platform)
• Enter the name of the server: kebnekaise-tl.hpc2n.umu.se and then enter your own username at HPC2N under “Username”:
  • If you don’t see the Options button, click on Advanced
  • Go to “Options” -> “Security” and check that authentication method is set to “password”.
  • Go to “Options” -> “Display” and mark “Windowed”
  • Go to “Options” -> “Local Devices” and uncheck Sound, Serial ports, Drives, Printer, Smart card readers
  • Enter your HPC2N password.
  • Click “Connect”
  • Click “Continue” when you are being told that “the server’s host key is not in the registry”.
  • After a short time, the ThinLinc desktop opens, running Mate. It is fairly similar to the Gnome desktop.
  • All your files on HPC2N should now be available.

Web Access desktop¶

On your local web browser, enter https://kebnekaise-tl.hpc2n.umu.se:300/ in the address bar. This will display the login box:

Here, you can type the username and password for HPC2N. This web browser version can be handy to get started with ThinLinc or if you do not want to install another software in your machine. Also, if you are working mainly with a tablet.

General ThinLinc usage (both versions)¶

Opening a Linux terminal in the ThinLinc desktop¶

To start a terminal window, go to the menu at the top. Click “Applications” → “System Tools” → “MATE Terminal”.

Disconnect or logout from the ThinLinc desktop¶

When you want to shutdown the ThinLinc connection, this can be done in two ways, either Disconnect or Logout.

• Disconnect
  • Keeps your thinlinc session running on the login node, making it possible for you to return to the same spot when you reconnect.
    • Only use this when you are actively working in e.g. Matlab over a few days, otherwise use “Logout”. Doing this keeps the login node quick and fast for active users.
  • Note! Always save your work before leaving since the login nodes will reboot now and then due to OS and security updates.
  • The following two ways are equivalent, both uses the top menu bar. Use one of them
    • “Applications” → “HPC2N” → “Disconnect ThinLinc Session”
    • “The blueish HPC2N icon to the right” → “Disconnect ThinLinc Session”
  • In the Web Access version, there is a button in the Toolbar to disconnect the session
• Logout
  • Will terminate your ThinLinc session on the login node.
  • Note! This does not affect any jobs in the batch queue or jobs running on the cluster, and any finished jobs will be available when you login again.
  • The following two ways are equivalent, both uses the top menu bar. Use one of them
  • “Applications” → “HPC2N” → “Logout ThinLinc Session”
    • “The blueish HPC2N icon to the right” → “Logout ThinLinc Session”

Reconnecting to an older ThinLinc session¶

If you have a running ThinLinc session (that you disconnected from) and there is a problem with the ThinLinc session when you connect again. The best way to solve this is to:

• Logout from the current ThinLinc session
• Open the client or the Web Access desktop again, but this time specify “End existing session” in the dialog or through the command options.
  • Do the final step and login

Connecting from Windows¶

If you are connecting to HPC2N from a Windows system, you need to install an ssh client to connect. The recommended way is by using ThinLinc, but in some cases using just a terminal window is preferred, and this section looks at SSH clients for that. Several exists, both commercial and free. Here are some of the more common ones:

• PuTTY (free)
• Cygwin (free)
• MobaXterm (Commercial, but basic feature version is free)

If you want to be able to open graphical displays (say for opening the Matlab graphical interface), you need an X11 server. These are commonly used:

• Xming (free)
• Cygwin (free)
• MobaXterm (Commercial, but basic feature version is free)

You also need to transfer files between your own home computer and HPC2N’s systems. You need to use a secure protocol, so either sftp or scp will work, but not standard ftp.

• WinSCP (Commercial)
• FileZilla (only sftp) (free)
• PSCP/PSFTP (free)
• Cyberduck (free)
• MobaXterm (Commercial. The free version has limits to the file transfers)

In this section we will give brief examples for Cyberduck, WinSCP, MobaXterm, PuTTy, Cygwin, and Xming.

In all cases, we strongly advice against saving passwords.

The simplest way to connect to HPC2N is to use either PuTTy together with Xming, or to use MobaXterm, unless you need a Linux-like environment on your Windows machine (CygWin).

SSH clients and X11 servers¶

PuTTY¶

• Download PuTTY from here.
• Get the Zip file which contains all of PuTTY, PSCP, and PSFTP.
• Unzip the downloaded zip-file, then run “putty.exe”.
• In the window that opens, under ‘Session’ enter the host name.
  • In the picture, it is entered for Kebnekaise (kebnekaise.hpc2n.umu.se).
• When you click ‘Open’ you will be prompted for your HPC2N username and password.
  • In the picture below, you can see how it can look when logged in.

PuTTy and X11 forwarding¶

If you need to open graphical interfaces from the remote system on your home computer then you need to enable X11 forwarding.

Example for Xming

• Download and install an X server (for instance Xming)
  • Start PuTTy
  • On the left side, scroll down to ‘Connection’ and click to open the tree if it is not opened already
  • Click to open the ‘SSH’ subcategory, and then click on ‘X11’.
  • Make sure ‘Enable X11 forwarding’ is checked. Note that this needs to be done for each saved session.
  • Some older versions of PuTTY does not work correctly with X11 forwarding from our systems. Try upgrading to version 0.69 (known to work) or newer.

Xming X server¶

In order to use X11 forwarding in PuTTy (or similar), you need to run Xming before starting PuTTy.

• Download from the Xming page or directly from Sourceforge
  • Install (default options should work)
  • Launch Xming

You can now launch (for instance) PuTTY SSH client and enable X11 forwarding as shown earlier on this page.

MobaXterm¶

This program has both a freeware and a paid version. The freeware version works well for most users. It combines SSH client, X11 server, and SFTP file browser. NOTE that the free version has a number of limits, such as a time-limit on the filebrowser. You may therefore wish to use either FileZilla or WinScp for file transfers instead because of that.

It exists both as an installable version and as a single executable that can be run from an USB stick.

• Download from here.
  • Get the Free / Home edition
  • Extract it

There is a demo on their homepage, but here are the basic steps to connect to HPC2N’s systems.

• Start the MobaXterm program
  
  
  
• Click ‘Session’ and then click ‘SSH’ in the new window that opens. Fill in the name of the remote host (kebnekaise.hpc2n.umu.se). Check ‘Specify username’ and fill in your own username (otherwise it will ask for your username when you connect to the system). Click ‘OK’. (Your settings will be saved and you can login again by clicking on the host name under ‘Saved sessions’ on the start up window).
  
  
  
• A new window will open, asking for your HPC2N password.
  
  
  
• When you have entered that, you will be logged on to the system (Kebnekaise). Note that there is a file browser on the left with your files on the HPC2N system.
  
  
  
• Since an X11 server is running and the display is sat automatically, you can now open new windows/displays/graphical interfaces from the host you are logged in to, on your own local screen. - You can also transfer files between your local system and the remote system (HPC2N) by using the file browser. Choosing download/upload or just drag-drop works. You can also do things like editing files on the remote system by double-clicking on a file in the file browser or right-clicking and choosing what to do. NOTE that there is a time-limit on the file browser in the free version, and you can not expect to do anything but minor edits through it this way.
  
  
  

Cygwin - installation¶

This is somewhat more involved, and mostly only worth it if you intend to use Cygwin locally on your Windows computer, in order to run a Linux-like environment. A longer description of the installation process can be found on Cygwin’s pages.

• Download “setup.exe” from the Cygwin page
• After the initial file downloads, you will get the option to ’Select Package’. Go through and check any you think you would like, as long as you make sure the ones below are selected from “X11” category
  • xorg-server (required, the Cygwin/X X Server)
  • xinit (required, scripts for starting the X server: xinit, startx, startwin (and a shortcut on the Start Menu to run it), startxdmcp.bat)
  • xorg-docs (optional, man pages)
  • X-start-menu-icons (optional, adds icons for “X Clients” to the Start menu)
  • You may also select any X client programs you want to use, and any fonts you would like to have available.
  • You may also want to ensure that the inetutils or openssh packages are selected if you wish to use telnet (not at HPC2N) or ssh connections to run remote X clients.
• Under “Graphics”, it is recommended to select opengl packages.
• Install

Cygwin - connecting¶

The custom XWin startup utility startxwin starts the X server in multiwindow mode. startxwin is included in the xinit package, which you should have installed if you followed the description above.

Run startxwin by doing one of:

• Using the “XWin Server” shortcut under “Cygwin-X” on the Start Menu
• Starting /usr/bin/startxwin in a Cygwin shell, by typing
  
  • startxwin

You can get more documentation for startxwin by typing man startxwin in the Cygwin shell.

File transfers¶

There are many options, some free, some commercial. Some of the more common ones are:

• WinSCP
• Cyberduck
• FileZilla

WinSCP¶

• Download from here. Pick ‘Installation package’.
• Install. During the setup you will be asked to choose between ‘Commander’ and ‘Explorer’. ‘Commander’ is probably the best for most people, but it is your choice.
  
  
  
• When the program has installed, start it. Click ‘New Session’. Enter the name of the remote host (kebnekaise.hpc2n.umu.se or abisko.hpc2n.umu.se). Put in your username and password. You can save the session settings so you do not have to enter it next time, but can just click it in the list that will be on the left, but we strongly recommend that you in that case do not save the password.
  
  
  
• When you log on to a remote host for the first time you will be asked if you want to continue connecting to an unknown server and add its host key to a cache. Say ‘Yes’. You will now be logged in to HPC2N, to your home directory. You can change directories by clicking, and you can upload/download files with drag-drop.
  

Cyberduck¶

• Download from here. Pick the “Cyberduck for Windows” even if you have Windows 10
• Install
• Start the program
  
  
  
• Click ‘Open Connection’ and enter the name of the remote host (kebnekaise.hpc2n.umu.se), Change the drop-down from ‘FTP’ to ‘SFTP’. Enter your username and password for HPC2N. We strongly recommend that you do NOT save the password.
  
  
  
• When you connect the first time to a remote host, you will be asked if you want to “Allow” or “Deny” an unknown fingerprint. Allow it.
• You are now logged in. You will end up in your home directory. You can change directories and you can upload/download files with drag-drop.
  
  
  

FileZilla¶

The FileZilla Client is free and supports FTP, FTP over TLS (FTPS) and SFTP. It is open source software distributed free of charge under the terms of the GNU General Public License. To connect to HPC2N, you need to use SFTP.

• Go to the FileZilla homepage and pick “Download FileZilla Client”.
• You will get to a page where you can pick “Download FileZilla Client” for your OS.
• Download and install.

Connecting from macOS¶

If you are connecting to HPC2N from a Mac, you have a number of options, aside from the built in SSH client “Terminal”. Several exists, both commercial and free. Here are some of the more common ones:

• ssh (built-in in “Terminal”)
• iTerm2 (free)

If you want to be able to open graphical displays (say for opening the Matlab graphical interface), you need an X11 server. It may or may not be installed as standard on Mac, depending on your version, but you can get it by installing XQuartz.

Another option would be to use ThinLinc which exists for all OS and gives you a desktop on Kebnekaise.

You also need to transfer files between your own home computer and HPC2N’s systems. You need to use a secure protocol, so either sftp or scp will work, but not standard ftp. These are some of the options:

• scp, sftp (built-in in “Terminal”)
• Cyberduck (free)
• FileZilla (free)

On this page we will give brief examples for ssh, Cyberduck and iTerm2, and also tell you how to get FileZilla.

In all cases, we strongly advice against saving passwords.

The simplest way to connect to HPC2N is to use the built-in ssh from “Terminal”.

SSH clients¶

ssh¶

• Launch “Terminal”
• Connect to Kebnekaise by doing:
  ssh -l username kebnekaise.hpc2n.umu.se
  where username is your username at HPC2N.
• If you need to open displays from the remote host on your local machine (say, for graphical interfaces to some software), you need to make sure XQuartz is installed and running. It should be set up automatically during install.

iTerm2¶

• Download iTerm2
• Install and launch
• Connect to Kebnekaise by doing:
  ssh -l username kebnekaise.hpc2n.umu.se
  where username is your username at HPC2N.
• You now have access to a number of nice features, like split panes, search, paste history, etc. Read more about that here.

File transfers¶

Cyberduck¶

• Download from here or from the Mac App Store
• Install
• Launch the program
• In the Open Connection dialog:
  • Select SFTP as protocol
  • Enter Server: kebnekaise.hpc2n.umu.se
  • Leave Port at default: 22
  • Enter your Username and Password at HPC2N
  • Click Connect
    
    
    
• When you connect the first time to a remote host, you will be asked if you want to “Allow” or “Deny” an unknown fingerprint. Allow it.
• You are now logged in. You will end up in your home directory. You can change directories and you can upload/download files with drag-drop. If you want, you can pick Bookmark -> New Bookmark from the top menu to save the connection settings for next time.
  
  
  

FileZilla¶

The FileZilla Client is free and supports FTP, FTP over TLS (FTPS) and SFTP. It is open source software distributed free of charge under the terms of the GNU General Public License. To connect to HPC2N, you need to use SFTP.

• Go to the FileZilla homepage and pick “Download FileZilla Client”.
• You will get to a page where you can pick “Download FileZilla Client” for your OS.
• Download and install.

Connecting from Linux/Unix¶

If you are connecting to HPC2N from a computer running Linux or Unix, you have a number of options. The most obvious and commonly used one is probably the built-in SSH client SSH. Several others exist, here are some of the more common ones:

• ssh (built-in in Linux terminal)
• PuTTY (free)

If you want to be able to open graphical displays (say for opening the Matlab graphical interface), you need an X11 server. It is installed per default on Linux/Unix systems.

Another option would be to use ThinLinc which exists for all OS and gives you a desktop on Kebnekaise.

You also need to transfer files between your own home computer and HPC2N’s systems. You need to use a secure protocol, so either sftp or scp will work, but not standard ftp. These are some of the options:

• scp, sftp (built-in in Linux terminal)
• cURL (free)
• FileZilla (free)
• PSFTP (Part of PuTTY. Free)

On this page we will give brief examples for ssh, scp/sftp, PuTTY, and FileZilla.

In all cases, we strongly advice against saving passwords.

The simplest way to connect to HPC2N is to use the built-in ssh from the terminal.

SSH clients¶

ssh¶

• Launch a terminal
• Connect to Kebnekaise by doing:
  ssh username@kebnekaise.hpc2n.umu.se
  where username is your username at HPC2N.
• If you need to open displays from the remote host on your local machine (say, for graphical interfaces to some software), you must use the flag -X (or -Y in some cases, if you need to type something in the display, like in MATLAB):
  ssh -X username@kebnekaise.hpc2n.umu.se

PuTTY¶

• Download PuTTY
• Unpack the tarball (For version 0.81 - adjust to fit: tar zxvf putty-0.81.tar.gz)
  • cd into the directory created by the above command (adjust to fit the version:

    cd unix/putty-0.81
    ./configure
    make
    

• It should build without problems. If you need the graphical utilities instead of just using it from the command line, you need Gtk+-1.2, Gtk+-2.0, or Gtk+-3.0 installed. More information can be found in the file README in the top putty directory.
  • Launch the graphical interface with ./putty from the unix directory under the PuTTY directory.
  • Enter kebnekaise.hpc2n.umu.se as the host:
    
    
    
  • The first time you connect you will be asked to accept the host key. Do so. Then login with your HPC2N username and password.
  • In order to use remote graphical interfaces, you need to enable X11 forwarding:
    • Scroll down in the left side of the PuTTY window to SSH.
    • Click the small arrow to get to the sub-options.
    • Click X11.
    • Check “Enable X11 forwarding”:
      
      
      

File transfers¶

scp/sftp¶

• scp and sftp should already be installed on your Linux installation

scp¶

scp - secure copy - copies files between hosts on a network. It uses ssh for data transfer.

For more info about scp, type: man scp on the command line.

sftp¶

sftp - secure file transfer program. Similar to FTP, but with many of the features of SSH included.

sftp username@remotehost

sftp username@remotehost:file ...

For more info about sftp, type: man sftp on the command line.

FileZilla¶

• Ubuntu: download and install with package manager (apt-get install filezilla)
• You can also download from FileZilla homepage if you are not using Ubuntu. Pick the one for “All platforms”. There is one for Debian (the executable is in the bin subdiretory and is called filezilla). If you are not using Debian or Ubuntu, you will probably have to compile from source.
• When building from source (You also need to download and install libfilezilla in much the same way):
  • uncompress the tarball (tar zxvf FILENAME), enter the directory created
  • mkdir compile
  • cd compile
  • ../configure
  • make
  • make install
• This is how it looks when FileZilla has started up:
  
  
  
• Connect by entering kebnekaise.hpc2n.umu.se in the “Host” field, then put in your HPC2N username under “Username”. We strongly recommend not saving your password.