Logging In

Storage quotas and rates take effect July 1, 2018. PIs and projects over quota in $CENTER1 and $ARCHIVE need to reduce data volumes or contact RCS immediately. Inaction will result in project member inability to read or write data starting July 1, 2018.

To log into Chinook, you will need a user account and Secure Shell (SSH) client program.

Use the SSH client you have chosen and installed to connect to chinook.alaska.edu. When prompted for a username, either interactively or while configuring the client, you should provide your UA username. You will be prompted for a password upon opening an SSH connection. When this happens, enter your UA password.

The Chinook login nodes are intended to provide access to the cluster, to compile and modify applications and workflows, to manage data between the mounted filesystems, and to manage jobs. Any processing should be very limited and short to avoid impacting other users' activities. Batch or interactive serial or parallel processing should take place on the compute nodes. RCS reserves the right to terminate user processes or sessions to maintain the normal working order of the login nodes and the cluster.

Chinook is a shared resource and users are asked to be neighborly to your fellow colleagues and students. Some helpful tips to keep in mind:

  • The login nodes are only to be used for compiling and modifying applications/workflows, managing data between the mounted filesystems and managing jobs
  • Computationally intensive work is to be done on the compute nodes or Linux workstations
  • Run code in the debug queue before submitting it to the small, standard, bio, or analysis partition to ensure that it works correctly and utilizes all the resources available to the job
  • Jobs that are serial in nature or interactive, such as MATLAB, sholid be run in the bio or analysis partition to ensure maximum utilization of our limited resources
  • Jobs submitted to the bio or analysis partition must include the amount of memory the job will use (#SBATCH --mem=<size[units]>)
  • Include a time limit in your batch scripts to help improve the performance of the scheduler in prioritizing jobs


Linux users should use the OpenSSH client, which is already installed on your computer. Open a terminal session and run the following command to connect to Chinook:

ssh uausername@chinook.alaska.edu

replacing uausername with your UA username (e.g. jsmith2).

To enable graphical displays with through an X Window run:

ssh -Y uausername@chinook.alaska.edu


Mac users, like Linux users, should use the pre-installed OpenSSH client. See above for directions.

Unlike Linux, Mac operating systems do not come with an X Window server pre-installed. If you want to run any graphical applications on Chinook, we recommend installing XQuartz on your Mac and use:

ssh -Y uausername@chinook.alaska.edu


Windows users will need to download and install a third-party SSH client in order to log into Chinook. Here are a few available options:

  • PuTTY (open source, MIT license)
  • Secure Shell (proprietary, UA credentials required for download)

Installing PuTTY

RCS recommends that Windows users download and install PuTTY, a free-and-open-source ssh/rsh/telnet client.

  1. Download PuTTY from the official site.
  2. Run the PuTTY installer, and select "Next".
  3. By default, the installer will install in C:\Program Files (x86)\PuTTY under 64-bit Windows, and C:\Program Files\PuTTY under 32-bit Windows. Select "Next".
  4. The installer will prompt you for a Start Menu folder in which to create shortcuts. Select "Next".
  5. Select "Create a desktop icon for PuTTY", and select "Next".
  6. The installer will allow you to review your choices. Select "Install" after you have done so.
  7. The installer will require only a few seconds to install PuTTY on your computer. Select "Finish". As it closes, the installer will by default open PuTTY's readme file, which contains additional information on using the additional tools included with PuTTY.

Using PuTTY

Establishing a remote login session over SSH using PuTTY is reasonably straightforward. The following steps describe how to do this, turn on X11 forwarding, and save connection settings.

Remote Login via SSH

  1. Open PuTTY using the icon placed on your desktop by the PuTTY installer.
  2. For "Host Name", enter chinook.alaska.edu.
  3. Select "Open" to initiate an SSH connection request.
  4. You may receive a security alert warning you that your client cannot establish authenticity of the host you are connecting to. This warning is always displayed the first time your SSH client connects to any computer it has never connected before. If you have never connected to Chinook using this PuTTY installation, select "Yes".
  5. A terminal window should open. You will be prompted for a username. Enter your UA username.
  6. You will be prompted for a password. Enter your UA password and continue.
  7. On successful authentication, a command prompt will appear and allow you to execute commands on Chinook.

Enabling Graphics

Some applications on Chinook, especially visualization applications, require a graphical display. It is possible to tunnel graphics over an SSH connection using X11 graphics forwarding, which is supported by PuTTY.

  1. Install a local X Window server. We recommend installing the last free version of XMing, which became proprietary software in May 2007.
  2. In PuTTY, define a connection to chinook.alaska.edu and navigate to "Connection-SSH-X11". Check the box labeled "Enable X11 forwarding".
  3. Initiate an SSH connection request and log in as outlined in the last section.
  4. Ensure that your local X server is running. Without this, any graphical application will fail to run properly.
  5. Run xlogo, a simple graphical application. If you see a window containing a black X on a white background, you have successfully enabled X11 forwarding.

Saving Connection Settings

  1. Configure your connection settings as desired
  2. Navigate to "Category-Session"
  3. Enter a name for your session in the "Saved Sessions" input box, and select "Save". Your session should now appear as a new line in the text box to the left of "Save".
  4. To load saved settings, select the session you want to load and then select "Load".

Optionally, PuTTY's command-line flags allow you to create shortcuts that load a particular connection.

  1. Copy your PuTTY shortcut icon
  2. Right click on the copy, and select "Properties"
  3. In the "Target" field, append -load followed by the connection name in quotation marks
  4. Select "Apply", and close the window
  5. Rename the modified shortcut appropriately


When I try to connect, PuTTY opens an alert box that says "Disconnected: No supported authentication methods available".

This message means that authentication by username failed. This is most likely caused by an incorrect username, or because you do not have access to Chinook. Please ensure that you received an email from RCS User Support (uaf-rcs@alaska.edu) notifying you of your Chinook account creation, and use the username provided in that email.

My application returns the error "X connection to localhost:10.0 broken (explicit kill or server shutdown)" (or similar).

This is an indication that your local X server is not running. Check the icons on the right-hand side of your task bar for the X server icon. If it is not present, ensure that you have installed an X server locally and that it is running. Once the icon is present, try opening your program again.

I received the "Unknown Host Key" popup alert, followed by another popup stating: "Server unexpectedly closed network connection".

This indicates that the server's SSH timeout was triggered. SSH servers are often configured to kill incoming connections that do not send data for a while. While you were responding to the "Unknown Host Key" popup, the remote host's connection timeout expired and it disconnected you. You should be able to reconnect without problem.

Using VNC to Login

To run graphical applications on RCS systems remotely, the Virtual Network Computing (VNC) application is available and provides some advantages beyond using X Windows over SSH such as a detachable session and better performance over a slow speed connection. Here is basic set up information required for this approach.

***Important Note: Please follow all of these steps with each new VNC session.***

Step 1: Install VNC on your local system

There are multiple VNC viewer programs available with unique interfaces and features. The application on RCS systems is TigerVNC.

MAC users can use the built in Apple "Screen Sharing" as a VNC client and do not have to install an additional client.

After installing the software, make sure ports 5900 and 5901 are open to allow VNC traffic through your host firewall.

Step 2: Setup port forwarding over SSH for the VNC session

On Linux or MAC systems:

  local$ ssh -L 5901:localhost:5901 username@remote.alaska.edu

On a Windows system:

Setup a SSH tunnel with PuTTY on Windows.

  1. On the left side of the PuTTY dialog box when you open PuTTY, choose Connection->SSH->Tunnels
  2. in Source Port enter 5901
  3. in Destination enter remote.alaska.edu:5901
  4. Click Add and you should see the following in the list of forwarded ports:

    L5901 remote.alaska.edu:5901

Step 3: Connect to the remote system and start the VNC server

Log onto the remote system over SSH and specify the appropriate ports for VNC client (your local system) and server (remote system) communication.

Launch a VNC server instance on the remote system. The initial vncserver instance will prompt you for a password to protect your session. Subsequent launches of vncserver will use the same password and you will not be prompted for a password.

  remote$ vncserver -localhost

  You will require a password to access your desktops.

  New 'remote:1 (username)' desktop is remote:1

  Creating default startup script /u1/uaf/username/.vnc/xstartup
  Starting applications specified in /u1/uaf/username/.vnc/xstartup
  Log file is /u1/uaf/username/.vnc/remote:1.log

Step 4: Open VNC on your local system

  1. Launch Apple "Screen Sharing" on a MAC.

    The Apple "Screen Sharing" connect to server dialog can be accessed with {apple key} K or Finder - Go - Connect to Server. Use "vnc://localhost:5901" as the "Server Address".

  2. Launch VNC on Windows from the menu or a launcher icon.

    On Windows, the VNC application should have installed a launcher somewhere in the menus and may have also installed an icon on the desk or start bar depending on options you chose when installing. Use the menu or icon to start VNC.

  3. Launch Linux VNC viewer from the command line

    Launch your VNC viewer program and connect to host "localhost" and port 5901. The example below shows how to launch the client using TigerVNC.

    local$ vncviewer localhost:5901

If you are using the TigerVNC GUI, enter "localhost:5901" into the "VNC server:" box then click the "Connect" button. You will then be prompted for the password created in Step 2. If your local VNC client connects successfully, you will then see your desktop on the remote system.

Your circumstances might require the use of different ports due to firewall issues or if you are running more than one VNC server session on the remote system. (Other people on the system might be running their own sessions as well and occupying the ports.) If this is the case, you may need to specify port 5902 or 5903 or ... Add 5900 to the display number to determine the correct remote port to use.

To determine whether the VNC viewer has successfully connected, check the log file noted when vncserver was started on the remote system.

After starting the server, the option exists to log out and back in again using different port forwarding parameters.

Note that some VNC viewer programs can automatically set up the SSH port forwarding through a command-line flag such as "-via" or some option in a graphical configuration menu.

Step 5: When finished, close the VNC session

To close your VNC session, view the open sessions on the remote system, then close the appropriate one.

  remote$ vncserver -list
  TigerVNC server sessions:
  :1                    252550
  remote$ vncserver -kill :1


  1. Orphaned Session

    If a previous VNC session remains open on the remote system, that old session will need to be closed prior to establishing a new connection using the same port. To identify and kill the old session, first obtain the processID of the "Xnvc" process, then issue the kill command.

      remote$ ps -elf | grep username | grep Xvnc
      0 S username    236193      1  0  80   0 - 24842 poll_s Nov09 ?        
            00:00:10 /usr/bin/Xvnc :1 -desktop remote:1 (username) 
            -auth /u1/uaf/username/.Xauthority -geometry 1024x768 
            -rfbwait 30000 -rfbauth /u1/uaf/username/.vnc/passwd 
            -rfbport 5901 -fp catalogue:/etc/X11/fontpath.d -pn -localhost
      remote$ kill 236193

  2. Locked Session

    Depending on your desktop settings on the remote system, the X screensaver may kick in and lock the session after a period of inactivity. If this happens, you'll be prompted for a password that doesn't exist. The xlock process can be killed from the command line. We recommend disabling X locking in the VNC displayed desktop settings to avoid this happening.

  3. Reset Server Password

    To change the VNC server password, use the 'vncpasswd' command on the remote system.

  4. More Information

    Run 'vncserver --help' and 'man vncserver' for more information on how to use the application.