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For overview information, see Atmosphere on the CyVerse website.

Atmosphere User Manual
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To keep your data safe, use a script to back up your data to the Data Store. For more information, see Backing Up and Restoring Your Data to the Data Store.

Important Notice about iPlant Cloud – Tucson
The iPlant Cloud – Tucson cloud provider is no longer available for new instance launches. If you did not back up your data on the iPlant – Tucson cloud, submit a request to support@cyverse.org for data migration to the new Marana cloud provider.
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You can log in to an instance using the Web Shell or Web Desktop, if available, as well as log in using SSH.

To learn about sharing your instance with other users via SSH or VNC, see Sharing an Instance with Other Users. For a basic introduction to instances and images, see Using Instances.

Web Shell

  1. In Atmosphere, click Projects at the top and then click to open the project to use.
  2. Click the name of the instance that is in Active status.

  3. Click Open Web Shell in the Actions menu.

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    If unavailable, try refreshing the page. If it is still not enabled, log in using SSH (steps for both below) or Web Desktop, if available. You also may want to read Why can't I open the Web Shell?

  4. Enter your CyVerse username and password.
  5. Click Connect and then enter your password again.

Web Desktop

Atmosphere's Web Desktop uses a VNC (Virtual Network Computing) that allows Atmosphere users to access an image you own in a graphical desktop environment. The image is run on CyVerse resources but accessed from your local machine. The underlying protocol works across operating systems and platforms, and allows remote users to access, use, and share a computer system. There are many free VNC clients or viewers, some of which are mentioned here.

Not all instances provide VNC access:

  • The instance must be running in Active status.
  • You must own the instance.
  • The image must have a graphical interface (most will have "GUI" in the title).

For more information, see Why can't I open the Web Desktop for my instance on the Atmosphere FAQs page.

  1. Click Projects on the menu bar and then click the project with the instance to view.
  2. Click the instance name to open the instance.
  3. Click Web Desktop in the Actions menu.

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    If Web Desktop is not available, try refreshing the page. If still not available, log in using SSH (steps for both below) or Web Shell. You also may want to read Why can't I open the Web Shell? on the FAQs page.

  4. If prompted to install updates, cancel out of the prompt.
  5. To terminate the session, click Send CtrlAltDel and then click Yes to shut down the system.

Changing screen resolution

Changing screen resolution for the VNC Viewer

  1. In the VNC Viewer window, click the System menu, point to Preferences, and then click Screen Resolution.
  2. In the Screen Resolution Preferences window, change the resolution, click Apply and then click Close.

Changing screen resolution using the command-line

Sometimes the Screen Resolution or Display Preferences may not work. You also can change the resolution of the using the command-line. For example, to change the resolution to 1024x768, use the following xrandr command within a terminal of your VNC session:

Example for changing resolution to 1024x768:

Only certain screen resolutions can be used by xrandr. To see a list of supported screen resolutions, enter 'xrandr' without any arguments.

 Example

Troubleshooting the VNC Viewer

A good source of information for issues with VNC Viewer or other Atmosphere issues is the Ask CyVerse questions about Atmosphere. The Atmosphere FAQs page also has some helpful information.

Restarting the VNC Viewer

Occasionally, there may be an issue in which the VNC connects but displays no desktop, OR the resumed instance's VNC session used to work (e.g., before suspending), but does not work now

We have seen some cases where the VNC web desktop session is not fully functional, although the VNC remote viewer and Web-based VNC viewer connect properly. Also, when suspended instances are resumed, the instance's IP address may change, causing the VNC server to fail; in this situation, you will need to restart the VNC web desktop server session.

  1. Log in to the instance via SSH and sudo to root:

  2. Sudo to root:

  3. Kill all processes that contain either "vnc" or "Xvnc":

  4. Exit sudo to return to your user account:

  5. Relaunch vncserver by typing:

  6. (Optional) If you encounter errors about the existence of files, you might need to delete (i.e., rm) the following files and attempt to relaunch the vncserver:
    • /tmp/.X1-lock
    • /tmp/.X11-unix/X1
  7. Attempt to reconnect to VNC; if the error still persists (sometimes it takes a couple of times), repeat the steps a few times.

 Feedback or questions about Atmosphere?

Go to Ask CyVerse for Atmosphere, or click Feedback & Support at the bottom right of the screen.

Having problems with your instance?

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SSH login

If Web Shell or Web Desktop are not available, you can log in to your instance via SSH for your operating system. To add a public SSH key, see Changing Settings and Configuring a Public SSH Key.

NOT FOR INTERACTIVE PROGRAMS

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This method is not recommended for interactive programs that run for an extended period of time and may result in network connection timeout.

Instead, use either:

Mac OS X SSH login

  1. Click Projects and then click the project with the instance to use.
  2. In the Instances list, copy the IP address for the instance.
  3. In a terminal window for Mac OS X:
    1. Enter the following command, using your CyVerse username and password, and the instance IP address you copied in step 3:

       Example
    2. If prompted to continue connecting, enter yes.
    3. Press Enter.

Windows SSH login

For Windows OS, use PuTTY, an SSH client for Windows. For a useful guide to using PuTTY, see PuTTY – Remote Terminal and SSH Connectivity.

  1. If you haven't already done so, download the PuTTY application.
  2. In Atmosphere, click Projects and then click the project with the instance to use.
  3. In the Instances list, copy the IP address for the instance.
  4. Launch PuTTY.
  5. Enter your username and paste the IP address.
  6. Click Connect.
  7. Enter your password and click Enter.

Windows SSH login using PuTTY

You can use PuTTY for logging in to an SSH window on a Windows operating system. PuTTY is an SSH client for Windows, and operates a bit differently than Terminal to make the initial SSH connection. For a useful guide to using PuTTY, see PuTTY – Remote Terminal and SSH Connectivity.

  1. Copy the instance IP address, either from the confirmation email or from the IP address displayed in your My Instances list.
  2. Download the PuTTY application.
  3. Launch PuTTY.
  4. Enter your username.
  5. Enter the IP address, either copied from your My Instances list or from the confirmation email, and then click Connect.
  6. Enter your password and click Enter.

Need help?

Click  at the bottom right of the screen to chat with an Atmosphere support team member during business hours. You also can go to Ask CyVerse for Atmosphere, or click Feedback & Support at the bottom of the screen.

2 Comments

  1. Do we no longer support the stand alone desktop VNC viewer? I though there used to be instructions for it here.

    1. Yes we do Ramona Walls - but the instructions are not here. And the instructions we do have here are a bit out of date. I'll log a ticket.