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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.

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This page contains a list of frequently asked questions about Atmosphere. You may also want to go to Ask CyVerse for answers to questions from other users about Atmosphere.

Volumes

For more information on volumes, see Using Volumes.

  • Volume lost its data

    There are several reasons why data might not appear in a volume as expected:
    • The volume was created with a partition: Although partitions are not required, some users prefer to format their volume with a partition. It is sometimes easy to forget that your volume was created with a partition. If your volume was created with a partition, you need to mount it with a 1, e.g., "mount /dev/xvdb1 /mydata".
    • The volume has a different file system than expected: The default mkfs command and the instructions provided by the Atmosphere documentation use ext2. Advanced users may opt to format the volume as a different file system. If you choose a different file system, please remember the file system you created for your volume.
    • The volume is corrupted: Corrupted volumes can occur when data is being written to the volume at the same time as an instance is being terminated. We highly recommend unmounting the volume before the termination of an instance for this very reason. The chances are low for recovery.
    • The volume was accidentally reformatted: You should execute the mkfs command only once per volume unless you intend to erase the existing data on that volume. There is no possibility of recovery in this situation.

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      Users are encouraged to back up any important data stored in instances and volumes to the Data Store using iCommands, or FUSE. You also can 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.

  • Volume has been suspended but I didn't suspend it

    An instance that has not performed significant computations measured by load average or that has not had an interactive session (via SSH or VNC) for more than three (3) days may be suspended, preserving the state but freeing the resources. You may resume a suspended instance at a later time, depending on available resources.
  • Volume is missing and need to find its data

    If you haven't accessed a volume within three (3) months, your volume may have been backed up to your CyVerse Data Store and the cloud storage reclaimed. The default location for volume backups is /iplant/home/username/atmo/vol-XXXXXX, where "username" is your CyVerse username and "vol-XXXXXX" is the original volume ID within Atmosphere. You can request a new volume and then copy your data back to the new volume. Contact CyVerse support staff at support@cyverse.org if you need assistance with restoring data to the new volume.

Instances

For more information about instances, see Using Instances.

  • Instance isn't working

    1. Read through the other questions and answers on this page.
    2. If you don't find an answer to your instance problem, you can report the problem.
    3. Go to Ask to see questions and answers submitted by other Atmosphere users.

  • Active instance lost connectivity and need to recover networking

    On rare occasions, an instance may lose connectivity after a maintenance period. Suspending and then resuming the instance should help restore the instance's networking. A short screencast to suspend and resume an instance can be found here: https://vimeo.com/100855170.
  • Receiving Warning: Remote Host Identification has changed!" message

When an IP address is reused quickly in cloud platforms, the IP address may be reused by an instance that you launched recently but terminated before launching a new instance. The result is the new instance now shows the same IP as the previously terminated one.

To resolve this issue, use ssh-keygen -R <ip-address-of-your-instance>, as in the following example with host of 128.196.64.136 and user nirav:


  • Can't open Web Shell for instance

    If Shell Unavailable is displayed, check the following:
    • The instance is not in Active status: The instance may be unavailable because it is not in Active status or has been terminated or suspended.
      Solution: Resume the instance. If the instance is not in Active status, you must wait until it is active. You may need to click in the My Instances list to refresh the status.
    • The instance failed to launch.
      Solution: Delete the instance and launch a new one.
    • The instance does not support Web Shell: The instance may be based on an old image that doesn't support Web Shell or the provider may not have provided it for the instance.
      Solution: Search for a newer version of the image. Connect using SSH or PuTTY

For more information, see Logging In to an Instance.

  • Can't open or issues with Web Desktop/VNC

    • If you can't open Web Desktop for instance or Web Desktop is not displayed, check the following:
      • Instance status is not Active: The instance may be unavailable because it is not in a status of Active or has been deleted. Try the following:
        1. Refresh your browser window.
        2. Wait until the instance is running and in Active status.
        3. You may need to launch a new instance.
      • Instance failed to launch
        1. Delete the instance.
        2. Launch a new one.
      • Instance does not provide a desktop interface
      • Need to find images tagged with VNC
        1. Click Launch New Instance.
        2. In the search field, enter vnc or gui and then click the image to use.

For more information on the Web Desktop, see Logging In to an Instance.

  • No Web desktop, or used to work but doesn't now

    • Either 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, the VNC remote desktop server session will need to be restarted.
      • Command-line workaround:
        1. Log in to the instance via SSH.
        2. Sudo to root by typing:

        3. Kill all processes with "vnc" or "Xvnc" by typing:

        4. Exit sudo to return to your user account by typing:

        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.

Information and definitions

Images

For more information on images, see Launching a New Instance in the Atmosphere manual.

  • Definition

    An image is a template for an instance. Each image comes preinstalled with an operating system, custom configuration, and related software that is specific to that image.Click any image to view its description and list of installed software, and then double-click the image to launch it with default settings.
  • Searching for an image

    You can search images by name, description, or ID number. You also can search by tag using the syntax tag:tag_to_find.

Instances

For more information on launching and using instances, see Using Instances.

  • Definition

    An instance is a specific virtual machine (VM) that exists on a physical compute node, and which has dedicated RAM, CPUs, and disk space. You can use an instance as you would use a physical computer for most tasks.

Volumes

For more information about volumes, see Using Volumes.

  • Definition

    A volume is like a virtual USB drive that helps you more easily transfer relatively small data between instances. You can create a volume with a capacity of up to 100 GB using the Create a Volume form. To store and transfer more data at once, store it in the CyVerse Data Store instead. You can mount the Data Store similarly to a volume.
  • Availability of a volume

    A volume is "available" when it is not attached to an instance. You must have at least one running instance in order to put a volume to use. Any newly created volume must be formatted and then mounted after it has been attached before you can use it.

Data and Atmosphere

  • Importing large data files for use in Atmosphere

    See this page on Ask CyVerse about the best way to import files for use in Atmosphere.

Other definitions

  • My Resource Usage definition

    Resource usage is determined by how many CPUs, GBs, and AUs of memory your instances are using cumulatively. You can reuse your resources only after the instance has been terminated and is no longer displayed in the My Instances list.
    For more information on resource usage, see Viewing Your Active Instances in the Atmosphere manual.
  • CPU hour definition

    A CPU hour is a CPU core used for one hour. For example, an instance that uses four CPU cores will consume four CPU hours for every hour that it is running. When your instance is stopped or paused, it will not contribute to the number of CPU hours your instances have used.
  • AU definition

    AU stands for Atmosphere Units, the number of Atmosphere CPU hours allocated for your account. One AU is roughly equivalent to one CPU-hour, or one CPU-core used per hour.

Other resources

  • Ask CyVerse is a question and answer forum that is moderated by CyVerse users.
  • The Atmosphere-users mailing list gives you access to postings by the Atmosphere-users group as well as to the collection of prior postings, and the ability to post messages to the Atmosphere group.
  • The main Frequently Asked Questions page provides answers to more general questions about using the Discovery Environment and CyVerse Data Store. You may find an answer to your question there as well.

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.