Troubleshoot Research Desktop

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Screen size issues

If the Research Desktop (RED) window covers your entire display, hiding control menus or positioning them off-screen, use the following keyboard shortcuts to either exit full-screen mode or terminate ThinLinc Client. Whichever method works for you, make sure to change the ThinLinc Client screen size settings before launching another RED session; for help, see Download, install, and configure ThinLinc Client to use Research Desktop (RED) at IU.

  • Exiting full-screen mode: Click the display background to make sure RED is the active window, press F8 to open the pop-up menu (depending on your system, you may need to press Fn-F8 or Win-F8), and then de-select Full screen.
  • Terminating ThinLinc Client: If you cannot exit full-screen mode, you may need to terminate or force quit the ThinLinc client. To do so, click the display background to make sure RED is the active window, and then:
    • In Windows, press Alt-F4 or Esc. Alternatively, press Ctrl-Alt-Delete or Ctrl-Shift-Esc, and then select Start Task Manager; then, on the Applications tab, select ThinLinc Client, and then click End Task.
    • In macOS, press Command-Option-Esc to open the "Force Quit" window, select ThinLinc Client, and then click Force Quit. Alternatively, press Command-Tab to switch to the last used application; then, from the Apple menu choose Force Quit..., select ThinLinc Client, and then click Force Quit.

      If you cannot force quit ThinLinc Client, you may need to log out of your macOS user account or reboot your computer. To log out of your user account, press Command-Shift-q. To reboot your computer, press Ctrl-Eject, and then select Restart.

Login issues

  • After five consecutive unsuccessful login attempts, you will be blocked from logging in for one hour. When this happens, you will see an error message similar to this:

    ThinLinc Client error message after too many failed login attempts

    If you receive an error similar to the one above and cannot log in, contact the RED development team for help.

  • Instead of logging in, a window appears with a message similar to one of the following:
    • Could not connect to session bus: Failed to connect to socket /tmp/dbus-fmw0GvVigr: Connection refused
    • ThinLinc login failed.
      (The SSH connection succeeded, but the ThinLinc server connection failed. Perhaps this server doesn't run a ThinLinc server?)

      RED connection error message

    Changing the PATH environment variable in your .bashrc file can often cause this issue.

    When changing the PATH in .bashrc, append rather than prepend any changes. For example, rather than entering:

    export PATH="/path/to/my/cool/program:$PATH"

    Instead, enter:

    export PATH="$PATH:/path/to/my/cool/program"

    Sometimes installing certain software (for example, Anaconda) will place a command that redefines the PATH environment variable in your .bashrc file. Even if you did not modify the file yourself, check to see if the file has a line redefining the PATH.

    To access the Research Desktop, you will need to log in directly to Carbonate using a terminal program, and then use an editing program such as vim or Emacs to edit your .bashrc file.

Issues with thindrives

  • If an exported local drive or directory in your thindrives folder is not responding, check the ThinLinc Client options to make sure you entered a valid path (see the Exporting local drives and folders section in Download, install, and configure ThinLinc Client to use Research Desktop (RED) at IU).
  • If you cannot copy files to an exported local drive or directory in your thindrives folder, check the ThinLinc Client options to make sure the path you entered is correct and has read/write permissions assigned.
  • Configuring ThinLinc Client to export local drives lets you select local paths that are specific to the computer on which you are currently working. Consequently, when you launch a RED session from that computer (for example, your desktop), you can access those local paths via the thindrives icon. However, if you disconnect from that session (without logging out), and then later re-connect to that session from another computer (for example, your laptop), the thindrives icon no longer will work, because it is still configured to access the local paths on your other computer (for example, your desktop).
  • If you are sure that you correctly exported a local folder, but it still does not display in your thindrives folder, try logging out of your RED session (not just disconnecting), and then log in again. To enable thindrives access to your personal computer's drives or folders, you must configure the ThinLinc Client's "Export Local Resources" option before connecting to a new session. If you configure "Export Local Resources" during a session that is already running, those local resources will not be available in the thindrives folder until you log out of the current session, and then log into a new session.

Issues with Box

Important:

Box cloud storage will be retired at Indiana University in spring 2021. Migration of IU's Box data began in June 2020. For details about cloud storage options at IU, see Storage @ IU.

After your files are migrated from Box, the Box versions become read-only. Migrations will be finished by March 2021, and access to Box will be terminated in May 2021.

You can create a Box desktop icon by using Applications > Storage > Box setup. The Box mount creates a connection between the Box cloud folder and RED via the internet. The mount makes the Box cloud folder appear as a local file system, but it is still a cloud folder with the data physically located on a faraway cloud; therefore, all file opens, reads, and writes take a long time compared to a traditional local disk or a networked file system.

  • This mount is only visible on the Research Desktop node where your RED session is running. It is not available on Carbonate login nodes or Carbonate compute nodes. Do not try to submit jobs that reference files that are visible across this mount. Instead, copy such files to your scratch or Slate space to use them for computational work.
  • If you run into issues with the Box mount on RED, run the Box setup command from the menu. You will be asked if you want to unmount, remount, or reset your Box folder. Try remounting first, and if that doesn't work, try resetting. This will often solve issues that you may be running into with your Box folder.
  • The Box mount on RED is meant to be a convenient option for easy data transfers between Box and other file systems mounted on RED file systems like Geode2, DC2, and Slate, where your home and scratch directories reside, respectively.

    For example, before your application run, you would transfer some input files from Box to Slate. After the run, you would transfer the output files to Box via the mount. This way, data on the Box cloud, accessible on RED via the mount, is not accessed during application runs.

  • The Box mount is suitable for small data transfers, under 1 GB. Larger data transfers might fail without any warning or error. In testing, we have observed a 10% failure rate for data transfers.
  • If you run any applications that are reading from or writing to your Box mount folder, they will likely throw an error. Even if they work, they will be at least 10 times slower than Slate, DC2, or Geode2. It is faster to copy the full data set to Slate, DC2, or Geode2 to compute against it rather than compute with the data residing on Box.

    For example, if all the I/O activity of your application takes 10 minutes out of a total run time of 60 minutes on DC2, using Box mount for I/O would make that I/O activity take 100 minutes, for an overall run time of 160 minutes.

    Note:
    UITS understands the importance of convenient Box access on RED for our users, and we are evaluating better data transfer options.

Other issues

  • If your computer's operating system is set to a language that is not supported, ThinLinc Client may not function properly. (See the Supported languages section of Research Desktop (RED) usage policies and interface features.)
  • You may encounter the following (or similar) message when you try to connect:

    The Thinlinc session is currently unreachable. Try again later or press "Abandon session" to abandon the session, in which case it will never be possible to connect to the session. The session will not be terminated, which means that the desktop environment and applications may continue to run.

    If you do not want to abandon the session, contact the RED development team for assistance. They may be able to restore the connection to your session.

Get help

If you have a question or need help with RED, contact the RED development team.

Support for IU research supercomputers, software, and services is provided by the Research Technologies division of UITS. To ask a question or get help, contact UITS Research Technologies.

This is document apxu in the Knowledge Base.
Last modified on 2020-06-11 11:26:42.

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