Research Desktop (RED) usage policies and interface features

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Usage policies

The instructions here are for using Research Desktop (RED) once you are already connected.

Note:
  • When Carbonate was retired on December 17, 2023, Research Desktop (RED) was reconfigured to use Quartz as its home directory. To use RED, you must have an account on Quartz If you do not already have a Quartz account, create one now using the instructions in Get additional IU computing accounts.
  • If you previously used RED with Carbonate, your Carbonate home directory files will continue to be available, but any software that you installed on Carbonate will need to be reinstalled to run on Quartz.

Fair share policy

RED nodes are login nodes. You should run parallel or compute-intensive applications on Quartz compute nodes.

Everyone who logs into RED shares dedicated nodes that are part of the Quartz research supercomputer. Because high loads on shared nodes can negatively impact system usability, be aware of how your processes use the system; see Analyzing memory and CPU consumption below.

IU uses a fair share policy that throttles processes and slows down applications for users who are consuming a high percentage of CPU resources; running highly parallel applications can lead to high CPU consumption. Although running such an application for a few minutes for testing purposes is fine, running it for hours can negatively impact the usability of RED for everyone on the node.

If you are going to use highly parallel applications on RED, do one of the following:

  • Limit the parallelism the applications use to 5 or fewer.
  • Run the applications via a normal batch job. You can do this in various ways, including an interactive batch job that allows for graphical output:
    srun -p interactive -A slurm-account-name --x11 ...
  • Only run such applications for short periods of time.

Users who don't follow these policies and fail to respond to requests to change how they use the system may have their jobs halted and lose their login privileges.

In addition, each user is limited to 100 GB of memory usage within the entire session. If user sessions reach 100 GB of memory consumption, one or more of their processes will be terminated to reduce usage.

Connection policies

ThinLinc Client lets you disconnect your RED session without terminating it; this keeps your session and any open applications running, allowing work to proceed while you are disconnected.

Note:
Disconnecting is not the same as logging out, which closes open applications, terminates your session on the server, and closes the remote desktop window.

Disconnected sessions are terminated after seven days of inactivity.

Only one RED session is allowed per user. When you connect, if you have no disconnected sessions running, ThinLinc Client automatically creates a new session. If you do have an existing session, you are automatically reconnected to that session. However, if you want a new session rather than your existing one, select End existing session before connecting; the existing session will be terminated and a new one created.

Monthly maintenance window

The scheduled monthly maintenance window for IU's high performance computing systems is the second Sunday of each month, 7am-7pm.

IU recommends saving your work and logging out before 7am on maintenance days. All sessions still open at 7am on maintenance day will be terminated.

Features

Desktop icons

When you connect to RED, the following icons appear by default on the remote desktop:

Desktop icons in RED that are explained in the text below

  • Disconnect ThinLinc Session: Double-click to close RED without terminating your remote session. This allows you to reconnect to the same session at a later time.
  • Log Out: Double-click to close RED and terminate your remote session. (For more, see the Logging out versus disconnecting your session section of Download, install, and configure ThinLinc Client to use Research Desktop (RED) at IU.)
  • Trash: Delete items by dragging and dropping them to Trash.
    Note:
    Items placed in Trash will continue to count toward your research computing storage quota until you permanently delete them. To view items in Trash, double-click Trash. To permanently delete all items, click Empty Trash, and then click Empty Trash again to confirm; to delete an individual item, right-click (or Ctrl-click) the item, select Delete Permanently, and then click Delete to confirm.
  • Home: Double-click to access your Quartz home directory. (When you're logged in, the Home icon's label will include your IU username.)
  • BR200 Login: Double-click to access options for logging into your Big Red 200 account.
  • Interactive Job: Double-click to open an interactive session on one of the compute nodes on Quartz. This opens a Terminal window and submits an interactive job request for four hours of wall time using eight cores and 32 GB of a single compute node. These jobs normally start within two or three minutes. When your job is ready, you will be placed at the compute node's command prompt.
    Note:
  • Slate Scratch: Double-click to access files in your Slate-Scratch space.
  • thindrives: Double-click to access drives and directories on (or connected to) your personal computer.
    Note:
    To enable thindrives access to drives and directories on your personal computer, before connecting to a new session you must configure the ThinLinc Client's "Export Local Resources" option.
  • RED Documentation: Double-click to access RED support documentation.
  • Feedback and Questions: Double-click to open a window that will let you send feedback and questions to the Research Desktop team.
  • Terminal: Double-click to open a Terminal window that logs you in automatically on the same node that is serving your RED session.

The RED pop-up menu lets you change your screen size settings, toggle full-screen view on and off, and access other connection settings during your RED session:

RED pop-up menu

To access the pop-up menu, press F8. (Depending on your local system, you may need to press Fn-F8 or Win-F8.)

To map the pop-up menu to another key:

  • Before opening a session: In the ThinLinc Client login window, click Options to open the "ThinLinc Client Options" window. On the Options tab, under "Session Options", make sure Send system keys is selected, use the Popup menu key selector to assign another key, and then click OK to return to the login window.
  • During your session: Open the pop-up menu, click Options, and then, on the Options tab, make sure Send system keys is selected. Use the Popup menu key selector to assign another key, and then click OK.

To disable the pop-up menu, do the same as above, but set the Popup menu key selector to None.

At the top of the screen, you can use the RED menu bar to launch installed applications, access local and remote resources, and set personal preferences.

  • Click Applications to browse and run installed software in several categories:
    • Analytics: Jupyter Notebook, Mathematica, MATLAB, RStudio, SAS, SAS Setup, SPSS, Stata
    • Coding and Editing: Arm Forge, Emacs, Geany, gedit, Pluma, Spyder, VS Code
    • Compute jobs: Interactive job, Quartz Job Manager, Slurm Info
    • Storage: Globus, Scholarly Data Archive (FileZilla), SDA on Globus
    • Utilities: File Browser, FileZilla, Firefox, MATE System Monitor, MATE Terminal, Spreadsheets, Take Screenshot, VLC Media Player
    • Visualization: Chimera, DSI Studio, Fiji, FSLeyes, Integrative Genomics Viewer, Metashape, ParaView, QGIS, VMD
    • IU HPC Slack Channel: Opens a Firefox browser tab to the IU HPC Slack Channel where the IU HPC user community can chat and communicate with one another and Research Technologies staff.
  • Click Places to access local and remote folders, browse bookmarked and local network locations, search for files, or connect to remote computers or shared disks.
  • Click System to access the Preferences menu, which includes several options for changing the appearance and behavior of your desktop.
  • Click the Caja icon (Caja file browser icon in RED menu bar) to access your Quartz home directory and browse the file system.
  • Click the Terminal icon (Terminal icon in RED menu bar) to open a Terminal window that logs you in automatically on the same node that is serving your RED session.
  • Click the Firefox icon (Firefox icon in RED menu bar) to open the Firefox web browser.

To customize your desktop, right-click (Windows) or Ctrl-click (Mac) on any part of the desktop or menu bar.

Note:

Some keyboard shortcuts used in the RED interface may differ slightly from the ones on your local computer and may vary from application to application. For example, to copy text, some applications use Shift-Ctrl-c, while others use Ctrl-c. Check the application's Edit menu to see which shortcuts it uses.

You can also change your RED session preferences, such as the keyboard layout or keyboard shortcuts. For example, to change the keyboard shortcuts, inside your RED session:

  1. From the RED menu bar, select System > Preferences > Hardware > Keyboard Shortcuts.
  2. In the "Keyboard Shortcuts" window, change your customized keyboard shortcuts.

Access your SDA or Slate storage

If you have an account on the Scholarly Data Archive (SDA) or on Slate, you can access it from RED:

  • SDA: From the RED menu bar, select Applications > Storage, and then choose how you want to connect:
    • Select Scholarly Data Archive (Filezilla) to open a virtual FileZilla window; when prompted, enter your IU passphrase to connect to your SDA account.
      Note:
      For SFTP connections to the SDA, RED uses a managed version of FileZilla that is safe to use; later versions of FileZilla have been identified as malware. If the FileZilla "Check for updates" window opens, click Close to close it and continue with your SDA session.
    • Select SDA on Globus to log into your SDA account via the IU Globus Web App.
  • Slate: On the RED desktop, double-click your Home icon, and then:
    1. In the file browser window, above the right pane, to the left of "Location", click the Toggle between button and text-based location bar icon to switch to the text-based location bar. The "Location" field should display your current location in the file system as /N/u/username/Quartz (where username is your IU username).
    2. In the "Location" text field, select and delete the displayed path, and then enter the path to your Slate account; for example (replace username with your IU username):
      /N/slate/username
    3. Press Enter or Return.

    Optionally, you can bookmark your Slate account. In the file browser menu, click Bookmarks, and then select Add Bookmark. A persistent link to your Slate account will be added to the Places list (under "Bookmarks") on the left side of the file browser.

Appearance customization

To customize the appearance of the RED interface, use the Appearance Preferences utility:

  1. From the RED menu bar, select System > Preferences > Look and Feel > Appearance.
  2. In the "Appearance Preferences" window, use the Theme, Background, Fonts, and Interface tabs to configure a personalized look and feel for the RED interface.
    Note:

    The available pre-set window and folder themes can be modified by selecting Customize, allowing you to specify your own color scheme, window appearance, icon appearance, icon style, and more.

Analyze memory and CPU consumption

To view current system status data, use the System Monitor utility:

  1. From the RED menu bar, select Applications > Utilities > MATE System Monitor.
  2. To view memory and CPU consumption for your processes and applications, select the Processes tab. By default, only your processes are displayed; to see processes besides your own, in the top right, click the menu icon (next to the search icon), and then select Active Processes or All Processes:

    System monitor in RED

  3. To add or remove information fields, in System Monitor menu, select Edit > Preferences, and then use the checkboxes to select the fields to display.

Supported languages

ThinLinc Client supports the following languages:

  • Brazilian Portuguese (pt_BR)
  • English (en_US)
  • Dutch (nl_NL)
  • French (fr_FR)
  • German (de_DE)
  • Italian (it_IT)
  • Russian (ru_RU)
  • Spanish (es_ES)
  • Swedish (sv_SE)
  • Turkish (tr_TR)
Note:
If your computer's operating system is set to an unsupported language, ThinLinc Client may not function properly.

To change your keyboard layout, inside your RED session:

  1. From the RED menu bar, select System > Preferences > Hardware > Keyboard.
  2. In the "Keyboard Preferences" window, on the Layouts tab, click Add.
  3. In the "Choose a Layout" window, on the By country or By language tab, use the drop-down lists to select a keyboard variant by country or language, and then click Add.

Get help

If you are using Research Desktop (RED) and need help or have questions, use this form to contact the Research Desktop development team directly.

This is document apxv in the Knowledge Base.
Last modified on 2024-02-23 16:47:18.