ARCHIVED: Karst Desktop usage policies and interface features

Following are instructions for using Karst Desktop once you are already connected.

• Usage policies
  • Fair share policy
  • Connection policies
• Features
  • Desktop icons
  • Pop-up menu
  • Menubar
• Analyzing memory and CPU consumption
• Supported languages
• Getting help

Usage policies

Fair share policy

Karst Desktop nodes are login nodes. You should run parallel or compute-intensive applications on Karst's compute nodes.

Everyone who logs into Karst Desktop shares dedicated nodes that are part of the Karst High Performance Computing Cluster. 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 Karst Desktop for everyone on the node.

If you are going to use highly parallel applications on Karst Desktop, 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:

  qsub -I -X -q interactive -l ...

• 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.

Connection policies

ThinLinc Client lets you disconnect your Karst Desktop session without terminating it; this suspends any currently open applications and keeps your session running on the server.

Disconnected sessions are terminated after seven days of inactivity.

Only one Karst Desktop 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.

Maintenance window

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 Karst Desktop, the following icons appear by default on the remote desktop:

• Double-click the Username's Home to access to your Karst home directory. (When you log in, the label will display your IU username.)
• Double-click DC2 Scratch to access your scratch directory on the ARCHIVED: Data Capacitor II high-throughput file system.
• Double-click File Browser to open the Karst Desktop file manager in browser mode. The browser window includes tools and menus for accessing and managing your files, folders, and your desktop.
• Double-click Interactive Job to open a terminal window on the desktop and automatically submit (qsub) an interactive job request for one hour of wall time on four cores on a single compute node. When your job is ready, you are given a command prompt on a Karst compute node:

  qsub: waiting for job 654321.m2 to start
  qsub: job 654321.m2 ready
  
  GMP arithmetic library version 5.1.1 loaded.
  MPFR version 3.1.1 loaded.
  Mpc version 1.0.1 loaded.
  gcc version 4.9.2 loaded.
  Moab Workload Manager scheduling and management system version 7.1.1 loaded.
  Python programming language version 2.7.3 loaded.
  Perl programming language version 5.16.2 loaded.
  [username@c5 ~]$
  

  These jobs are routed to an interactive queue and normally should start within two or three minutes. If your job does not start after two or three minutes, notify the Karst Desktop development team.

  Note:

  The Interactive Job shortcut is intended to provide a convenient method for logging into a Karst compute node. If you need help using this tool, or have questions, email the Karst Desktop development team.

• Double-click Karst Desktop Help to access support documentation.
• Double-click Karst Job Manager to open the "PBS Tools GUI" window, a graphical interface for using TORQUE (OpenPBS) to monitor and manage your jobs running on Karst:

  

• Double-click Terminal to open a terminal window that logs you in automatically on the same node as is serving your Karst Desktop session.
• Double-click the SDA icon to access your account on the Scholarly Data Archive (SDA).
• Double-click thindrives to access any local drives or directories that you are exporting from your personal computer. (These are configured in the ThinLinc Client options; for instructions, see the ARCHIVED: Exporting local drives and directories section in ARCHIVED: Download, install, and configure ThinLinc Client to use Karst Desktop at IU.)
• To delete items, drag and drop (or click and drag) them to the Trash icon. However, items in Trash count toward your storage quota, unless they are from your Data Capacitor II scratch space (in which case, they will be permanently deleted). You can empty the trash by double clicking on the icon and selecting Empty Trash.
• Double-click Disconnect Desktop Session to close Karst Desktop without terminating your remote session; this allows you to reconnect to the same session at a later time.
• Double-click Log Out to close Karst Desktop and terminate your remote session. (For more, see the ARCHIVED: Logging out versus disconnecting section in ARCHIVED: Download, install, and configure ThinLinc Client to use Karst Desktop at IU.)

Pop-up menu

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

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.

Menubar

At the top of the screen, you can use the Karst Desktop menubar 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 (Mathematics, MATLAB, rstudio, SAS, SPSS, and Stata)
  • Geographic Information Systems (GRASS, QBrowser, and QGIS)
  • Performance Analysis (Alinea Forge, ddd, TotalView, and Vampir)
  • Utilities (Emacs, File Browser, gedit Text Editor, Screen Shot, Spreadsheets, System Monitor, Terminal, and Wire Shark)
  • Visualization (Chimera, FSL View, Integrative Genomics Viewer, meshlab, paraview, and VMD)
• 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.

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

Some keyboard shortcuts used in the Karst Desktop 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.

Analyzing memory and CPU consumption

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

• To access the System Monitor, from the menubar, select Applications, then Utilities, and then System Monitor.

  

• 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, from the View menu, select Active Processes or All Processes.

  

• To add or remove information fields, from the Edit menu, select Preferences, and then, under "Information Fields", use the checkboxes to select the fields to display.

  

Supported 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)

Getting help

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