NC State Open OnDemand

Connecting to Open OnDemand

1. Open your preferred web browser and navigate to https://servood2.hpc.ncsu.edu.
2. If you have not yet saved a campus, you will be prompted to select an identity provider from a presented menu.
   

File Explorer

The File Explorer feature allows users to browse and manage files stored on NC State\'s HPC system effectively. The following steps outline how to use it:

1. Access the File Explorer function by clicking on the "Files" menu. A familiar interface will be displayed.
2. Choose a location to browse, typically your Home directory. This will launch a file browsing interface.
3. Within the File Explorer:
   • To navigate directories, simply click on the desired directory.
   • To return to the previous directory, use the up arrow option.
   • The current directory path is displayed at the top, enabling easy navigation.
   • The Change Directory button allows users to directly access a specific directory.
4. Create new files and directories using the New File and New Directory buttons as needed.
5. To edit a file, select it and click the Edit button in the menu. After making changes, be sure to save your work.
6. File uploads can be easily accomplished via the Upload button, which allows for dragging and dropping files or browsing for files to upload. Users can also upload directories.

To download files or directories, use the checkboxes to select the desired items, followed by the Download button. A dialog box will prompt you to select a location on your local system for saving the items.

Job Management

Users can easily check and manage their jobs through the Jobs menu: The functionalities include:

1. The Active Jobs option displays jobs that have been submitted. Users can manage their jobs based on their needs, displaying either their own jobs or all jobs in progress.
2. The Job Composer facilitates the creation of simple jobs, allowing users to configure and submit computational tasks based on their specific requirements.

Shell Access

To access the Linux command line, users should click on the Clusters menu, followed by selecting the "NCSU Hazel Cluster Shell Access" option. This action will present an interface for interacting with the system using a command-line interface.

RStudio

RStudio is a powerful interactive environment dedicated to the R programming language. To utilize RStudio within Open OnDemand, follow these steps:

1. Select Interactive Apps from the main menu and then click on "R Studio Server".
2. Fill out the required session configuration form: The various parameters mean:
   • Queue: Usually, this field can be left empty unless a specific queue needs to be selected.
   • Number of hours: Indicates the duration for which the session will be active.
   • Number of processors: Specifies how many processors the session will utilize.
   • Exclusive Node Option: Requests exclusive access to a node; select multiple processors for scheduling, understanding that it may delay job initiation.
   • Amount of memory requested: Specify memory requirements, such as “1GB” for one gigabyte.
   • Version of R container: Select the appropriate R version for the session.
   • Path to User Libraries: Define where user-installed libraries are stored; it\'s advised to separate this location from standard libraries to prevent conflicts.
3. After finalizing the configuration, click on the Launch button. Job initiation time may vary based on resource allocation. Once ready, select the Connect to RStudio Server button to access the RStudio application.

Working within RStudio

Upon clicking the Connect to RStudio Server button, the RStudio application interface will appear, offering familiar functionalities and features. Users are encouraged to utilize RStudio as they typically would in local environments with a few caveats.

Installing Packages

The version of RStudio utilized in the compute nodes supports package installation. Packages can be sourced from the NC State CRAN mirror or the Duke CRAN mirror.

Resuming Interrupted Sessions

In instances where your session is still active, you can re-establish the connection (useful in case of broken connections) via the My Interactive Sessions menu.
Any currently running sessions will be listed, and users can reconnect by clicking the Connect to RStudio Server button.

Exiting RStudio

To properly exit your RStudio session, follow these steps:

1. Click the Power button located in the RStudio interface.
2. Close the RStudio window to end your session.
3. Finally, back in the My Interactive Session window, click the Delete option to remove the session from active job listings.

Limitations of OOD RStudio

While Open OnDemand with RStudio offers substantial advantages, it does come with inherent limitations, including:

• Limited Internet Connectivity: Not all websites and services may be accessed, impacting functionalities that rely on external resources.
• Restricted CRAN Mirrors: Access to CRAN mirrors is limited, which may affect package installations.
• Potential Configuration Conflicts: Some of the user configurations from local environments may clash with the OOD version settings, leading to unexpected behaviors.
• Missing Full Internet Connection Resources: Certain components, particularly those requiring a full internet connection such as the Connections panel (ODBC, Spark), may encounter errors or be non-operational.
• Inability to Install Certain R Packages: Packages that have compiled components, such as shiny or learnr, cannot be installed due to absent dependencies and components required for configuration.

502 Errors

If you encounter a 502 Proxy error, it is advisable to check the connection speed of your account logins via the SSH Shell. Slow login times can often lead to Open OnDemand timeout issues. A common culprit is the inclusion of certain commands within the .bashrc file, which may significantly delay login speeds.

For example, users who have added code for Anaconda will need to remove the code from the .bashrc file and relocate it to an alternative file, such as .conda.bashrc, for efficient sourcing when necessary.