Navigating Open OnDemand

After creating your Cheaha account, going to rc.uab.edu will take you to the Open OnDemand (OOD) homepage:

The landing page contains information about current updates to the system, a message of the day with links to our support email and documenation, as well as a helpful partition table to help you determine which partition to submit your jobs to. You can access all of the different features of OOD using the navigation tabs at the top of the screen. The most commonly used features are covered below.

File Browser

You can open a file browser in a new tab by clicking the Files dropdown and selecting which default directory you would like to access from HOME, USER_DATA, or USER_SCRATCH.

Note

USER_SCRATCH is shown as both /scratch and /data/scratch. /data/scratch is just a symbolic link to /scratch. You can use either, but /scratch is preferred since it's an actual folder instead of a symlink.

You can see the current working directory at the top (green) along with its file and folder list (black). There are also control bars for both working with files (blue) as well as the file browser itself (orange).

Renaming/Moving File

You can use the Rename/Move button in the control bar to either rename a selected file with a desired name or move it to a preferred location by specifying the full path of the destination.

Danger

Make sure you never leave the box empty while renaming the files! If it's left empty, you risk losing the files, which cannot be recovered. This problem has been noted in OOD version < 2.0.0.

Below is an example that shows how leaving the box empty while renaming the folder "test_rename" results in the loss of the folder itself.

OOD Command Menu

Uploading Data

Data can be uploaded from your local machine using this interface. Use the Upload button in the OOD Command Menu at the top right to select files from your local browser.

Important

This should be limited to small files only (< 1 MB). For large files or datasets, please use Globus instead.

Opening a Terminal

You can also open a bash terminal in the current directory using the >_Open in Terminal command. This should only be used for small tasks since the terminal is running on the login node. For compute-intensive tasks, either request an interactive session in the terminal or request an HPC Desktop session through the Interactive Apps and use the terminal there.

Show Dotfiles

Selecting the Show Dotfiles option will show the hidden files (those beginning with .) in the current folder.

Show Owner

Selecting the Show Owner/Mode option will show the permissions for the files in the working directory. These permissions (mode) can be used to investigate permission issues in shared spaces like /data/project directories. The owner column shows the Unix ID for the user who owns the file or directory. There is not a known way to change it to the username so its use is limited.

Interactive Apps

There are two tabs used to interact with applications in OOD, the Interactive Apps dropdown, used to select resources and start jobs, and the My Interactive Sessions tab, used to view currently running interactive apps. As shown below.

Creating an Interactive Job

The Interactive Apps dropdown has a list of specific software setup to run on Cheaha that you can interact with through a browser window such as RStudio, MATLAB, and Jupyter. There is also an HPC Desktop app that provides a general VNC desktop to run all available software on Cheaha. See the quickstart for how to create an example HPC Desktop job. Below, you can see a general form for selecting job resources.

The interactive apps have the following fields to customize the resources for your job:

1. Number of Hours: the maxmimum number of hours the job will run for. Interactive apps will stay allocated for this amount of time unless the job is manually deleted or crashes. The selected number of hours should be less than or equal to the max runtime for your selected partition.
2. Partition: the partition the job will be allocated in. See here for more information about which partition to choose for your job.
3. Number of GPUs: Total number of GPUs to request (max of 4 on pascalnodes or 2 on amperenodes)
4. Numer of CPUs: Total number of CPUs to request
5. Memory Per CPU (GB): GB of memory multiplied by the requested number of CPUs.

Note

The "number of GPUs" field is ignored if a partition is selected that has no GPUs.

Tip

You can decrease wait time in the queue by choosing resources carefully. The closer your request is to actual usage, the more optimal your wait time will be. Please see our section on Job Efficiency for more information.

Every interactive app has resources only allocated on a single node, and resources are shared among all processes running in the app. Make sure the amount of memory you request is less than or equal to the max amount per node for the partition you choose. We have a table with memory available per node for each partition.

Environment Setup Window

In addition to requesting general resources, for some apps you will have the option to add commands to be run during job startup in an Environment Setup Window. See below for an example showing how to load CUDA into a Jupyter job so it can use a GPU.

For jobs such as RStudio and Jupyter, some modules like CUDA need to be loaded beforehand so the application has access to it. This can also include loading compiler modules such as CMake and GCC for compiling package installations or editing your $PATH specifically for the interactive app without needing to edit your .bashrc. See the software specific pages for more examples on how to use the Environment Setup.

My Interactive Sessions

The My Interactive Sessions page lists the available apps and your current interactive sessions. If you are logged out, disconnected, or lose track of an interactive application (because of a closed tab or computer shutdown) you can reconnect to running applications on this page. The My Interactive Sessions page looks like:

For each job running via Open OnDemand, there will be a card listed on this page. Each card has basic information about the number of cores, node assignment, and time remaining for the job. Also shown are the Job ID in the top-left part of the job card, and a Session ID link near the center of the card. The Job ID and Session ID are important for diagnosing issues you may encounter on Cheaha while using Open OnDemand.

Bug

If your job fails to launch, see debugging OOD jobs for instructions on how to access OOD job data and submit a support ticket.

Click the Launch Desktop in new tab button to open your interactive VNC session. You may have to wait for the card to change from blue to green to launch the job. You can also click the button in the Host field to open a terminal directly. This terminal is opened on the compute node and so can run any commands you need.

These interactive jobs can be stopped early by clicking Delete on the right side of the job card.

Debugging OOD Job Failures

On occasion, interactive jobs created in OOD will crash on startup and cause the job card to disappear. Most of these failures are caused by improper environment setup prior to job creation. If you experiencing OOD job failures, retrieve the OOD job info using the following steps:

1. Create a new job with the same setup as the job that failed.

2. When the job is in queue, click the link in the Session ID field in the job card before the job fails (see the image below for an example). This will open a file browser in a new tab.

   

3. Wait for the job to fail. Afterwards, refresh the file browser, select all of the files (do not include the desktops or .. folders), and click Download.

4. Take all of the files that were downloaded, put them in a new folder, and zip the folder.

Submit a ticket to us explaining the issue with the zip folder created in Step 4 attached to the email, and we will be happy to assist. If you would like to inspect the log yourself for debugging, the output.log typically will contain the relevant error messages.