For questions, please open a UAService ticket and assign to the Tools Team.
File Browser
Overview
The file browser provides easy access to your /home, /xdisk, and /groups directories and allows you to view, edit, copy, and rename your files. You may also transfer small files between HPC and your local workstation using this interface. For larger transfers, see our section on Transferring Data for more efficient methods.
Access Files
In the browser at the top of the screen, select the Files dropdown
You will be able to select your home directory, /groups, or /xdisk. If you select /groups or /xdisk, enter your PI's NetID in the Filter field to find your shared group space.
Editing Files
First, navigate to the file you wish to edit. Then, click the vertical ellipses on the right-hand side and select Edit
This will open a file editor in your browser where you may select your color theme, text size, and syntax highlighting.
The OnDemand file manager is a quick easy way to transfer small files (<1GB). For larger files, see:
Transferring Data
Uploading Files
In the file browser, navigate to the directory where you would like to upload your files, then select "Upload" :
This will bring up a popup where you can open a file browser to search for your files. Alternatively, you can drag/drop files/directories onto the tile.
Downloading Files
To download small files from your HPC account to your local workstation, navigate to the file(s) you'd like to to transfer and check the box(es) on the left. Clicking download will initiate the transfer to your local Downloads directory.
Job Viewer and Composer
Job Viewer
The Job Viewer allows you to check the status and time remaining of your running jobs. You can also cancel your jobs using this interface. Note: be careful looking at All Jobs since this will likely timeout trying to organize them all. To use the Job Viewer, navigate to the Jobs dropdown and select Active Jobs.
This will open a new page listing all your running and pending jobs. You may delete them by clicking the red trash icon under Actions, or view more information about individual jobs using the dropdown on the left next to the ID.
Job Composer
The Job Composer lets you create and run a SLURM script on any of our three clusters. It should be noted that the Job Composer creates a special string of directories in your /home starting with ondemand/ which is where both your submission scripts and output files will be stored. Make note of the path to your files on the right-hand side of the Job Composer screen under Script location.
Command Line Access
Need command line access to a terminal on HPC? No problem! Simply select the Clusters dropdown menu to connect to one of HPC's login nodes.
Interactive Graphical Applications
Overview
Open OnDemand provides access to graphical interfaces for some popular software. These can be found under Interactive Apps through the Open OnDemand web browser. The process of starting and accessing these applications is the same.
Web Form
First, select the desired application from Interactive Apps. This will take you to a form where you will enter your job information. This includes the entries in the following table:
| Field | Description | Example Value |
|---|---|---|
| Cluster | Select which cluster to submit the job request to. | ElGato |
| Run Time | The maximum number of hours the job can run. | 4 |
| Core Count on a single node | The number of CPUs needed. This affects the amount of memory your job is allocated. The maximum that can be requested is dependent on which cluster you choose. | 16 |
| Memory per core | The amount of memory needed per core. The amount that can be requested is dependent on which cluster you choose and your desired node type. Warning: if you request more than is available on a standard node, you may be allocated a high memory node. The wait times for these machines can be significantly longer. | 4 |
| GPUs required | The number of GPUs needed for your job, if any. This field may be left blank or set to 0 if no GPU is desired. Up to 4 may be requested on a single Puma node, 1 may be requested on Ocelote, and 0 on ElGato. | 1 |
| PI Group | Your accounting group. If you do not know your group name, you can either check in the user portal, or can run va on the command line. If the group you entered does not exist, you will receive an error "sg: group 'foo' does not exist" | your_group |
| Queue | The queue, or partition, to use. Standard is the most common. If your group has buy-in hours, you may use High Priority. | Standard |
Once you've entered all your details, click Launch at the bottom of the page. This will take you to a tile with information about your job including job ID and session ID. This information can used for debugging purposes.
When you first submit your job, it will show as having a status of "Queued". Once your job reaches the front of the queue, it will show a status of "Starting". When your session is ready, you can launch the application using Connect at the bottom of the tile.
Graphical Applications
Interactive Virtual Desktops
One nice feature of Open OnDemand is the ability to interact with HPC using a virtual Desktop environment. This provides a user-friendly way to run applications, perform file management, and navigate through your directories as though you were working with a local computer. Additionally, it eliminates the need to use X11 forwarding when working with GUI applications allowing an easy way to interact with software such as Matlab, VisIt, or Anaconda.
Jupyter Notebooks
The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text.
Kernels
Various Kernels are available to use through this OOD Application including Python, R, and Bash. Additionally, you have the ability to create your own python kernels to control python version and provide access to your own custom environments. You can also create kernels to enable access to other software applications. For example, if you want to add a kernel for Julia, you can log into an interactive terminal session and use the Julia module to add IJulia. When you log into your next Jupyter session, you should see the kernel in the "new" dropdown menu:
$ module load julia
$ julia
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.6.1 (2021-04-23)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> using Pkg
julia> Pkg.add("IJulia")
Default Directory
When you start a Jupyter notebook, by default your working directory will be your home. If you would like to change this so that your session starts in a different location, you'll need to add a line to the hidden file ~/.bashrc in your home. To do this, open your ~/.bashrc in a text editor and add the following, substituting your desired path in for /path/to/directory:
export NOTEBOOK_ROOT=/path/to/directory
RStudio
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. For an overview of the RStudio IDE, see: https://www.rstudio.com/products/RStudio/. Additionally, practice examples are available from https://www.rstudio.com/products/RStudio/.
For information on using R on HPC, see our online documentation on Using and Customizing R Packages.
Matlab
A GUI for multiple versions of Matlab is available. You can select which version to use in the web form when specifying your resources.
Ansys
Multiple versions of the engineering application Ansys are available. You can specify which version to use in the web form when specifying your resources. To receive Ansys-specific support: Getting Help
