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Code Server and UVA HPC
Description Run VS Code on any machine anywhere and access it in the browser. Software Category: tools
For detailed information, visit the Code Server
website.
Available Versions To find the available versions and learn how to load them, run:
module spider code-server The output of the command shows the available Code Server
module versions.
For detailed information about a particular Code Server
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider code-server/4.16.1 ModuleVersion Module Load Command code-server4.16.1 module load apptainer/1.2.2 code-server/4.16.1 code-server4.16.1 module load code-server/4.16.1 code-server4.92.2 module load code-server/4.
Jupyter Lab and UVA HPC
Overview Jupyter Notebooks are documents which can combine executable code, formatted text, and interactive graphics into a single file. Because Notebooks can be shared, they provide developers with a tool for capturing and explaining their computational results. To use a Jupyter Notebook, a web application, such as JupyterLab, is needed.
We now provide a web portal where JupyterLab can be accessed on Rivanna and Afton.
However, to use JupyterLab, you must have an account on UVA HPC.
Accessing JupyterLab To access JupyterLab, you will begin by connecting to our Open OnDemand portal:
Open a web browser and go to https://ood.hpc.virginia.edu. Use your Netbadge credentials to log in.
Nvidia Clara Parabricks and UVA HPC
Overview Nvidia Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. It contains GPU-enabled versions of popular bioinformatics tools such as the aligners BWA-Mem and STAR.
Loading the container On the HPC system, Clara Parabricks is available as an Apptainer container. To load the clara-parabricks container module, you can type:
module load apptainer clara-parabricks The load command will load a default version of Clara Parabricks, unless another version is specified. To see the available versions, type:
module spider clara-parabricks Running Clara Parabricks tools The Clara Parabricks container on the HPC system includes many bioinformatics tools for genomics and transcriptomics.
R and RStudio and UVA HPC
Overview R is a programming language that often is used for data analytics, statistical programming, and graphical visualization.
Loading the R module On the UVA HPC system, R is available through our module system. For example, to load R, you can type:
module load goolf R Notice that we included goolf in the load command. There are two reasons why including goolf is important:
R was built with a compiler, an interface to OpenMPI, and other utilities. The goolf module will ensure that each of these items is loaded.
R has many computationally-intensive packages that are built with C, C++, or Fortran.
RStudio Server and UVA HPC
Overview RStudio Server is a web-based interface to RStudio – a development environment for R programming.
Research Computing provides a web portal where RStudio Server can be accessed on the HPC system. However, to use RStudio Server, you must have an account on UVA HPC. Instructions for setting up an account can be found here.
Accessing RStudio Server To access RStudio Server, you will begin by connecting to our Open OnDemand portal:
Open a web browser and go to URL: https://ood.hpc.virginia.edu. Use your “Netbadge” credentials to log in. On the top right of the menu bar of the Open OnDemand dashboard, click on “Interactive Apps”.
Blender and UVA HPC
Description Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline,
modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video
editing and game creation.
Software Category: vis For detailed information, visit the Blender
website.
Available Versions The current installation of Blender
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider blender The output of the command shows the available Blender
module versions.
For detailed information about a particular Blender
module, including how to load the module, run the module spider command with the module’s full version label.
Matlab and UVA HPC
MATLAB is an integrated technical computing environment from the MathWorks that combines array-based numeric computation, advanced graphics and visualization, and a high-level programming language. Separately licensed toolboxes provide additional domain-specific functionality.
Mathworks provides MATLAB examples and tutorials for all experience levels here.
Available Versions To find the available versions and learn how to load them, run:
module spider matlab The output of the command shows the available MATLAB
module versions. To load the most recent version of MATLAB
, at the terminal window prompt run:
module load matlab For detailed information about a particular MATLAB
module, including how to load the module, run the module spider command with the module’s full version label.
Open OnDemand Desktop
Overview The Open OnDemand Desktop app provides a full Linux Desktop environment launched on user-specified allocated hardware resources which may include a compute node equipped with graphical processing units (GPUs).
This is the preferred mechanism to start compute intensive applications that require a graphical user interface (GUI) on the HPC system.
Accessing the Desktop App To access the app and start a desktop session, connect to our Open OnDemand portal:
Open a web browser and go to https://ood.hpc.virginia.edu. Use your Netbadge credentials to log in. On the top right of the menu bar of the Open OnDemand dashboard, click on Interactive Apps.
ParaView and UVA HPC
Description ParaView is a scientific parallel visualizer. Software Category: vis
For detailed information, visit the ParaView
website.
Available Versions To find the available versions and learn how to load them, run:
module spider paraview The output of the command shows the available ParaView
module versions.
For detailed information about a particular ParaView
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider paraview/5.11.0 ModuleVersion Module Load Command paraview5.11.0 module load gcc/11.4.0 openmpi/4.1.4 paraview/5.11.0 Interactive Sessions through Open Ondemand Interactive sessions of ParaView
can be launched through the HPC web portal, Open OnDemand.
