/category/hpc
Python and UVA HPC
Overview Python is an integrated technical computing environment that combines sophisticated computation, advanced graphics and visualization, and a high-level programming language.
Learning Python Research Computing offers an online “Introduction to Programming in Python” course. Click here to start learning Python.
Python on the HPC System The default Python is required for system purposes and is generally too old for applications. We offer Python through the Miniforge distribution.
View our Miniforge on the HPC System documentation for details.
VASP and UVA HPC
Description The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling.
Local support is not available. The package is supported by its developers through their documentation site. VASP is licensed software and licenses are issued to individual research groups. Each group must build and maintain its own copy of the code.
Software Category: chem
For detailed information, visit the VASP
website.
Available Versions To find the available versions and learn how to load them, run:
module spider vasp The output of the command shows the available VASP
module versions.
For detailed information about a particular VASP
Image Processing with Fiji and UVA HPC
Description Fiji is an image processing package—a ‘batteries-included’ distribution of
ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
This release is based on ImageJ-2.1.0 and Fiji-2.1.1
Software Category: vis
For detailed information, visit the Fiji
website.
Available Versions The current installation of Fiji
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider fiji The output of the command shows the available Fiji
module versions.
For detailed information about a particular Fiji
module, including how to load the module, run the module spider command with the module’s full version label.
Perl and UVA HPC
Overview Perl is a general-purpose interpreted programming language, originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and bioinformatics.
Available Versions The default Perl is required for system purposes and is generally too old for applications. We offer more recent versions of Perl as modules. To find the available versions and learn how to load them, run:
module spider perl The output of the command shows the available Perl
module versions.
For detailed information about a particular Perl
module, including how to load the module, run the module spider command with the module’s full version label.
AlphaFold and UVA HPC
Description Open source code for AlphaFold
Software Category: bio
For detailed information, visit the AlphaFold
website.
Available Versions The current installation of AlphaFold
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider alphafold The output of the command shows the available AlphaFold
module versions.
For detailed information about a particular AlphaFold
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider alphafold/2.3.0 ModuleVersion Module Load Command alphafold2.3.0 module load apptainer/1.2.2 alphafold/2.3.0 AlphaFold Installation Details Dockerfile We prepared a Docker image based on the official Dockerfile with some modifications.
Cell Ranger and UVA HPC
Description A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Software Category: bio
For detailed information, visit the Cell Ranger
website.
Available Versions To find the available versions and learn how to load them, run:
module spider cellranger The output of the command shows the available Cell Ranger
module versions.
For detailed information about a particular Cell Ranger
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider cellranger/8.0.0 ModuleVersion Module Load Command cellranger8.0.0 module load cellranger/8.0.0
Cell Ranger ATAC and UVA HPC
Description Cell Ranger ATAC is a set of analysis pipelines that process
Chromium Single Cell ATAC data.
Software Category: bio
For detailed information, visit the Cell Ranger ATAC
website.
Available Versions To find the available versions and learn how to load them, run:
module spider cellranger-atac The output of the command shows the available Cell Ranger ATAC
module versions.
For detailed information about a particular Cell Ranger ATAC
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider cellranger-atac/2.0.0 ModuleVersion Module Load Command cellranger-atac2.0.0 module load cellranger-atac/2.0.0
CellProfiler and UVA HPC
Description CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Software Category: bio
For detailed information, visit the CellProfiler
website.
Available Versions The current installation of CellProfiler
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider cellprofiler The output of the command shows the available CellProfiler
module versions.
For detailed information about a particular CellProfiler
module, including how to load the module, run the module spider command with the module’s full version label. For example:
Chemistry and UVA HPC
Overview Many popular software packages for computational chemistry are available on Rivanna and Afton.
General considerations Most computational chemistry packages utilize MPI for parallel execution. Accordingly, the Slurm job scripts should contain the following two SBATCH directives:
#SBATCH -N <M> # request M nodes (replace with a number) #SBATCH –ntasks-per-node=<L> # request L MPI processes per node You should launch your program with srun as the MPI executor, for example for Quantum Espresso
srun pw.x -in mymol.in Please see the page of the particular package you wish to use for more details.
VASP Users
The Vienna Ab-Initio Simulation Package, is licensed by individual groups and we do not have a common installation.
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.
Engineering and UVA HPC
Overview Several software packages for computer-aided engineering are available on the UVA HPC system.
General considerations Some engineering software packages utilize single node, multicore or multi-node MPI for parallel execution. Accordingly, the Slurm job scripts should contain either of the following two SBATCH directives:
Single Node Multi-Core
#SBATCH -N 1 # request single node #SBATCH –cpus-per-task=<X> # request X multiple cpu cores Replace <X> with the actual number of cpu cores to be requested.
Multi Node MPI
#SBATCH -N <M> # request M nodes (replace with a number) #SBATCH –ntasks-per-node=<L> # request L MPI processes per node You should launch your program with srun as the MPI executor, for example for Quantum Espresso
Gaussian and UVA HPC
Description Gaussian is a suite of electronic-structure codes.
Software Category: chem
For detailed information, visit the Gaussian
website.
Available Versions The current installation of Gaussian
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider gaussian The output of the command shows the available Gaussian
module versions.
For detailed information about a particular Gaussian
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gaussian/g16 ModuleVersion Module Load Command gaussiang16 module load gaussian/g16 gaussiangrads16 module load gaussian/grads16 License and Permission We have a site license.
GROMACS and UVA HPC
Description GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Software Category: chem
For detailed information, visit the GROMACS
website.
Available Versions To find the available versions and learn how to load them, run:
module spider gromacs The output of the command shows the available GROMACS
module versions.
For detailed information about a particular GROMACS
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider gromacs/2023.2 ModuleVersion Module Load Command gromacs2023.2 module load gcc/11.
Gurobi and UVA HPC
Gurobi The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multicore processors, using the most advanced implementations of the latest algorithms.
Available Versions To find the available versions and learn how to load them, run:
module spider gurobi The output of the command shows the available Gurobi
module versions. To load the most recent version of Gurobi
, at the terminal window prompt run:
module load gurobi For detailed information about a particular Gurobi
module, including how to load the module, run the module spider command with the module’s full version label.
IDEs and Editors
Editors Several text editors are available on the HPC system. Most provide features such as syntax coloring.
Vim (Vi iMproved) Vim is an updated version of the early Unix text editor vi (for “visual”). It provides many extensions over plain vi. On the HPC system, the vi command is equivalent to the vim command. Vim is primarily utilized through keyboard commands. Once learned, it is extremely efficient to use. Many tutorials can be found online such as https://vim.fandom.com/wiki/Tutorial.
Emacs Emacs is another well-known Unix text editor. Like vim, it is largely operated through the keyboard. It can run a compiler and debugger so has some of the capabilities of an IDE.
Intel and UVA HPC
Description Intel C and C++ compilers
Software Category: compiler
For detailed information, visit the Intel
website.
Available Versions To find the available versions and learn how to load them, run:
module spider intel The output of the command shows the available Intel
module versions.
For detailed information about a particular Intel
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider intel/18.0 ModuleVersion Module Load Command intel18.0 module load intel/18.0 intel2023.1 module load intel/2023.1 intel2024.0 module load intel/2024.0 The 2024.0 version is experimental. Most users should load an older version for the time being.
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.
LAMMPS and UVA HPC
Description LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular-dynamics code. The code is designed to be easy to modify or extend with new functionality. LAMMPS can run on a single core but is designed to be highly efficient running on a large number of cores in parallel using message-passing techniques and a spatial decomposition of the simulation domain. It solves systems ranging from single atoms through polymers and proteins to rigid collections of particles. A variety of force fields is supported.
Local support is not available. LAMMPS has documentation and tutorials at its Website. It has a large and active community of users; to search or join the mailing list see the instructions here.
Libraries and UVA HPC
Available Software Libraries To get an up-to-date list of the installed software libraries, log on to UVA HPC and run the following command in a terminal window:
module keyword lib To get more information about a specific module version, run the module spider command, for example:
module spider hdf5 List of Software Library Modules
Module Category Description
Math & Statistics and UVA HPC
Overview Many popular math and statistics software packages are available on the HPC system.
General considerations Available Math & Statistics Software To get an up-to-date list of the installed math applications, log on to UVA HPC and run the following command in a terminal window:
module keyword math To get more information about a specific module version, run the module spider command, for example:
module spider mathematica List of Math & Statistics Software Modules
Module Category Description clapack math C version of LAPACK eigen math Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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”.
The Bioconda Environment and UVA HPC
Bioconda Python packages Many bioinformatics Python packages are now maintained and available for the popular Anaconda Python distribution. Python packages for the Anaconda distribution are distributed through a variety of different bundles, called channels. The bioconda channel is specifically set up for the maintenance and distribution of popular bioinformatics packages.
Available Versions The current installation of Bioconda
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider bioconda The output of the command shows the available Bioconda
module versions.
For detailed information about a particular Bioconda
module, including how to load the module, run the module spider command with the module’s full version label.
BerkeleyGW and UVA HPC
Description Local support is not available. For detailed documentation and tutorials, visit the BerkeleyGW website. The user forum can be found here. Software Category:
Available Versions To find the available versions and learn how to load them, run:
module spider berkeleygw The output of the command shows the available BerkeleyGW
module versions.
For detailed information about a particular BerkeleyGW
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider ModuleVersion Module Load Command Users may build their own versions of BerkeleyGW if they wish to use a different compiler+MPI combination, or to choose individual optional packages.
Yambo and UVA HPC
Description YAMBO implements Many-Body Perturbation Theory (MBPT) methods (such as GW and BSE) and Time-Dependent Density Functional Theory (TDDFT), which allows for accurate prediction of fundamental properties as band gaps of semiconductors, band alignments, defect quasi-particle energies, optics and out-of-equilibrium properties of materials.
Local support is not available. For detailed documentation and tutorials, visit the Yambo
website. The user forum can be found here.
Software Category: phys
Available Versions To find the available versions and learn how to load them, run:
module spider yambo The output of the command shows the available Yambo
module versions.
For detailed information about a particular Yambo
The Make Tool
Overview Make is a program used primarily on Unix systems to manage compiling and linking (building) programs written in C, C++, Fortran, or other compiled languages. Make operates on targets using rules to create those targets. It has a set of built-in rules but users may write their own or override the default rules. Make scans the dependencies of each target looking for files newer than the target. If it finds them, it recreates the target. Targets may and usually do depend on other targets; make will work its way through the chain to rebuild the final target, which is typically an executable.
Spark and UVA HPC
Description Spark is Hadoop MapReduce done in memory
Software Category: devel
For detailed information, visit the Spark
website.
Available Versions To find the available versions and learn how to load them, run:
module spider spark The output of the command shows the available Spark
module versions.
For detailed information about a particular Spark
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider spark/3.4.1 ModuleVersion Module Load Command spark3.4.1 module load spark/3.4.1 Using Spark interactively There are three ways to use Spark interactively:
Shell prompt Open OnDemand PySpark Open OnDemand Desktop If you need the Web UI you must use the third method (OOD Desktop).
DeepLabCut and UVA HPC
Description DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
Software Category: bio
For detailed information, visit the DeepLabCut
website.
Available Versions To find the available versions and learn how to load them, run:
module spider deeplabcut The output of the command shows the available DeepLabCut
module versions.
For detailed information about a particular DeepLabCut
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider deeplabcut/3.0.0rc4 ModuleVersion Module Load Command deeplabcut3.0.0rc4 module load apptainer/1.2.2 deeplabcut/3.0.0rc4 Dockerfile We cannot use the official Docker image on the UVA HPC system because:
Snakemake and UVA HPC
Description The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Software Category: tools For detailed information, visit the Snakemake
website.
Available Versions The current installation of Snakemake
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider snakemake The output of the command shows the available Snakemake
module versions.
For detailed information about a particular Snakemake
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider snakemake/7.24.2 ModuleVersion Module Load Command snakemake7.24.2 module load snakemake/7.
Workflow Managers and UVA HPC
Workflow managers are used to create reproducible and scalable analysis pipelines. These managers are useful when you have a series of scripts that you want to tie together in the form of a pipeline.
The most popular workflow managers on the HPC system are listed below:
Snakemake Snakemake is a workflow management system written in Python. It integrates with both conda environments and singularities. Cromwell Cromwell is a Workflow Management System geared towards scientific workflows Nextflow Nextflow enables scalable and reproducible scientific workflows using software containers
RAPIDS and UVA HPC
Description The RAPIDS suite of open source software libraries and APIs gives you the ability to execute end-to-end data science and analytics pipelines entirely on GPUs. Licensed under Apache 2.0, RAPIDS is incubated by NVIDIA based on extensive hardware and data science science experience. RAPIDS utilizes NVIDIA CUDA primitives for low-level compute optimization, and exposes GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces.
Software Category: data For detailed information, visit the RAPIDS
website.
Available Versions To find the available versions and learn how to load them, run:
module spider rapidsai The output of the command shows the available RAPIDS
ANSYS and UVA HPC
Description ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater.
Software Category: cae
Local support is minimal; users should make an account at the student forum through the ANSYS
website for technical support and for obtaining detailed information.
Available Versions The current installation of ANSYS
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider ansys The output of the command shows the available ANSYS
module versions.
For detailed information about a particular ANSYS
Code Debugging and UVA HPC
TotalView TotalView is a full-featured, source-level, graphical debugger for applications written in C, C++, Fortran (77 and 90/95/2003), assembler, and mixed source/assembler codes. It is a multiprocess, multithread debugger that supports multiple parallel programming paradigms including MP and OpenMP. The University has a near-site license (256 tokens) for Totalview on all versions of Linux. Visit the TotalView website for detailed documentation.
Available Versions To find the available versions and learn how to load them, run:
module spider totalview The output of the command shows the available TotalView
module versions.
For detailed information about a particular TotalView
module, including how to load the module, run the module spider command with the module’s full version label.
NAMD and UVA HPC
Description NAMD is a parallel molecular dynamics code designed for high-performance simulation of
large biomolecular systems.
Software Category: chem
For detailed information, visit the NAMD
website.
Available Versions The current installation of NAMD
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider namd The output of the command shows the available NAMD
module versions.
For detailed information about a particular NAMD
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider namd/2.14 ModuleVersion Module Load Command namd2.14 module load gcc/11.
ORCA and UVA HPC
Description ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry
with specific emphasis on spectroscopic properties of open-shell molecules.
It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single-
and multireference correlated ab initio methods.
It can also treat environmental and relativistic effects.
Software Category: chem
For detailed information, visit the ORCA
website.
Available Versions The current installation of ORCA
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider orca The output of the command shows the available ORCA
Samtools and UVA HPC
Description SAM Tools provide various utilities for manipulating alignments in the SAM format,
including sorting, merging, indexing and generating alignments in a per-position format.
Software Category: bio
For detailed information, visit the Samtools
website.
Available Versions To find the available versions and learn how to load them, run:
module spider samtools The output of the command shows the available Samtools
module versions.
For detailed information about a particular Samtools
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider samtools/1.17 ModuleVersion Module Load Command samtools1.17 module load samtools/1.17 Build Your Own Version Users may build their own versions of Samtools
SageMath and UVA HPC
Description SageMath (previously Sage or SAGE, “System for Algebra and Geometry Experimentation”[3]) is a computer algebra system with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, numerical analysis, number theory, calculus and statistics. Ref: wikipedia.org
SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
Its mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. Ref: sagemath.
High Performance Computing
Research Computing supports all UVA researchers who are interested in writing code to address their scientific inquiries. Whether these programming tasks are implemented interactively, in a series of scripts or as an open-source software package, services are available to provide guidance and enable collaborative development. RC has specific expertise in object-oriented programming in Matlab, R, and Python.
Examples of service areas include:
Collaborating on package development Reviewing and debugging code Preparing scripts to automate or expedite tasks Developing web interfaces for interactive data exploration Advising on integration of existing software tools UVA has three local computational facilities available to researchers: Rivanna, Afton, and Ivy.
GnuPG and UVA HPC
Description Software Category: For detailed information, visit the GnuPG
website.
Available Versions To find the available versions and learn how to load them, run:
module spider gnupg The output of the command shows the available GnuPG
module versions.
For detailed information about a particular GnuPG
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider ModuleVersion Module Load Command Generate a key To generate a key, execute the following command:
gpg –full-generate-key and follow the on-screen instructions.
If it ends abruptly with this message:
gpg: agent_genkey failed: No pinentry Key generation failed: No pinentry please follow these steps:
OpenFoam and UVA HPC
Description OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Software Category: cae
For detailed information, visit the OpenFOAM
website.
Available Versions To find the available versions and learn how to load them, run:
module spider openfoam The output of the command shows the available OpenFOAM
module versions.
For detailed information about a particular OpenFOAM
module, including how to load the module, run the module spider command with the module’s full version label. For example:
Image Processing & Scientific Visualization and UVA HPC
Available Software To get an up-to-date list of the installed image processing and visualization tools, log on to UVA HPC and run the following command in a terminal window:
module keyword vis To get more information about a specific module version, run the module spider command, for example:
module spider blender/2.78c List of Image Processing and Visualization Software Modules
Module Category Description at-spi2-atk vis AT-SPI 2 toolkit bridge at-spi2-core vis Assistive Technology Service Provider Interface. atk vis ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
Image Processing & Scientific Visualization on the HPC system
Available Software To get an up-to-date list of the installed image processing and visualization tools, log on to UVA HPC and run the following command in a terminal window:
module keyword vis To get more information about a specific module version, run the module spider command, for example:
module spider blender/2.78c List of Image Processing and Visualization Software Modules
Module Category Description at-spi2-atk vis AT-SPI 2 toolkit bridge at-spi2-core vis Assistive Technology Service Provider Interface. atk vis ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
Bioinformatics and UVA HPC
Overview Many commonly used bioinformatics software packages on the HPC clusters are available as individual modules or as Python packages bundled in the bioconda modules.
Please see our HowTo for more information about using this software on the HPC system.
Software Availability If a particular package is not available, several options are available. If it is sufficiently widely used, Research Computing staff will install it as a new module. If we determine that it is too specialized, you can install it yourself. Please use permanent storage such as your home directory to install software. If you have difficulty we can assist you to install the package.
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.
Physics and UVA HPC
Abinit and UVA HPC
Description ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Software Category: chem
For detailed information, visit the Abinit
website.
Available Versions The current installation of Abinit
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider abinit The output of the command shows the available Abinit
module versions.
For detailed information about a particular Abinit
module, including how to load the module, run the module spider command with the module’s full version label.
Amber and UVA HPC
Description Amber (originally Assisted Model Building with Energy Refinement) is software for performing
molecular dynamics and structure prediction.
Software Category: chem
For detailed information, visit the Amber
website
Local support is not available.
Available Versions To find the available versions and learn how to load them, run:
module spider amber The output of the command shows the available Amber
module versions.
For detailed information about a particular Amber
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider amber/22.0 ModuleVersion Module Load Command amber22.0 module load gcc/11.4.0 openmpi/4.1.4 amber/22.
Bowtie2 and UVA HPC
Description Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Software Category: bio
For detailed information, visit the Bowtie2
website.
Available Versions The current installation of Bowtie2
incorporates the most popular packages.
BWA and UVA HPC
Description Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference sequence such as the human genome.
BWA provides three alignment algorithms:
BWA-backtrack BWA-SW BWA-MEM The BWA-backtrack algorithm is exclusively used for short sequence reads up to 100bp, the latter two can be used for sequence reads of up to 1MB. The BWA-MEM algorithm can also be used for high-quality short Illumina sequence reads (< 100bp) in many cases with better performance compared to the original BWA-backtrack algorithm. Therefore, the more universal BWA-MEM algorithm is recommended as a starting point for most alignment scenarios.
Cromwell and UVA HPC
Description Cromwell is a Workflow Management System geared towards scientific workflows.
Software Category: tools For detailed information, visit the Cromwell
website.
Available Versions The current installation of Cromwell
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider cromwell The output of the command shows the available Cromwell
module versions.
For detailed information about a particular Cromwell
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider cromwell/30.1 ModuleVersion Module Load Command cromwell30.1 module load cromwell/30.1 The Backend Configuration In order to allow Cromwell to interact with the HPC system (via SLURM), we need to define a backend to dispatch jobs.
GATK and UVA HPC
Description The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
with a primary focus on variant discovery and genotyping as well as strong emphasis on
data quality assurance. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size.
Software Category: bio
For detailed information, visit the GATK
website.
For a GitHub reference, visit: https://github.com/broadinstitute/gatk
Available Versions The current installation of GATK
incorporates the most popular packages. To find the available versions and learn how to load them, run:
Julia and UVA HPC
Description Julia is a high-level programming language designed for high-performance numerical analysis and computational science. Distinctive aspects of Julia’s design include a type system with parametric polymorphism and types in a fully dynamic programming language and multiple dispatch as its core programming paradigm. It allows concurrent, parallel and distributed computing, and direct calling of C and Fortran libraries without glue code. A just-in-time compiler that is referred to as “just-ahead-of-time” in the Julia community is used. [Ref: Wikipedia](https://en.wikipedia.org/wiki/
Software Category: lang
For detailed information, visit the julia
website.
Available Versions To find the available versions and learn how to load them, run:
Mathematica and UVA HPC
Description Mathematica is an integrated technical computing environment that combines numeric and symbolic computation, advanced graphics and visualization, and a high-level programming language.
There are several website resources with Mathematica tutorials and parallel Mathematica training sessions.
Software Category:
For detailed information, visit the Mathematica
website.
Available Versions To find the available versions and learn how to load them, run:
module spider mathematica The output of the command shows the available Mathematica
module versions.
For detailed information about a particular Mathematica
module, including how to load the module, run the module spider command with the module’s full version label. For example:
NCBI Blast and UVA HPC
Description Basic Local Alignment Search Tool, or BLAST, is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences.
Software Category: bio
For detailed information, visit the NCBI Blast
website.
Available Versions The current installation of NCBI Blast
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider blast The output of the command shows the available NCBI Blast
module versions.
For detailed information about a particular NCBI Blast
module, including how to load the module, run the module spider command with the module’s full version label.
Picard and UVA HPC
Description A set of tools (in Java) for working with next generation sequencing data in the BAM format. Software Category: bio
For detailed information, visit the Picard
website.
Available Versions To find the available versions and learn how to load them, run:
module spider picard The output of the command shows the available Picard
module versions.
For detailed information about a particular Picard
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider picard/2.27.5 ModuleVersion Module Load Command picard2.27.5 module load picard/2.27.5
QuantumEspresso and UVA HPC
Description Quantum ESPRESSO is an integrated suite of computer codes
for electronic-structure calculations and materials modeling at the nanoscale.
It is based on density-functional theory, plane waves, and pseudopotentials
(both norm-conserving and ultrasoft).
Local support is not available. For detailed documentation and tutorials, visit the QuantumEspresso website. QuantumEspresso (QE) has a large and active community of users; to search or join the mailing list see the instructions here. Software Category: chem
Available Versions We built versions of QE incorporating the most popular optional packages. To find the available versions and learn how to load them, run:
module spider quantumespresso The output of the command shows the available QuantumEspresso
SAS and UVA HPC
Description Statistical analysis package
Software Category: math
For detailed information, visit the SAS
website.
Available Versions To find the available versions and learn how to load them, run:
module spider sas The output of the command shows the available SAS
module versions.
For detailed information about a particular SAS
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider sas/9.4 ModuleVersion Module Load Command sas9.4 module load sas/9.4 Note: SAS scripts may be run on the HPC system through the Slurm queueing system in batch mode, but production interactive jobs on the frontend are not permitted.
SmrtLink and UVA HPC
Description PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule,
Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI
or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through
the extensive set of APIs provided
Software Category: bio
For detailed information, visit the SmrtLink
website.
Available Versions To find the available versions and learn how to load them, run:
module spider smrtlink The output of the command shows the available SmrtLink
module versions.
For detailed information about a particular SmrtLink
module, including how to load the module, run the module spider command with the module’s full version label.
TeX Live and UVA HPC
Description TeX Live is TeX Live is intended to be a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
Software Category: tools
For detailed information, visit the TeX Live
website.
Available Versions To find the available versions and learn how to load them, run:
module spider texlive The output of the command shows the available TeX Live
WDLTool and UVA HPC
Description A Java command-line tool co-developed with WDL that performs utility functions, including syntax validation and generation of input JSON templates.
Software Category: tools For detailed information, visit the WDLTool
website.
Available Versions To find the available versions and learn how to load them, run:
module spider wdltool The output of the command shows the available WDLTool
module versions.
For detailed information about a particular WDLTool
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider wdltool/0.14 ModuleVersion Module Load Command wdltool0.14 module load wdltool/0.14
