/category/software
BerkeleyGW on Rivanna
Description The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. Local support is not available. For detailed documentation and tutorials, visit the BerkeleyGW website. The user forum can be found here.
Software Category: URL: https://www.berkeleygw.org
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.
Yambo on Rivanna
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: URL: https://www.yambo-code.org/
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 module, including how to load the module, run the module spider command with the module’s full version label.
Cell Ranger on Rivanna
Description A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
Software Category: URL: https://www.10xgenomics.com/
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/5.0.0 ModuleVersion Module Load Command cellranger5.0.0 module load cellranger/5.
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 on Rivanna
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/3.1.2 ModuleVersion Module Load Command spark3.1.2 module load spark/3.1.2 Using Spark interactively Please request an ijob or a Desktop session.
Cell Ranger ATAC on Rivanna
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.
DeepLabCut on Rivanna
Description DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
Software Category: URL: https://github.com/DeepLabCut/DeepLabCut
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/2.2.1.1-anipose ModuleVersion Module Load Command deeplabcut2.2.1.1-anipose module load singularity/3.7.1 deeplabcut/2.2.1.1-anipose deeplabcut2.2 module load singularity/3.
AlphaFold on Rivanna
Description Open source code for AlphaFold
Software Category: URL: https://github.com/deepmind/alphafold 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/2.1.2 ModuleVersion Module Load Command alphafold2.1.2 module load singularity/3.7.1 alphafold/2.1.2 alphafold2.2.0 module load singularity/3.
Snakemake on Rivanna
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/6.0.5 ModuleVersion Module Load Command snakemake6.
Workflow Managers on Rivanna
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 Rivanna 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 on Rivanna
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 module versions.
ANSYS on Rivanna
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 module, including how to load the module, run the module spider command with the module’s full version label.
Code Debugging on Rivanna
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 on Rivanna
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.
ORCA on Rivanna
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 module versions.
Samtools on Rivanna
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/1.10 ModuleVersion Module Load Command samtools1.10 module load samtools/1.
SageMath on Rivanna
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.
The Bioconda Environment on Rivanna
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. On Rivanna, we offer two bioconda modules, one using Python 2.7 and the other using Python 3.6.
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.
Building Your Code on Rivanna
Building your Application Creating an executable from source with a compiled language requires two steps, compiling and linking. The combination of these is generally called building. The output of the compiler is generally an object file, which on Unix will end in a .o suffix. Object files are machine code and are not human-readable, but they are not standalone and cannot be executed. The linker, which is usually invoked through the compiler, takes all object files, along with any external libraries, and creates the executable (also called a binary).
Compilers are invoked on source files with a line such as
Intel on Rivanna
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 intel20.0 module load intel/20.0 intel2022.11 module load intel/2022.11 Compiler For general information on building code using compilers, please see our How-To pages:
GnuPG on Rivanna
Description GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880 (also known as PGP). GnuPG allows you to encrypt and sign your data and communications; it features a versatile key management system, along with access modules for all kinds of public key directories. Software Category: tools
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.
CellProfiler on Rivanna
Description CellProfiler is an image processing package to generate morphometric measurements.
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:
module spider cellprofiler/3.1.8 ModuleVersion Module Load Command cellprofiler3.1.8 module load singularity/3.7.1 cellprofiler/3.
OpenFoam on Rivanna
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: URL: http://www.openfoam.org/
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 on Rivanna
Available Software To get an up-to-date list of the installed image processing and visualization tools, log on to Rivanna 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
function searchFunction() { var input, filter, table, tr, td, i, txtValue; input = document.getElementById(“searchInput”); filter = input.value.toUpperCase(); table = document.getElementById(“moduleTable”); tr = table.getElementsByTagName(“tr”); for (i = 0; i -1) { tr[i].style.display = “"; } else { tr[i].style.display = “none”; } } } } Module Category Description atk vis ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.
Image Processing & Scientific Visualization on Rivanna
Available Software To get an up-to-date list of the installed image processing and visualization tools, log on to Rivanna 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
function searchFunction() { var input, filter, table, tr, td, i, txtValue; input = document.getElementById(“searchInput”); filter = input.value.toUpperCase(); table = document.getElementById(“moduleTable”); tr = table.getElementsByTagName(“tr”); for (i = 0; i -1) { tr[i].style.display = “"; } else { tr[i].style.display = “none”; } } } } Module Category Description atk vis ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.
IDEs and Editors
Editors Several text editors are available on Rivanna. 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 Rivanna, 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.
Bioinformatics on Rivanna
Overview Many commonly used bioinformatics software packages on Rivanna 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 Rivanna.
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 on Rivanna
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: URL: https://www.blender.org 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.
Chemistry on Rivanna
Overview Many popular software packages for computational chemistry are available on Rivanna.
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.
Engineering on Rivanna
Overview Several software packages for computer-aided engineering are available on Rivanna.
General considerations Some engineering software packages utilize single node, multi-core 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
Gurobi on Rivanna
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 multi-core 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.
Jupyter Lab on Rivanna
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.
However, to use JupyterLab, you must have an account on Rivanna.
Accessing JupyterLab To access JupyterLab, you will begin by connecting to our Open OnDemand portal:
Open a web browser and go to https://rivanna-portal.hpc.virginia.edu. Use your Netbadge credentials to log in.
Libraries on Rivanna
Available Software Libraries To get an up-to-date list of the installed software libraries, log on to Rivanna 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 hdf5/1.10.4
List of Software Library Modules
function searchFunction() { var input, filter, table, tr, td, i, txtValue; input = document.getElementById(“searchInput”); filter = input.value.toUpperCase(); table = document.getElementById(“moduleTable”); tr = table.getElementsByTagName(“tr”); for (i = 0; i -1) { tr[i].style.display = “"; } else { tr[i].style.display = “none”; } } } } Module Category Description armadillo numlib Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.
Math & Statistics on Rivanna
Overview Many popular math and statistics software packages are available on Rivanna.
General considerations Available Math & Statistics Software To get an up-to-date list of the installed math applications, log on to Rivanna 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/12.1
List of Math & Statistics Software Modules
function searchFunction() { var input, filter, table, tr, td, i, txtValue; input = document.getElementById(“searchInput”); filter = input.value.toUpperCase(); table = document.getElementById(“moduleTable”); tr = table.getElementsByTagName(“tr”); for (i = 0; i -1) { tr[i].
Matlab on Rivanna
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 Rivanna.
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://rivanna-portal.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 on Rivanna
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/5.6.0 ModuleVersion Module Load Command paraview5.6.0 module load gcc/9.2.0 openmpi/3.1.6 paraview/5.6.0 paraview5.6.0 module load intel/18.0 intelmpi/18.0 paraview/5.6.0 Interactive Sessions through Rivanna’s Web Portal Interactive sessions of ParaView can be launched through Rivanna’s web portal, Open OnDemand.
Perl on Rivanna
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 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. For example:
module spider perl/5.24.0 ModuleVersion Module Load Command perl5.24.0 module load perl/5.
Physics on Rivanna
Python on Rivanna
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 Rivanna The default Python is required for system purposes and is generally too old for applications. We offer Python through the Anaconda distribution from Continuum Analytics. Anaconda bundles a large number of popular modules and packages, as well as the Spyder IDE, an iPython console, and Jupyter notebooks.
View our Anaconda on Rivanna documentation for details.
R and RStudio on Rivanna
Overview R is a programming language that often is used for data analytics, statistical programming, and graphical visualization.
Loading the R module On Rivanna, R is available through our module system. For example, to load R, you can type:
module load goolf/7.1.0_3.1.4 R Notice that we included goolf version 7.1.0_3.1.4 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. Also, because 7.1.0_3.1.4 is no longer the default version, we must specify the version of goolf.
RStudio Server on Rivanna
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 Rivanna. However, to use RStudio Server, you must have an account on Rivanna. Instructions for setting up an acccount 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://rivanna-portal.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”.
Abinit on Rivanna
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 on Rivanna
Description A suite of biomolecular simulation programs. It began in the late 1970’s, and is maintained by an active development community. Software Category: bio
For detailed information, visit the Amber website.
Local support is not available.
Available Versions The current installation of Amber lags behind the latest release due to license restrictions. To find the available versions and learn how to load them, run:
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:
Bowtie2 on Rivanna
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 on Rivanna
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 on Rivanna
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.
GATK on Rivanna
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: URL: http://www.broadinstitute.org/gatk/
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:
Gaussian on Rivanna
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 on Rivanna
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/2021.2 ModuleVersion Module Load Command gromacs2021.
Image Processing with Fiji on Rivanna
Description Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Software Category: tools
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. For example:
module spider fiji/1.52 ModuleVersion Module Load Command fiji1.
Julia on Rivanna
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:
Keras on Rivanna
Description Keras is a high-level neural networks application programming interface (API), written in Python and capable of running on top of TensorFlow, CNTK, or Theano. On Rivanna, we provide TensorFlow containers that include the Keras API. Since version 1.12.0, TensorFlow contains its own Keras API implementation as described on the TensorFlow website.
Using Keras with TensorFlow containers Like TensorFlow itself, Python code that utlizes the Keras package can be run interactively as Jupyter Notebooks, in interactive shell jobs, or non-interctively as Slurm batch jobs. Rivanna provides several nodes with graphics processing units (GPUs) that should be used when running Keras code.
LAMMPS on Rivanna
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.
Mathematica on Rivanna
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 on Rivanna
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 on Rivanna
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/2.23.4 ModuleVersion Module Load Command picard2.23.4 module load picard/2.23.4
QuantumEspresso on Rivanna
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 module versions.
SAS on Rivanna
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 Rivanna through the Slurm queueing system in batch mode, but production interactive jobs on the frontend are not permitted.
SmrtLink on Rivanna
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:
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 on Rivanna
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 module versions.
VASP on Rivanna
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 module, including how to load the module, run the module spider command with the module’s full version label.
WDLTool on Rivanna
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
