/tag/multi-core
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
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.
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:
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.
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.
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
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).
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
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.
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
