/tag/multi-core

  • 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.
  • 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/2.2.0 ModuleVersion Module Load Command cellprofiler2.2.0 module load singularity/2.6.1 cellprofiler/2.
  • 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:
  • 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: 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.
  • 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.
  • 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.
  • 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: 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:
  • 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 GaussView The GaussView graphical interface is available on Rivanna.
  • 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:
  • 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 (http://samtools.github.io/hts-specs) 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/2.1.1 ModuleVersion Module Load Command picard2.1.1 module load picard/2.1.1 picard2.
  • 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.
  • 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: 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/1.4.1 ModuleVersion Module Load Command samtools1.4.1 module load gcc/7.
  • 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