Applications

Research Computing offers a wide range of applications on the HPC clusters. Not all clusters have the same set of applications, as some clusters are more narrowly focused on a particular discipline.

  • Applications
    ABAQUS ABAQUS is used for both the modeling and analysis of mechanical components and assemblies (pre-processing) and visualizing the finite element analysis result.
    available modules: abaqus/6.10-2, abaqus/6.13-4(default)
    ABySS ABySS, Assembly by Short Sequences, is a de novo, parallel, paired-end sequence assembler that is designed for short reads.
    available modules: abyss/1.9.0, abyss/1.9.0-ib
    ALLPATHS‐LG ALLPATHS‐LG is a whole‐genome shotgun assembler that can generate high‐quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.
    available modules: allpathslg/52488
    ANSA ANSA is an advanced multidisciplinary CAE pre-processing tool that provides all the necessary functionality for full-model build up, from CAD data to ready-to-run solver input file, in a single integrated environment. (13.1.3 / 64-bit)
    available modules: ansa/13.1.3
    ART ART (art_Illumina Q version) is a simulation program to generate sequence read data of Illumina sequencers. (03.19.15 / 64-bit / binary pkg)
    available modules: art/03.19.15
    AsciiDoc AsciiDoc is a presentable text document format for writing articles, UNIX man pages and other small to medium sized documents. The asciidoc(1) command translates AsciiDoc files to HTML, DocBook and LinuxDoc formats.
    available modules: asciidoc/8.6.9
    Bazel Bazel is Google’s own build tool. Bazel has built-in support for building both client and server software, and also provides an extensible framework that you can use to develop your own build rules.
    available modules: bazel/0.3.0
    Bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
    available modules: bioconductor/3.2
    BLAST NCBI BLAST (Basic Local Alignment Search Tool) is a suite of programs for aligning query sequences against those present in a selected target database.
    available modules: blast/2.2.29+, blast/2.3.0+
    Bowtie2 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 to relatively long (e.g. mammalian) genomes.
    available modules: bowtie2/2.1.0
    BWA BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
    available modules: bwa/0.7.12
    Caffe Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors.
    available modules: caffe/1.0.0rc3, caffe/1.0.0rc3-cuda
    CG2AT-Traj CG2AT-Traj is a program to convert a coarse-grained molecular dynamics simulation trajectory to an all-atom trajectory. This project started on Sat Oct 17 2015 as part of a ‘hack day’ at the CECAM workshop for ‘setting up simulations’.
    available modules: cg2at/traj
    ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences.
    available modules: clustalw/2.1, clustalw-mpi/0.13
    CMake CMake is a cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
    available modules: cmake/3.4.1
    CNAnalysis Constraint Network Analysis (CNAnalysis) is a graph theory-based rigidity analysis approach that analyzes global and local flexibility and rigidity characteristics of proteins by carrying out thermal unfolding simulations.
    available modules: cna/2.0
    Eclipse Eclipse provides IDEs and platforms nearly every language and architecture, including Java, C/C++, JavaScript and PHP
    available modules: eclipse/4.3.2
    Espresso Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
    available modules: espresso/5.3.0-intel-mpi, espresso/5.3.0-mpi
    ExAML This code implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.
    available modules: examl/3.0.16
    FASTX-Toolkit The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
    available modules: fastx_toolkit/0.0.14
    FFmpeg FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. It contains libavcodec, libavutil, libavformat, libavfilter, libavdevice, libswscale and libswresample which can be used by applications. As well as ffmpeg, ffserver, ffplay and ffprobe which can be used by end users for transcoding, streaming and playing.
    available modules: ffmpeg/3.0
    Gaussian Gaussian 03 provides state-of-the-art capabilities for electronic structure modeling.
    available modules: gaussian/03
    GRASS GRASS (Geographic Resources Analysis Support System), is a free and open source GIS software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.
    available modules: grass/7.0.3
    GROMACS 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.
    available modules: gromacs/5.0, gromacs/5.0-mpi-ib, gromacs/5.1.2-mpi-cuda, gromacs/5.0-cuda, gromacs/5.1.2, gromacs/5.1.2-mpi-ib, gromacs/5.0-mpi, gromacs/5.1.2-cuda, gromacs/5.0-mpi-cuda, gromacs/5.1.2-mpi
    ITK ITK is an open-source software toolkit for performing registration and segmentation. Segmentation is the process of identifying and classifying data found in a digitally sampled representation.
    available modules: itk/4.9.0
    LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Packages built: no-all yes-molecule yes-class2 yes-opt yes-shock yes-replica yes-manybody yes-kspace yes-mc yes-peri yes-user-reaxc yes-xtc yes-user-misc yes-user-phonon
    available modules: lammps/15May15, lammps/16Feb16(default)
    MAFFT Multiple alignment program for amino acid or nucleotide sequences. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of<∼200 sequences), FFT-NS-2 (fast; for alignment of<∼30,000 sequences), etc. (7.273woe)
    available modules: mafft/7.055woe, mafft/7.273woe(default)
    Mathematica Mathematica is a software package which is ideal for communicating scientific ideas, whether this is visualization of a concept in an intro-level course, or creating a simulation of a new idea related to research.
    available modules: mathematica/8.0
    MATLAB MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming.
    available modules: matlab/R2014a, matlab/R2015b(default)
    MEME Multiple Em for Motif Elicitation. The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
    available modules: meme/4.9.1, meme/4.9.1-ib
    Modeller MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
    available modules: modeller/9.16
    MPIBlast Open-Source Parallel BLAST (Basic Local Alignment Search Tool). BLAST is a suite of programs provided by NCBI for aligning query sequences against those present in a selected target database.
    available modules: mpiblast/1.6.0, mpiblast/1.6.0-ib
    MPP-Dyna LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems.
    available modules: mpp-dyna/7.1.1, mpp-dyna/8.0.0(default), mpp-dyna/7.1.1-ib, mpp-dyna/8.0.0-ib
    MrBayes MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
    available modules: mrbayes/3.2.2(default), mrbayes/3.2.2-ib
    NAMD NAMD (2.11 x86_64 mpi) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
    available modules: namd/2.11-mcore, namd/2.11-mcore-cuda, namd/2.11-mpi(default)
    NCO The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.
    available modules: nco/4.4.8
    NetBeans NetBeans is a free, open source IDE that allows you to quickly and easily develop desktop, mobile and web applications with Java, HTML5, PHP, C/C++ and more.
    available modules: netbeans/8.0.2 netbeans/8.1(default)
    NetLogo NetLogo is a multi-agent programmable modeling environment.
    available modules: netlogo/5.0.4, netlogo/5.1.0(default)
    Node.js Node.js is a JavaScript runtime built on Chrome’s V8 JavaScript engine. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient.
    available modules: node.js/4.4.0
    Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
    available modules: openbabel/2.3.2
    OpenCV OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
    available modules: opencv/3.1.0, opencv/3.1.0-cuda
    OpenFOAM OpenFOAM is a free, open source CFD software package developed by OpenCFD Ltd at ESI Group and distributed by the OpenFOAM Foundation. (3.0+ / 64-bit / gnu-compiled)
    available modules: openfoam/3.0+, openfoam/3.0+ib
    Paraview ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques.
    available modules: paraview/5.0.0-mpi
    PDL PDL (‘Perl Data Language’) gives standard Perl the ability to compactly store and speedily manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing.
    available modules: pdl/2.015
    Peridigm Peridigm is an open-source computational peridynamics code developed at Sandia National Laboratories for massively-parallel multi-physics simulations.
    available modules: peridigm/1.4.1-mpi
    PEtot PEtot parallel total Energy (Etot) is a parallel plane wave pseudopotential program for atomistic total energy calculation based on density functional theory.
    available modules: petot/v3
    PLINK PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
    available modules: plink/1.90b3.32
    POY POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned).
    available modules: poy/5.0.1, poy/5.1.2, poy/5.0.1-ib, poy/5.1.2-ib(default)
    QIIME QIIME (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
    available modules: qiime/1.9.1
    QuickFlash QuickFlash provides high-performance data access and processing routines for large, multi-dimensional datasets in environments where memory and access to other software may be limited, such as on desktop computers or parallel supercomputer nodes.
    available modules: quickflash/1.0.0, quickflash/1.0.0-ib
    R R is a free software environment for statistical computing and graphics.
    available modules: R/3.1.1, R/3.2.3(default), R/3.3.1
    RAxML RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
    available modules: raxml/7.4.2, raxml/8.2.4(default), raxml/7.4.2-mpi, raxml/8.2.4-mpi
    Rosetta Rosetta is a comprehensive software suite for modeling macromolecular structures.
    available modules: rosetta/2015.02, rosetta/2016.10(default)
    RStudio RStudio IDE is a powerful and productive user interface for R.
    available modules: rstudio/0.99
    Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data, allowing you to read/write/edit/index/view SAM/BAM/CRAM format.
    available modules: samtools/0.1.18, samtools/1.3(default)
    SAS SAS (Statistical Analysis System) is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
    available modules: sas/9.4
    SEER SEER, Sequence Element (kmer) Enrichment Analysis, finds sequence elements (words/kmers) that are enriched in samples with a given phenotype, which may be binary or continuous.
    available modules: seer/1.1.1-intel
    Siesta SIESTA,a first-principles materials simulation code using DFT,is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
    available modules: siesta/3.2, siesta/4.0(default)
    SMOG SMOG v2 is a software package designed to allow the user to start with a structure of a biomolecule (i.e. a PDB file) and construct a structure-based model, which is then simulated using Gromacs, or NAMD.
    available modules: smog/2.0.2
    SOWHat SOWHat automates the SOWH phylogenetic topology test. It works on amino acid, nucleotide, and binary character state datasets. Partitions (including codon position partitioning) can be specified.
    available modules: sowhat/0.36
    SPAdes SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
    available modules: spades/2.5., 1spades/3.7.1(default)
    StarCCM+ StarCCM+ (11.04) is much more than just a CFD solver, STAR-CCM+ is an entire engineering process for solving problems involving flow (of fluids or solids), heat transfer and stress.
    available modules: starccm/10.04, starccm/11.04(default), starccm/9.02
    STATA loads the env for stata 11.0
    available modules: stata/11
    UDUNITS The UDUNITS package supports units of physical quantities. Its C library provides for arithmetic manipulation of units and for conversion of numeric values between compatible units.
    available modules: udunits/2.2.19
    VCFtools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
    available modules: vcftools/0.1.10
    VisIt VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
    available modules: visit/2.10.0(default), visit/2.9.0, visit/2.10.0-ib, visit/2.9.0-ib
    VTK The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, modeling, image processing, volume rendering, scientific visualization, and information visualization.
    available modules: vtk/6.2.0, vtk/7.0.0
    WHAM WHAM is a fast, memory efficient implementation of the Weighted Histogram Analysis Method (WHAM).
    available modules: wham/2.0.9
    WRF The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs.
    available modules: wrf/3.7.1-intel(default), wrf/3.7.1-intel-serial, wrf/3.7.1-intel-ib, wrf2grads/2.0-intel
    WRF2Grads Generate IEEE files from WRF netCDF files. All WRF input, output and static (real and idealized data) in netCDF format can be converted.
    available modules: wrf2grads/2.0-intel
    XCrySDen XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
    available modules: xcrysden/1.5.60
    Yices Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted function symbols with equality, linear real and integer arithmetic, bitvectors, scalar types, and tuples.
    available modules: yices/2.4.2
    Z3 Z3 Theorem Prover is an efficient, high-performance SMT Solver being developed at Microsoft Research.
    available modules: z3/4.4.1
  • Languages/Compilers
    GNU Compilers The GNU Compiler Collection includes front ends for C, C++, Objective-C, and Fortran, as well as libraries for these languages (libstdc++, libgcj,…).
    system version: 4.8.5; available modules: gcc/4.9.3, gcc/5.3.0(default)
    GHC The Glasgow Haskell Compiler (GHC) is a state-of-the-art, open source compiler and interactive environment for the functional language Haskell. Haskell is a polymorphically statically typed, lazy, purely functional computer programming language.
    available modules: ghc/7.10.3
    Intel Compilers Intel’s suite of compilers facilitates native code development in C++/C and Fortran for parallel computing. Parallel programming enables software programs to take advantage of multi-core processors from Intel and other processor vendors.
    available modules: intel/14.0.3, intel/16.0.0(default)
    PGI Compilers The Portland Group offers optimizing parallel FORTRAN 2003, C99 and C++ compilers and tools for workstations, servers and clusters running Linux, including support for NVIDIA CUDA GPGPU
    available modules: pgi/14.4, pgi/15.9(default)
    PyPy PyPy is a replacement for CPython. PyPy implements Python 2.7.10. It supports all of the core language, passing the Python test suite (with minor modifications that were already accepted in the main python in newer versions). It is built using the RPython language that was co-developed with it. The main reason to use it instead of CPython is speed: it runs generally faster.
    available modules: pypy/5.3.1
    Python Python is an interpreted, object-oriented, high-level programming language with dynamic semantics. Its high-level built in data structures, combined with dynamic typing and dynamic binding, make it very attractive for Rapid Application Development, as well as for use as a scripting or glue language to connect existing components together.
    system version: 2.7.5; available modules: python/3.5.1
    Scala Scala is an acronym for ‘Scalable Language’. Scala is a pure-bred object-oriented language. Conceptually, every value is an object and every operation is a method-call. The language supports advanced component architectures through classes and traits.
    available modules: scala/2.11.7
    YASM YASM, an assembler and disassembler for the Intel x86 architecture, is a complete rewrite of the NASM assembler. YASM currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, 32 and 64-bit Mach-O, RDOFF2, COFF, Win32, and Win64 object formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats.
    available modules: yasm/1.3.0
  • Additional Libraries
    clBLAS clBLAS is a software library containing BLAS functions written in OpenCL.
    available modules: clblas/1.10
    CUDA Toolkit The NVIDIA CUDA Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications.
    available modules: cuda/7.5
    GLEW The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file.
    available modules: glew/1.13.0
    Google Libs Various Google codes, including Gflags (Google’s commandline flags library); Glog (C++ implementation of the Google logging module); LevelDB (A fast key-value storage library); Protocol Buffers (Google’s language-neutral, platform-neutral, extensible mechanism for serializing structured data)
    available modules: google-code/2015
    HDF Hierarchical Data Format (HDF4; also known as HDF) is a library and multi-object file format for storing and managing data between machines.
    available modules: hdf/4.2.11(default), hdf/4.2.11-intel, hdf/4.2.11-pgi
    HDF5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
    available modules: hdf5/1.8.16(default), hdf5/1.8.16-mpi, hdf5/1.8.16-intel, hdf5/1.8.16-intel-mpi, hdf5/1.8.16-pgi, hdf5/1.8.16-pgi-mpi
    LibGPUarray A common GPU ndarray(n dimensions array) that can be reused by all projects.
    available modules: libgpuarray/0.9997
    NetCDF NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
    available modules: netcdf/4.3.3.1, netcdf/4.3.3.1-mpi, netcdf/4.3.3.1-intel, netcdf/4.3.3.1-intel-mpi, netcdf/4.3.3.1-pgi, netcdf/4.3.3.1-pgi-mpi, netcdf/4.4.0(default), netcdf/4.4.0-mpi, netcdf/4.4.0-intel, netcdf/4.4.0-intel-mpi, netcdf/4.4.0-pgi, netcdf/4.4.0-pgi-mpi
    OpenBLAS Hierarchical Data Format (OPENBLAS4; also known as OPENBLAS) is a library and multi-object file format for storing and managing data between machines.
    available modules: openblas/0.2.18
    Trilinos Trilinos is an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
    available modules: trilinos/11.14.1-mpi, trilinos/12.6.1-mpi(default)
  • MPI
    Open MPI The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
    available modules: openmpi/1.8.1, openmpi/1.8.1-ib, openmpi/1.8.1-intel14, openmpi/1.8.1-intel14-ib, openmpi/1.8.1-intel, openmpi/1.8.1-intel-ib, openmpi/1.8.1-pgi, openmpi/1.8.1-pgi-ib, openmpi/1.10.0(default), openmpi/1.10.0-ib, openmpi/1.10.0-intel, openmpi/1.10.0-intel-ib, openmpi/1.10.0-pgi, openmpi/1.10.0-pgi-ib
    Platform MPI IBM Platform MPI is a high performance, production–quality implementation of the Message Passing Interface (MPI)—supporting the broadest range of industry standard platforms, interconnects and operating systems to help ensure that parallel applications can run on any platform.
    available modules: platform-mpi/9.01

Cluster users may request additional applications to be installed and supported by URC staff, and research groups are also provided with shared storage suitable for installing and maintaining their own discipline specific applications.