Modules
From HPC
Applications
The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license visit: Applications requiring special licenses.
If you are looking for how to use a module use the Quickstart.
An up-to-date list of all modules available on Viper can be found at Module List
Click on the links below for support on the individual applications:
| Package | Description |
| ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. |
| Anaconda | Anaconda is the leading open data science platform powered by Python. |
| Arnold | Monte Carlo ray tracing renderer. |
| Autotools | Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 . |
| BayesTraits | BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. |
| Bison | Bison, is a parser generator that is part of the GNU Project. |
| Blender | Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation. |
| Bowtie1 | The aligner is typically used with short reads and a large reference genome, or for whole-genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences. |
| Bowtie2 | Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method. |
| Bridger | Bridger is an efficient de novo transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference. |
| Centrifuge | Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. |
| CMake | CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method. |
| Crop | CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate. |
| CP2K | CP2K is a quantum chemistry and solid-state physics software package that can perform atomistic simulations of solid-state, liquid, molecular, periodic, material, crystal, and biological systems. |
| CUDA | CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes. |
| Cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| Delft3D | Delft3D is a world-leading 3D modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. |
| FDS-SMV | Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations. |
| ffmpeg | FFmpeg is a very fast video and audio converter that can also be grabbed from a live audio/video source. |
| Flex | Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognize lexical patterns in text. |
| Fiji | Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community. |
| gcc | GCC (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more. |
| GNUplot | Gnuplot is a portable command-line-driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. |
| Grace | Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr. |
| Guppy | Local accelerated basecalling for Nanopore data. |
| HyPhy | HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. |
| Intel Parallel Studio | Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing. |
| IQtree | stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood. |
| Java | Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented. |
| Mafft | MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), and FFT-NS-2 (fast; for alignment of <∼30,000 sequences). |
| Maker | MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases. |
| Matlab | Numerical Computing Environment. |
| Mercurial | Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap. |
| Modflow | Program and framework developed to provide a platform for supporting multiple models and multiple types of models within the same simulation. |
| Mpich | MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard. |
| Miniconda | Miniconda is a lite version of Anaconda used for creating virtual environments. |
| Minimap2 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. |
| Mono | .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime. |
| MrBayes | MrBayes: Bayesian Inference of Phylogeny |
| Mvapich2 | MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance. |
| Ncbi blast | It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. |
| Netcdf-c | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data. |
| Nwchem | NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems. |
| Obitools | The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering taxonomic information. |
| Openfoam | OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. |
| Orca | ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules. |
| Packmol | PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations. |
| Paraview | ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques. |
| Perl | Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries. |
| Prinseq-lite | PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data. |
| Python | Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython. |
| Qiime2 | QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed. |
| R | R is an open-source programming language and software environment for statistical computing and graphics. |
| RaXML | RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. |
| Readline | GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash. |
| RStudio | RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment. |
| Samtools | Tools (written in C using htslib) for manipulating next-generation sequencing data |
| Savu | Python package to assist with the processing and reconstruction of parallel-beam tomography data. |
| Scalapack | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers |
| Siesta | SIESTA 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. |
| STAR | Ultrafast universal RNA-seq aligner. |
| Star-ccm+ | Star-ccm+ package. |
| Tophat | It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons. |
| Transabyss | Software pipeline for analysing ABySS-assembled transcriptome contigs |
| Transrate | Transrate is software for de-novo transcriptome assembly quality analysis |
| Trinityrnaseq | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
| Utilities | General utility module including zip, wget and git utilities. |
| Voxfe | VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised easily. |
| Yt | yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography. |
Libraries
Library software listed here refers to those listed in the libs section of the typing module avail.
| Library | Description |
| Boost | C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. |
| Cuda | CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. |
| Expat | Expat XML parser library in C |
| Fftw3 | FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT). |
| Gsl | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. |
| Hdf5 | HDF5 is a data model, library, and file format for storing and managing data. |
| Hypre | A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers. |
| Libbeagle | BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. |
| Libgd | The module LibGD is an open-source code library for the dynamic creation of images. |
| Libjpeg-turbo | The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression |
| Libpng | The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files. |
| Ncurses | ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner. |
| OpenACC | OpenACC is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran. |
| Openblas | OpenBLAS is an optimized BLAS library (based on GotoBLAS2 1.13 BSD version). |
| OpenCL | A framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), and field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. |
| OpenMP | OpenMP is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran. |
| OpenMPI | Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes. |
| Parmetis | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, and meshes, and for computing fill-reducing orderings of sparse matrices. |
| Qt | Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper. |
| Zlib | zlib is a software library used for data compression. |
Test Modules
The test-modules module does not provide access to a specific application, instead, it provides access to a further set of modules that are in a development state.
These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.
If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module.
[username@login01 ~]$ module add test-modules [username@login01 ~]$ module avail --------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------- dot module-git module-info modules null use.own --------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles --------------------------------------------- abyss/1.5.2/gcc-4.9.3 gsl/gcc/2.1 java/jdk1.8.0_102 ospray/0.10.1 <standard output> -------------------------------------------- /trinity/clustervision/CentOS/7/test-modules --------------------------------------------- SAS/9.4 gettext/gcc/0.19.8.1 netcdf-c/intel/intelmpi/4.4.1 ansys/v170_test glib/gcc/2.50.2 netcdf-f/intel/intelmpi/4.4.4 ansys/v172sj grackle/gcc/serial/2.2 ood/anaconda/2021.11 cairo/1.14.6 harfbuzz/gcc/1.3.3 openfoam-org/10.0/openmpi-4.0.5/gcc-7.3.0 comsol/52a libffi/gcc/3.2.1 pango/1.40.3 comsol/53 libxml2/gcc/2.9.4 pcre/gccc/8.38 comsol/53a matlab/2021a pixman/0.34.0 comsol/54 matlab/test ruby/2.3.1 enzo/gcc/2016-09-28 mercurial/3.9.1-2016-09-28 singularity/3.5.3/gccc-8.2.0 fontconfig/gcc/2.12.1 mpich/3.2/gcc-5.2.0 scotch/7.0.1/openmpi-4.05/gcc-7.3.0 fontconfig/gcc/2.8.0 music/gcc/1.53 transabyss/1.5.5 freetype/2.7 nas./gcc/2.12.02