Modules specific to Niagara
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| Module | Versions (2018a) | Documentation | Description |
|---|---|---|---|
| anaconda2 | 5.1.0 | Python | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture
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| anaconda3 | 5.2.0 5.1.0 2018.12 | Python | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture
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| antlr | 2.7.7 | ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions
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| ants | 2.3.1 | ANTs extracts information from complex datasets that include imaging
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| armadillo | 8.500.1 | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use
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| arpack-ng | 3.5.0 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
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| aspect | 2.1.0-pre 2.0.1 2.0.0 | Finite element parallel code to simulate problems in thermal convection in both 2D and 3D models
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| aspera-client | 3.8.1 | Command-line interface for Aspera, a data transport and streaming technology
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| autotools | 2017 | The standard GNU build tools: autoconf, automake and libtool
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| bayestraits | 3.0.1 | 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
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| bazel | 0.15.0 0.11.1 | Bazel is a build tool that builds code quickly and reliably
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| bedops | 2.4.35 | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale
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| bedtools | 2.27.1 | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage
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| blast+ | 2.7.1 | 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
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| boost | 1.67.0 1.66.0 1.63.0 | Boost provides free peer-reviewed portable C++ source libraries
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| boost-mpi | 1.67.0 | Boost provides free peer-reviewed portable C++ source libraries
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| bwa | 0.7.17 | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome
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| cdo | 1.9.4 | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data
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| cereal | 1.2.2 | A C++11 library for serialization
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| cfitsio | 3.430 | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
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| chaiscript | 6.1.0 | Embedded Scripting Language Designed for C++
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| cmake | 3.11.1 3.11.0 3.10.3 | CMake, the cross-platform, open-source build system
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| cp2k | 6.1 | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems
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| dakota-mpi | 6.7.0 | The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and Unicertainly Quantification
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| ddt | 18.2 18.1.2 | Parallel Debugging with DDT | DDT debugger and MAP profiler
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| diamond | 0.9.23 | Accelerated BLAST compatible local sequence aligner
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| eigen | 3.3.4 | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
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| elpa | 2018.05.001 2017.05.003 2016.05.003 | Eigenvalue SoLvers for Petaflop-Applications
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| esmf | 7.1.0r | The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models
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| fastme | 2.1.6.1 | FastME: a comprehensive, accurate and fast distance-based phylogeny inference program
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| fenics | 2018.1.0 2017.2.0 | FEniCS is a computing platform for solving partial differential equations
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| fetk | 1.5 | The Finite Element ToolKit is a collaboratively developed, evolving collection of adaptive finite element method software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations
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| ffmpeg | 3.4.2 | A complete, cross-platform solution to record, convert and stream audio and video
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| fftw | 3.3.7 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data
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| fftw-mpi | 3.3.7 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data
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| fmt | 4.1.0 3.0.2 | fmt (formerly cppformat) is an open-source formatting library
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| foam-extend | 4.0 | The foam-extend project is a fork of the OpenFOAM open source library for Computational Fluid Dynamics
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| freesurfer | 6.0.0 5.3.0 | FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
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| gamess | 14Feb2018 | GAMESS | General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package
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| gc | 7.6.6 | The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new
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| gcc | 7.3.0 4.9.4 | Niagara Quickstart | The GNU Compiler Collection C, C++, and Fortran
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| gdb | 8.1 | Performance And Debugging Tools: Niagara | The GNU Project Debugger
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| git | 2.16.3 | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency
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| glib | 2.22.5 | GLib is one of the base libraries of the GTK+ project
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| g_mmpbsa | 5.1.2 | Molecular mechanics/Poisson-Bolzmann surface area method for GROMACS
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| gmp | 6.1.2 | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers
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| gnu-parallel | 20180322 | Running Serial Jobs on Niagara | GNU parallel is a shell tool for executing (usually serial) jobs in parallel
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| gnuplot | 5.2.2 | Portable interactive, function plotting utility
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| googletest | 1.8.0 | Google's C++ test framework
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| gromacs | 5.1.4 2019.1 2016.5-plumed-2.4.1 2016.5 | GROMACS | GROMACS is a versatile package to perform molecular dynamics, i
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| gsl | 2.4 | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
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| guile | 2.2.3 | Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts
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| harminv | 1.4.1 | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids
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| hdf5 | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
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| hdf5-mpi | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
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| hisat2 | 2.1.0 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)
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| hpcx | 2.2-mofed-4.4 | Mellanox HPC-X Software Toolkit
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| hpn-ssh | 7.7p1-14v15 | Optimized ssh protocol
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| htseq | 0.11.1 | A framework to process and analyze data from high-throughput sequencing (HTS) assays
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| imake | 1.0.7 | imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems
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| intel | 2018.3 2018.2 2018.1 2017.7 | Niagara Quickstart | Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries
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| intelmpi | 2018.3 2018.2 2018.1 2017.7 | Niagara Quickstart | Intel MPI library with compiler wrappers for C, C++, and Fortran
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| intel-mpi-benchmarks | 2018.1 | a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard
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| intelpython2 | 2018.2 | Python | Intel Python distribution for python 2, based on anaconda
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| intelpython3 | 2018.2 | Python | Intel Python distribution for python 3, based on anaconda
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| itk | 4.13.0 | Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data
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| jasper | 2.0.14 | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard
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| java | 1.8.0_162 | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers
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| julia | 1.1.0 1.0.0 | A high-level, high-performance dynamic language for technical computing
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| lammps | 22Sep2017 11May2018 | The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
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| libatomic_ops | 7.6.4 | C/C++ Library for semi-portable access to hardware-provided atomic memory update operations on a number of architectures
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| libconfig | 1.7.2 | Libconfig is a simple library for processing structured configuration files
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| libctl | 4.1.2 4.0.1 | libctl is a free Guile-based library implementing flexible control files for scientific simulations
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| libevent | 2.1.8 | The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached
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| libffi | 3.2.1 | The libffi library provides a portable, high level programming interface to various calling conventions
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| libint | 1.1.6 1.1.5 | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory
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| libtiff | 4.0.9 | tiff: Library and tools for reading and writing TIFF data files
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| libunistring | 0.9.9 | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard
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| libxc | 4.0.5 4.0.3 3.0.0 | Libxc is a library of exchange-correlation functionals for density-functional theory
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| libxslt | 1.1.32 | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform)
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| libxsmm | 1.9 | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86)
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| libyaml | 0.1.7 | LibYAML is a YAML 1
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| lmdb | 0.9.22 | OpenLDAP's Lightning Memory-Mapped Database (LMDB) library
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| makedepend | 1.0.5 | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies
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| mcl | 14-137 | The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs
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| mcr | R2018a | MATLAB | The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
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| meep | 1.5.0 1.4.3 | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems
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| meep-mpi | 1.5.0 1.4.3 | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems
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| mercurial | 4.6 | Mercurial is a free, distributed source control management tool
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| metis | 5.1.0 | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices
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| mkl | 2018.3 2018.2 2018.2 2017.7 | Niagara Quickstart | Intel Math Kernel Library
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| mmseqs2 | 7-4e23d | MMseqs2: ultra fast and sensitive search and clustering suite
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| mosh | 1.3.2 | Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes
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| mpb | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
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| mpb-mpi | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
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| mpfr | 4.0.1 | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding
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| mumps | 5.1.2 | A parallel sparse direct solver
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| mysql | 8.0.13 | MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS)
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| namd | 2.13 | NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
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| ncl | 6.4.0 | NCL is an interpreted language designed specifically for scientific data analysis and visualization
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| nco | 4.7.6 4.7.4 | Python bindings for NCO
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| ncview | 2.1.7 | Ncview is a visual browser for netCDF format files
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| netcdf | 4.6.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
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| netcdf-mpi | 4.6.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
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| neuron | 7.6.2 | Empirically-based simulations of neurons and networks of neurons
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| octave | 4.4.0 | Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations
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| openblas | 0.2.20 | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1
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| opencv | 4.1.0 2.4.13.6 | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library
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| openfoam | 6 5.0-debug 5.0 4.1 18.12 18.06 17.12 | OpenFOAM is a free, open source CFD software package
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| openmpi | 3.1.1 3.1.0rc4 3.1.0rc3 3.1.0 3.0.2 3.0.1 2.1.4 2.1.3 1.10.7 | Niagara Quickstart | The Open MPI Project is an open source MPI-2 implementation
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| orthofinder | 2.2.7 | Program for identifying orthologous protein sequence families
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| osu-micro-benchmarks | 5.4.3 | OSU Micro-Benchmarks
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| paraview | 5.5.0 | Visualization | ParaView is a scientific parallel visualizer
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| paraview-offscreen | 5.6.0 | Visualization | Off-screen rendering with ParaView, a scientific parallel visualizer
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| parmetis | 4.0.3 | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices
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| perf-reports | 18.2 | ARM performance reports
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| perl | 5.26.1 5.20.3 | Larry Wall's Practical Extraction and Report Language
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| petsc | 3.9.2 3.8.4-debug 3.8.4 | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations
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| pgplot | 5.2.2-x 5.2.2 | Graphics subroutine library for C/C++ and Fortran
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| pism | 1.0 | Parallel Ice Sheet Model is open source and capable of high resolution
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| plink | 1.07 | PLINK is a whole-genome association analysis toolset
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| plumed | 2.4.1 | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines
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| pnetcdf | 1.9.0 | Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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| protobuf | 3.6.1 | Google Protocol Buffers
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| python | 3.6.5 2.7.15 2.7.14 | Python | Python is a programming language that lets you work more quickly and integrate your systems more effectively
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| qbatch | 2.1 | qbatch is a tool for executing commands in parallel across a compute cluster
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| qhull | 2015.2 | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
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| qt | 5.11.1 | Qt is a comprehensive cross-platform C++ application framework
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| quantum-espresso | 6.3 6.2.1 | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
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| r | 3.5.1 3.5.0 | R is a free software environment for statistical computing and graphics
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| rarray | 1.2 | Library for runtime multi-dimensional arrays in C++
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| rsync | 3.1.3 | Data Management | Fast, versatile, remote file-copying tool
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| rtk | 1.4.0 | An open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit
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| rust | 1.28.0 1.26.1 | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety
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| samtools | 1.8 | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
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| scalapack | 2.0.2 | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
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| scons | 3.0.1 | SCons is a software construction tool
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| scotch | 6.0.6 | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning
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| shengbte | 1.1.1 | Software package for solving the Boltzmann Transport Equation for phonons
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| silo | 4.10.2-bsd | Silo is a library for reading and writing a wide variety of scientific data to binary, disk files
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| singularity | 2 (=2.6.1) | Singularity | Singularity is a portable application stack packaging and runtime utility.
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| spades | 3.13.0 | Genome assembler for single-cell and isolates data sets
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| spglib | 1.10.3 | Spglib is a C library for finding and handling crystal symmetries
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| sqlite | 3.23.0 | SQLite: SQL Database Engine in a C Library
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| stacks | 2.2 | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform
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| star | 2.6.1b | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays
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| stringtie | 1.3.5 | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
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| su2 | 6.1.0 6.0.0 5.0.0 | An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems
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| subversion | 1.9.7 | Subversion is an open source version control system
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| sundials | 3.1.0 2.7.0 2.6.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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| sundials-mpi | 3.1.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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| swig | 3.0.12 | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages
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| thirdorder | 1.1.1 | Set of scripts to help users of ShengBTE and almaBTE create FORCE_CONSTANTS_3RD files in an efficient and convenient manner
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| trilinos | 12.12.1 | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems
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| trinityrnaseq | 2.8.1 | Trinity RNA-Seq de novo transcriptome assembly
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| udunits | 2.2.26 | UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement
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| valgrind | 3.14.0 3.13.0 | Introduction To Performance | Valgrind provides debugging and profiling tools
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| visit | 2.13.1 | Visualization | An open-source, interactive, scalable, visualization, animation and analysis tool
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| vmd | 1.9.4a12 | Visualization | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
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| vtk | 8.1.1 | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
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