Modules specific to Niagara
Jump to navigation
Jump to search
| 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
|
| 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
|
| 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
| |
| ants | 2.3.1 | ANTs extracts information from complex datasets that include imaging
| |
| 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
| |
| arpack-ng | 3.5.0 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
| |
| 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
| |
| aspera-client | 3.8.1 | Command-line interface for Aspera, a data transport and streaming technology
| |
| autotools | 2017 | The standard GNU build tools: autoconf, automake and libtool
| |
| 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
| |
| bazel | 0.15.0 0.11.1 | Bazel is a build tool that builds code quickly and reliably
| |
| 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
| |
| bedtools | 2.27.1 | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage
| |
| 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
| |
| boost | 1.67.0 1.66.0 1.63.0 | Boost provides free peer-reviewed portable C++ source libraries
| |
| boost-mpi | 1.67.0 | Boost provides free peer-reviewed portable C++ source libraries
| |
| 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
| |
| cdo | 1.9.4 | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data
| |
| cereal | 1.2.2 | A C++11 library for serialization
| |
| 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
| |
| chaiscript | 6.1.0 | Embedded Scripting Language Designed for C++
| |
| cmake | 3.11.1 3.11.0 3.10.3 | CMake, the cross-platform, open-source build system
| |
| 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
| |
| dakota-mpi | 6.7.0 | The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and Unicertainly Quantification
| |
| ddt | 18.2 18.1.2 | Parallel Debugging with DDT | DDT debugger and MAP profiler
|
| diamond | 0.9.23 | Accelerated BLAST compatible local sequence aligner
| |
| eigen | 3.3.4 | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
| |
| elpa | 2018.05.001 2017.05.003 2016.05.003 | Eigenvalue SoLvers for Petaflop-Applications
| |
| esmf | 7.1.0r | The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models
| |
| fastme | 2.1.6.1 | FastME: a comprehensive, accurate and fast distance-based phylogeny inference program
| |
| fenics | 2018.1.0 2017.2.0 | FEniCS is a computing platform for solving partial differential equations
| |
| 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
| |
| ffmpeg | 3.4.2 | A complete, cross-platform solution to record, convert and stream audio and video
| |
| 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
| |
| 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
| |
| fmt | 4.1.0 3.0.2 | fmt (formerly cppformat) is an open-source formatting library
| |
| foam-extend | 4.0 | The foam-extend project is a fork of the OpenFOAM open source library for Computational Fluid Dynamics
| |
| freesurfer | 6.0.0 5.3.0 | FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
| |
| gamess | 14Feb2018 | GAMESS | General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package
|
| 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
| |
| gcc | 7.3.0 4.9.4 | Niagara Quickstart | The GNU Compiler Collection C, C++, and Fortran
|
| gdb | 8.1 | Performance And Debugging Tools: Niagara | The GNU Project Debugger
|
| 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
| |
| glib | 2.22.5 | GLib is one of the base libraries of the GTK+ project
| |
| g_mmpbsa | 5.1.2 | Molecular mechanics/Poisson-Bolzmann surface area method for GROMACS
| |
| gmp | 6.1.2 | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers
| |
| gnu-parallel | 20180322 | Running Serial Jobs on Niagara | GNU parallel is a shell tool for executing (usually serial) jobs in parallel
|
| gnuplot | 5.2.2 | Portable interactive, function plotting utility
| |
| googletest | 1.8.0 | Google's C++ test framework
| |
| 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
|
| gsl | 2.4 | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
| |
| 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
| |
| 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
| |
| hdf5 | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
|
| hdf5-mpi | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
|
| 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)
| |
| hpcx | 2.2-mofed-4.4 | Mellanox HPC-X Software Toolkit
| |
| hpn-ssh | 7.7p1-14v15 | Optimized ssh protocol
| |
| htseq | 0.11.1 | A framework to process and analyze data from high-throughput sequencing (HTS) assays
| |
| imake | 1.0.7 | imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems
| |
| 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
|
| intelmpi | 2018.3 2018.2 2018.1 2017.7 | Niagara Quickstart | Intel MPI library with compiler wrappers for C, C++, and Fortran
|
| intel-mpi-benchmarks | 2018.1 | a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard
| |
| intelpython2 | 2018.2 | Python | Intel Python distribution for python 2, based on anaconda
|
| intelpython3 | 2018.2 | Python | Intel Python distribution for python 3, based on anaconda
|
| itk | 4.13.0 | Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data
| |
| 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
| |
| java | 1.8.0_162 | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers
| |
| julia | 1.1.0 1.0.0 | A high-level, high-performance dynamic language for technical computing
| |
| lammps | 22Sep2017 11May2018 | The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
| |
| libatomic_ops | 7.6.4 | C/C++ Library for semi-portable access to hardware-provided atomic memory update operations on a number of architectures
| |
| libconfig | 1.7.2 | Libconfig is a simple library for processing structured configuration files
| |
| libctl | 4.1.2 4.0.1 | libctl is a free Guile-based library implementing flexible control files for scientific simulations
| |
| 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
| |
| libffi | 3.2.1 | The libffi library provides a portable, high level programming interface to various calling conventions
| |
| 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
| |
| libtiff | 4.0.9 | tiff: Library and tools for reading and writing TIFF data files
| |
| libunistring | 0.9.9 | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard
| |
| libxc | 4.0.5 4.0.3 3.0.0 | Libxc is a library of exchange-correlation functionals for density-functional theory
| |
| libxslt | 1.1.32 | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform)
| |
| libxsmm | 1.9 | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86)
| |
| libyaml | 0.1.7 | LibYAML is a YAML 1
| |
| lmdb | 0.9.22 | OpenLDAP's Lightning Memory-Mapped Database (LMDB) library
| |
| makedepend | 1.0.5 | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies
| |
| 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
| |
| 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
|
| 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
| |
| 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
| |
| mercurial | 4.6 | Mercurial is a free, distributed source control management tool
| |
| 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
| |
| mkl | 2018.3 2018.2 2018.2 2017.7 | Niagara Quickstart | Intel Math Kernel Library
|
| mmseqs2 | 7-4e23d | MMseqs2: ultra fast and sensitive search and clustering suite
| |
| mosh | 1.3.2 | Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes
| |
| mpb | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
| |
| mpb-mpi | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
| |
| mpfr | 4.0.1 | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding
| |
| mumps | 5.1.2 | A parallel sparse direct solver
| |
| mysql | 8.0.13 | MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS)
| |
| namd | 2.13 | NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
|
| ncl | 6.4.0 | NCL is an interpreted language designed specifically for scientific data analysis and visualization
| |
| nco | 4.7.6 4.7.4 | Python bindings for NCO
| |
| ncview | 2.1.7 | Ncview is a visual browser for netCDF format files
| |
| 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
| |
| 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
| |
| neuron | 7.6.2 | Empirically-based simulations of neurons and networks of neurons
| |
| octave | 4.4.0 | Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations
|
| openblas | 0.2.20 | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1
| |
| 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
| |
| openfoam | 6 5.0-debug 5.0 4.1 18.12 18.06 17.12 | OpenFOAM is a free, open source CFD software package
| |
| 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
|
| orthofinder | 2.2.7 | Program for identifying orthologous protein sequence families
| |
| osu-micro-benchmarks | 5.4.3 | OSU Micro-Benchmarks
| |
| paraview | 5.5.0 | Visualization | ParaView is a scientific parallel visualizer
|
| paraview-offscreen | 5.6.0 | Visualization | Off-screen rendering with ParaView, a scientific parallel visualizer
|
| 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
| |
| perf-reports | 18.2 | ARM performance reports
| |
| perl | 5.26.1 5.20.3 | Larry Wall's Practical Extraction and Report Language
| |
| 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
| |
| pgplot | 5.2.2-x 5.2.2 | Graphics subroutine library for C/C++ and Fortran
| |
| pism | 1.0 | Parallel Ice Sheet Model is open source and capable of high resolution
| |
| plink | 1.07 | plink-1
| |
| 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
| |
| pnetcdf | 1.9.0 | Parallel netCDF: A Parallel I/O Library for NetCDF File Access
| |
| protobuf | 3.6.1 | Google Protocol Buffers
| |
| 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
|
| qbatch | 2.1 | qbatch is a tool for executing commands in parallel across a compute cluster
| |
| 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
| |
| qt | 5.11.1 | Qt is a comprehensive cross-platform C++ application framework
| |
| 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
| |
| r | 3.5.1 3.5.0 | R is a free software environment for statistical computing and graphics
| |
| rarray | 1.2 | Library for runtime multi-dimensional arrays in C++
| |
| rsync | 3.1.3 | Data Management | Fast, versatile, remote file-copying tool
|
| rtk | 1.4.0 | An open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit
| |
| rust | 1.28.0 1.26.1 | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety
| |
| 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
| |
| scalapack | 2.0.2 | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
| |
| scons | 3.0.1 | SCons is a software construction tool
| |
| 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
| |
| shengbte | 1.1.1 | Software package for solving the Boltzmann Transport Equation for phonons
| |
| silo | 4.10.2-bsd | Silo is a library for reading and writing a wide variety of scientific data to binary, disk files
| |
| singularity | 2 (=2.6.1) | Singularity | Singularity is a portable application stack packaging and runtime utility.
|
| spades | 3.13.0 | Genome assembler for single-cell and isolates data sets
| |
| spglib | 1.10.3 | Spglib is a C library for finding and handling crystal symmetries
| |
| sqlite | 3.23.0 | SQLite: SQL Database Engine in a C Library
| |
| stacks | 2.2 | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform
| |
| star | 2.6.1b | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays
| |
| stringtie | 1.3.5 | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
| |
| 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
| |
| subversion | 1.9.7 | Subversion is an open source version control system
| |
| sundials | 3.1.0 2.7.0 2.6.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
| |
| sundials-mpi | 3.1.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
| |
| 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
| |
| 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
| |
| 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
| |
| trinityrnaseq | 2.8.1 | Trinity RNA-Seq de novo transcriptome assembly
| |
| 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
| |
| valgrind | 3.14.0 3.13.0 | Introduction To Performance | Valgrind-3
|
| visit | 2.13.1 | Visualization | An open-source, interactive, scalable, visualization, animation and analysis tool
|
| 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
|
| vtk | 8.1.1 | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
|