Modules specific to Niagara

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

Module	Versions	Documentation	Description
anaconda2	5.1.0		Description: 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. Homepage: https://www.continuum.io/anaconda-overview
anaconda3	5.1.0 5.2.0		Description: 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. Homepage: https://www.continuum.io/anaconda-overview
ants	2.3.1		Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: http://stnava.github.io/ANTs/
armadillo	8.500.1		Description: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Homepage: http://arma.sourceforge.net/
arpack-ng	3.5.0		Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: http://forge.scilab.org/index.php/p/arpack-ng/
aspect	2.0.0 2.0.1		Description: An extensible code written in C++ to support research in simulating convection in the Earth mantle and elsewhere. Homepage: https://aspect.geodynamics.org/
aspera-client	3.8.1		Description: Homepage:
autotools	2017		Description: This bundle collect the standard GNU build tools: Autoconf, Automake and libtool Homepage: http://autotools.io
bayestraits	3.0.1		Description: 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. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. Homepage: http://www.evolution.reading.ac.uk/BayesTraitsV1.html
bazel	0.11.1 0.15.0		Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: http://bazel.io/
blast+	2.7.1		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. Homepage: http://blast.ncbi.nlm.nih.gov/
boost	1.63.0 1.66.0 1.67.0		Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/
boost-mpi	1.67.0		Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/
cdo	1.9.4		Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo
cereal	1.2.2		Description: Header-only C++11 serialization library. Homepage: https://uscilab.github.io/cereal
cfitsio	3.430		Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/
chaiscript	6.1.0		Description: Easy to use embedded scripting language for C++. Homepage: http://chaiscript.com
cmake	3.10.3 3.11.0 3.11.1		Description: open-source, cross-platform family of tools designed to build, test and package software Homepage: https://cmake.org
cp2k	5.1		Description: 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. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. Homepage: http://www.cp2k.org/
dakota-mpi	6.7.0		Description: Toolkit for advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. Homepage: https://dakota.sandia.gov
ddt	18.1.2 18.2		Description: ARM's HPC development tools: Distributed Debugging Tool and MAP Profiler Homepage: https://www.arm.com/products/development-tools/hpc-tools/cross-platform/forge
eigen	3.3.4		Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: http://eigen.tuxfamily.org/index.php?title=Main_Page
elpa	2016.05.003 2017.05.003 2018.05.001		Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: http://elpa.rzg.mpg.de
fenics	2017.2.0 2018.1.0		Description: Computing platform for solving partial differential equations. Homepage: https://fenicsproject.org
fetk	1.5		Description: Finite Element ToolKit. Homepage: http://www.fetk.org
ffmpeg	3.4.2		Description: A complete, cross-platform solution to record, convert and stream audio and video. Homepage: https://www.ffmpeg.org/
fftw	3.3.7		Description: 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. Homepage: http://www.fftw.org
fftw-mpi	3.3.7		Description: 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. Homepage: http://www.fftw.org
fmt	3.0.2 4.1.0		Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/
foam-extend	4.0		Description: Homepage:
freesurfer	6.0.0		Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. Homepage: http://freesurfer.net/
gamess	14Feb2018		Description: Homepage:
gc	7.6.6		Description: The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. Homepage: http://hboehm.info/gc/
gcc	7.3.0		Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: http://gcc.gnu.org/
gdb	8.1		Description: The GNU Project Debugger Homepage: http://www.gnu.org/software/gdb/gdb.html
git	2.16.3		Description: 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. Homepage: http://git-scm.com/
glib	1.10.3 2.22.5		Description: GLib is one of the base libraries of the GTK+ project Homepage: http://www.gtk.org/
g_mmpbsa	5.1.2		Description: Homepage:
gmp	6.1.2		Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. Homepage: http://gmplib.org/
gnu-parallel	20180322		Description: Tools for running commands in parallel on one or more nodes. Homepage: https://www.gnu.org/software/parallel/
gnuplot	5.2.2		Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net/
googletest	1.8.0		Description: Welcome to Google Test, Google-s C++ test framework! Please see the project page for more information as well as the mailing list for questions, discussions, and development. There is also an IRC channel on OFTC. Getting started information for Google Test is available in the Google Test Primer documentation. Google Mock is an extension to Google Test for writing and using C++ mock classes. See the separate Google Mock documentation. More detailed documentation for googletest (including build instructions) are in its interior googletest/README.md file. Homepage: https://github.com/google/googletest
gromacs	2016.5 2016.5-plumed-2.4.1 5.1.4		Description: 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. This is CPU only build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org
gsl	2.4		Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. Homepage: http://www.gnu.org/software/gsl/
guile	2.2.3		Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile
harminv	1.4.1		Description: 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. Homepage: http://ab-initio.mit.edu/wiki/index.php/Harminv
hdf5	1.10.2 1.8.20		Description: 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. Homepage: https://support.hdfgroup.org/HDF5/
hdf5-mpi	1.10.2 1.8.20		Description: 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. Homepage: https://support.hdfgroup.org/HDF5/
hisat2	2.1.0		Description: 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). Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml
hpn-ssh	7.7p1-14v15		Description: Homepage:
imake	1.0.7		Description: imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. Homepage: http://www.x.org/
intel	2017.7 2018.2 2018.3		Description: Compiler toolchain including Intel compilers and Intel Math Kernel Library (MKL). Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe
intelmpi	2017.7 2018.2 2018.3		Description: Intel's (MPICH-based) MPI implementation. Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe
intel-mpi-benchmarks	2018.1		Description: Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
intelpython2	2018.2		Description: Homepage:
intelpython3	2018.2		Description: Homepage:
java	1.8.0_162		Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://java.com/
julia	1.0.0		Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org
lammps	11May2018 22Sep2017		Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -KIM, -MSCG, -KOKKOS, -USER-QUIP, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/
libatomic_ops	7.6.4		Description: Homepage:
libconfig	1.7.2		Description: Libconfig is a simple library for processing structured configuration files Homepage: http://www.hyperrealm.com/libconfig/
libctl	4.0.1 4.1.2		Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations. Homepage: http://ab-initio.mit.edu/libctl
libevent	2.1.8		Description: 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. Furthermore, libevent also support callbacks due to signals or regular timeouts. Homepage: http://libevent.org/
libffi	3.2.1		Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. Homepage: http://sourceware.org/libffi/
libint	1.1.5 1.1.6		Description: 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. Homepage: https://sourceforge.net/p/libint/
libunistring	0.9.9		Description: This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. Homepage: http://www.gnu.org/software/libunistring/
libxc	3.0.0 4.0.3 4.0.5		Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
libxslt	1.1.32		Description: Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). Homepage: http://xmlsoft.org/
libyaml	0.1.7		Description: LibYAML is a YAML parser and emitter written in C. Homepage:
lmdb	0.9.22		Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. Homepage: https://symas.com/lmdb
makedepend	1.0.5		Description: The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html
mcr	R2018a		Description: 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. Homepage: http://www.mathworks.com/products/compiler/mcr/
meep	1.4.3 1.5.0		Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. Homepage: http://ab-initio.mit.edu/wiki/index.php/Meep
meep-mpi	1.4.3 1.5.0		Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. Homepage: http://ab-initio.mit.edu/wiki/index.php/Meep
mercurial	4.6		Description: Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. Homepage: http://mercurial.selenic.com/
metis	4.0.3 5.1.0		Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
mkl	2017.7 2018.2 2018.2.lua 2018.3		Description: Intel's Math Kernel Library, for use with gcc modules (the intel modules include mkl already). Homepage: http://software.intel.com/en-us/intel-mkl/
mpb	1.6.2		Description: Homepage:
mpb-mpi	1.6.2		Description: Homepage:
mpfr	4.0.1		Description: The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. Homepage: http://www.mpfr.org
mumps	5.1.2		Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/
ncl	6.4.0		Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: http://www.ncl.ucar.edu
nco	4.7.4		Description: Python bindings for NCO Homepage: https://github.com/nco/pynco
netcdf	1.9.0 4.6.1		Description: 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. Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf-mpi	4.6.1		Description: 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. Homepage: http://www.unidata.ucar.edu/software/netcdf/
octave	4.4.0		Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: http://www.gnu.org/software/octave/
openblas	0.2.20		Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/
openfoam	17.12 4.1 5.0 5.0-debug		Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.com/
openmpi	1.10.7 2.1.3 2.1.4 3.0.1 3.0.2 3.1.0 3.1.0rc3 3.1.0rc4 3.1.1		Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/
osu-micro-benchmarks	5.4.3		Description: Homepage:
paraview	5.5.0		Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org
parmetis	4.0.3		Description: 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. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
perf-reports	18.2		Description: Homepage:
perl	5.20.3 5.26.1		Description: Larry Wall's Practical Extraction and Report Language Homepage: http://www.perl.org/
petsc	3.8.4 3.8.4-debug 3.9.2		Description: 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. Homepage: http://www.mcs.anl.gov/petsc
pgplot	5.2.2 5.2.2-x		Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: http://www.astro.caltech.edu/~tjp/pgplot/
plink	1.07		Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/
plumed	2.4.1		Description: 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. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org
pnetcdf	1.9.0		Description: Parallel netCDF: A Parallel I/O Library for NetCDF File Access Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf
python	2.7.14 3.6.5		Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/
qhull	2015.2		Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Homepage:
qt	5.11.1		Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/
quantum-espresso	6.2.1 6.3		Description: Homepage:
r	1.1.1 3.5.0 4.0.1 6.0.0 R2018a		Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/
rarray	1.2		Description: Homepage:
rsync	3.1.3		Description: Utility that provides fast incremental file transfer; this module provides a newer version than is present in the operating system. Homepage: https://rsync.samba.org/
rust	1.26.1 1.28.0		Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org
samtools	1.8		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. Homepage: http://www.htslib.org/
scalapack	2.0.2		Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: http://www.netlib.org/scalapack/
scons	3.0.1		Description: SCons is a software construction tool. Homepage: http://www.scons.org/
scotch	6.0.6		Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: http://gforge.inria.fr/projects/scotch/
shengbte	1.1.1		Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/
silo	4.10.2-bsd		Description: Silo is a library for reading and writing a wide variety of scientific data to binary, disk files Homepage: https://wci.llnl.gov/codes/silo/
singularity	2.5.2		Description: Singularity is a portable application stack packaging and runtime utility. Homepage: http://singularity.lbl.gov
spglib	1.10.3		Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: http://spglib.sourceforge.net/
sqlite	3.23.0		Description: SQLite: SQL Database Engine in a C Library Homepage:
su2	5.0.0 6.0.0 6.1.0		Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu
subversion	1.9.7		Description: Subversion is an open source version control system. Homepage: http://subversion.apache.org/
sundials	2.6.0 2.7.0 3.1.0		Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: http://computation.llnl.gov/projects/sundials
sundials-mpi	3.1.0		Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: http://computation.llnl.gov/projects/sundials
swig	3.0.12		Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/
thirdorder	1.1.1		Description: Homepage:
trilinos	12.12.1		Description: 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. A unique design feature of Trilinos is its focus on packages. Homepage: http://trilinos.sandia.gov/
trinityrnaseq	2.8.1		Description: Homepage:
valgrind	3.13.0		Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org
visit	2.13.1		Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit
vmd	1.9.4a12		Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: http://www.ks.uiuc.edu/Research/vmd
vtk	8.1.1		Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org

Message Passing Interface

Intel Math Kernel Library, a software library of optimized math routines