Difference between revisions of "Modules specific to Niagara"

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FEniCS Project is a collection of free and open-source software components with the common goal to enable automated solution of differential equations. The components provide scientific computing tools for working with computational meshes, finite-element variational formulations of ordinary and partial differential equations, and numerical linear algebra.<br />Homepage: https://fenicsproject.org/</div>
 
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FEniCS Project is a collection of free and open-source software components with the common goal to enable automated solution of differential equations. The components provide scientific computing tools for working with computational meshes, finite-element variational formulations of ordinary and partial differential equations, and numerical linear algebra.<br />Homepage: https://fenicsproject.org/</div>
 
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| align="center" | [ fetk]
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| align="center" | [http://www.fetk.org/ fetk]
 
| align="center" | 1.5
 
| align="center" | 1.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage: </div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Finite Element ToolKit (FETK) is a collaboratively developed, evolving collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE).<br />Homepage: http://www.fetk.org/ </div>
 
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| align="center" | [https://www.ffmpeg.org/ ffmpeg]
 
| align="center" | [https://www.ffmpeg.org/ ffmpeg]

Revision as of 20:41, 2 August 2018

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

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
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:
Homepage:
[ aspect] 2.0.0 2.0.1

Description:
Homepage:
autotools 2017

Description: This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
Homepage: http://autotools.io
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
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/
cmake 3.10.3 3.11.0 3.11.1

Description: CMake, the cross-platform, open-source build system. CMake is a 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:
Homepage:
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

Description: FEniCS Project is a collection of free and open-source software components with the common goal to enable automated solution of differential equations. The components provide scientific computing tools for working with computational meshes, finite-element variational formulations of ordinary and partial differential equations, and numerical linear algebra.
Homepage: https://fenicsproject.org/
fetk 1.5

Description: The Finite Element ToolKit (FETK) is a collaboratively developed, evolving collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE).
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:
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: calculates components of binding energy using MM-PBSA method except the entropic term and energetic contribution of each residue to the binding using energy decomposition scheme.
Homepage: https://rashmikumari.github.io/g_mmpbsa/
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

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
[ 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/
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: This package provides semi-portable access to hardware-provided atomic memory update operations on a number of architectures.
Homepage: https://github.com/ivmai/libatomic_ops
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

Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations.
Homepage: http://ab-initio.mit.edu/libctl
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

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

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 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: MPB is a free and open-source software package for computing electromagnetic band structures and modes.
Homepage: http://ab-initio.mit.edu/wiki/index.php/MPB
mpb-mpi 1.6.2

Description: MPB is a free and open-source software package for computing electromagnetic band structures and modes.
Homepage: http://ab-initio.mit.edu/wiki/index.php/MPB
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
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 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/
paraview 5.5.0

Description: ParaView is a scientific parallel visualizer.
Homepage: http://www.paraview.org
[ 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: http://www.qhull.org/
quantum-espresso 6.2.1 6.3

Description: Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Homepage: https://www.quantum-espresso.org/
r 1.1.1 3.5.0 4.0.1 R2018a

Description: R is a free software environment for statistical computing and graphics.
Homepage: http://www.r-project.org/
rarray 1.2

Description: rarray is a C++ library for multidimensional arrays. It is a header-only implementation that uses templates, which allows most compilers to generate fast code.
Homepage: https://github.com/vanzonr/rarray
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

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/
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: https://www.sqlite.org/
su2 5.0.0 6.0.0

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/
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