Modules specific to Niagara
From SciNet Users Documentation
2018a
Module  Versions (2018a)  Documentation  Description 

anaconda2  5.1.0  Python  Built to complement the rich, open source Python community, the Anaconda platform provides an enterpriseready 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 enterpriseready 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 opensource C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use
 
arpackng  3.5.0  ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
 
aspect  2.1.0pre 2.0.1 2.0.0  Finite element parallel code to simulate problems in thermal convection in both 2D and 3D models
 
asperaclient  3.8.1  Commandline 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 opensource commandline 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 aminoacid sequences of different proteins or the nucleotides of DNA sequences
 
boost  1.67.0 1.66.0 1.63.0  Boost provides free peerreviewed portable C++ source libraries
 
boostmpi  1.67.0  Boost provides free peerreviewed portable C++ source libraries
 
bwa  0.7.17  BurrowsWheeler 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 crossplatform, opensource 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
 
dakotampi  6.7.0  The Dakota project delivers both stateoftheart research and robust, usable software for optimization and Unicertainly Quantification
 
ddt  19.1  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 PetaflopApplications
 
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 distancebased 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, crossplatform 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
 
fftwmpi  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 opensource formatting library
 
foamextend  4.0  The foamextend 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 BoehmDemersWeiser 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/PoissonBolzmann 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
 
gnuparallel  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 2016.5plumed2.4.1 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 plugins, modules, or scripts
 
harminv  1.4.1  Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion  given a discretetime, finitelength signal that consists of a sum of finitelymany 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

hdf5mpi  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 nextgeneration sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)
 
hpcx  2.2mofed4.4  Mellanox HPCX Software Toolkit
 
hpnssh  7.7p114v15  Optimized ssh protocol
 
htseq  0.11.1  A framework to process and analyze data from highthroughput sequencing (HTS) assays
 
imake  1.0.7  imake is a Makefilegenerator 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

intelmpibenchmarks  2018.1  a set of elementary benchmarks that conform to MPI1, MPI2, and MPI3 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 opensource initiative to provide a free softwarebased reference implementation of the codec specified in the JPEG2000 Part1 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 highlevel, highperformance dynamic language for technical computing
 
lammps  22Sep2017 11May2018  The 'Largescale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
 
libatomic_ops  7.6.4  C/C++ Library for semiportable access to hardwareprovided 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 Guilebased 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 twobody 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 exchangecorrelation functionals for densityfunctional 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 matrixmatrix multiplications targeting Intel Architecture (x86)
 
libyaml  0.1.7  LibYAML is a YAML 1
 
lmdb  0.9.22  OpenLDAP's Lightning MemoryMapped Database (LMDB) library
 
makedepend  1.0.5  The makedepend package contains a Cpreprocessor like utility to determine buildtime dependencies
 
mcl  14137  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 finitedifference timedomain (FDTD) simulation software package developed at MIT to model electromagnetic systems
 
meepmpi  1.5.0 1.4.3  Meep (or MEEP) is a free finitedifference timedomain (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.lua 2018.2 2017.7  Niagara Quickstart  Intel Math Kernel Library

mmseqs2  74e23d  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 PhotonicBands: computation of photonic band structures in periodic media
 
mpbmpi  1.6.2  MIT PhotonicBands: computation of photonic band structures in periodic media
 
mpfr  4.0.1  The MPFR library is a C library for multipleprecision floatingpoint 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 opensource relational database management system (RDBMS)
 
namd  2.13  NAMD  NAMD is a parallel molecular dynamics code designed for highperformance 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 machineindependent data formats that support the creation, access, and sharing of arrayoriented scientific data
 
netcdfmpi  4.6.1  NetCDF (network Common Data Form) is a set of software libraries and machineindependent data formats that support the creation, access, and sharing of arrayoriented scientific data
 
neuron  7.6.2  Empiricallybased simulations of neurons and networks of neurons
 
octave  4.4.0  Octave  GNU Octave is a highlevel 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 5.0debug 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 MPI2 implementation

orthofinder  2.2.7  Program for identifying orthologous protein sequence families
 
osumicrobenchmarks  5.4.3  OSU MicroBenchmarks
 
paraview  5.5.0  Visualization  ParaView is a scientific parallel visualizer

paraviewoffscreen  5.6.0  Visualization  Offscreen rendering with ParaView, a scientific parallel visualizer

parmetis  4.0.3  ParMETIS is an MPIbased parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fillreducing orderings of sparse matrices
 
perfreports  18.2  ARM performance reports
 
perl  5.26.1 5.20.3  Larry Wall's Practical Extraction and Report Language
 
petsc  3.9.2 3.8.4debug 3.8.4  PETSc, pronounced PETsee (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  5.2.2x 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 is a wholegenome association analysis toolset
 
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, furthestsite Delaunay triangulation, and furthestsite Voronoi diagram
 
qt  5.11.1  Qt is a comprehensive crossplatform C++ application framework
 
quantumespresso  6.3 6.2.1  An integrated suite of OpenSource computer codes for electronicstructure 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 multidimensional arrays in C++
 
rsync  3.1.3  Data Management  Fast, versatile, remote filecopying tool

rtk  1.4.0  An opensource and crossplatform software for fast circular conebeam 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 perposition 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  4.10.2bsd  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 singlecell 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 shortread sequences, such as those generated on the Illumina platform
 
star  2.6.1b  STAR aligns RNAseq reads to a reference genome using uncompressed suffix arrays
 
stringtie  1.3.5  StringTie is a fast and highly efficient assembler of RNASeq alignments into potential transcripts
 
su2  6.1.0 6.0.0 5.0.0  An opensource collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDEconstrained 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
 
sundialsmpi  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 highlevel 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 objectoriented software framework for the solution of largescale, complex multiphysics engineering and scientific problems
 
trinityrnaseq  2.8.1  Trinity RNASeq 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 provides debugging and profiling tools

visit  2.13.1  Visualization  An opensource, 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 3D graphics and builtin scripting

vtk  8.1.1  The Visualization Toolkit (VTK) is an opensource, freely available software system for 3D computer graphics, image processing and visualization

2019b
Module  Versions (2019b)  Documentation  Description 

ants  2.3.1  ANTs extracts information from complex datasets that include imaging
 
autotools  2018b 2018  The standard GNU build tools: autoconf, automake and libtool
 
boost  1.69.0  Boost provides free peerreviewed portable C++ source libraries
 
cfitsio  3.450  CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
 
cmake  3.13.4  CMake, the crossplatform, opensource build system
 
ddt  19.1  Parallel Debugging with DDT  DDT debugger and MAP profiler

eigen  3.3.7  Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
 
ffmpeg  3.4.2  A complete, crossplatform solution to record, convert and stream audio and video
 
fftw  3.3.8  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
 
gcc  8.3.0  Niagara Quickstart  The GNU Compiler Collection C, C++, and Fortran

gdal  2.4.1  GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation
 
geos  3.7.1  GEOS (Geometry Engine  Open Source) is a C++ port of the Java Topology Suite (JTS)
 
git  2.21.0  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
 
gmp  6.1.2  GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers
 
gnuparallel  20190322  Running Serial Jobs on Niagara  GNU parallel is a shell tool for executing (usually serial) jobs in parallel

gromacs  2018.6  GROMACS  GROMACS is a versatile package to perform molecular dynamics, i

gsl  2.5  The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
 
hdf5  1.8.21 1.10.5  HDF5  HDF5 is a data model, library, and file format for storing and managing data

intel  2019u4 2019u3  Niagara Quickstart  Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries

intelmpi  2019u4 2019u3  Niagara Quickstart  Intel MPI library with compiler wrappers for C, C++, and Fortran

intelpython2  2019u4 2019u3  Python  Intel Python distribution for python 2, based on anaconda

intelpython3  2019u4 2019u3  Python  Intel Python distribution for python 3, based on anaconda

itk  4.13.2  Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data
 
java  1.8.0_201  Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers
 
julia  1.1.0  A highlevel, highperformance dynamic language for technical computing
 
mkl  2019u4 2019u3  Niagara Quickstart  Intel Math Kernel Library

mpfr  4.0.2  The MPFR library is a C library for multipleprecision floatingpoint computations with correct rounding
 
netcdf  4.6.3  NetCDF (network Common Data Form) is a set of software libraries and machineindependent data formats that support the creation, access, and sharing of arrayoriented scientific data
 
openmpi  4.0.1 3.1.3  Niagara Quickstart  The Open MPI Project is an open source MPI2 implementation

osumicrobenchmarks  5.6.1  OSU MicroBenchmarks
 
perl  5.28.1  Larry Wall's Practical Extraction and Report Language
 
petsc  3.10.5  PETSc, pronounced PETsee (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  Graphics subroutine library for C/C++ and Fortran
 
pnetcdf  1.11.0  Parallel netCDF: A Parallel I/O Library for NetCDF File Access
 
proj  6.0.0 4.9.3  Cartographic projections and coordinate transformations library
 
python  3.6.8 2.7.15  Python  Python is a programming language that lets you work more quickly and integrate your systems more effectively

r  3.5.3  R is a free software environment for statistical computing and graphics
 
samtools  1.9  SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a perposition format
 
sqlite  3.23.0  SQLite: SQL Database Engine in a C Library
 
swig  3.0.12  SWIG is a software development tool that connects programs written in C and C++ with a variety of highlevel programming languages
 
trilinos  12.12.1  The Trilinos Project is an effort to develop algorithms and enabling technologies within an objectoriented software framework for the solution of largescale, complex multiphysics engineering and scientific problems
 
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  Introduction To Performance  Valgrind3
