Modules specific to Niagara

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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 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 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 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.lua  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 is a whole-genome 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, 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 provides debugging and profiling tools
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

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 peer-reviewed 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 cross-platform, open-source 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, cross-platform 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
gnu-parallel 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 high-level, high-performance 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 multiple-precision floating-point computations with correct rounding
netcdf 4.6.3
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
openmpi 4.0.1  3.1.3 Niagara Quickstart
The Open MPI Project is an open source MPI-2 implementation
osu-micro-benchmarks 5.6.1
OSU Micro-Benchmarks
perl 5.28.1
Larry Wall's Practical Extraction and Report Language
petsc 3.10.5
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
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 per-position 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 high-level programming languages
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
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
Valgrind-3