Modules specific to Niagara
From SciNet Users Documentation
2019b
Module  Versions (2019b)  Documentation  Description 

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. ANTs is useful for managing, interpreting and visualizing multidimensional data.
 
armadillo  9.700.2  Armadillo is an opensource 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.
 
arpackng  3.7.0  ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
 
autotools  2018b 2018  The standard GNU build tools: autoconf, automake and libtool.
 
bedtools  2.29.0  The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widelyused file formats: BED, GFF/GTF, VCF, and SAM/BAM.
 
blast+  2.9.0  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.
 
blitz++  1.0.1  Blitz++ is a (LGPLv3+) licensed metatemplate library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an objectoriented interface
 
boost  1.70.0 1.69.0  Boost provides free peerreviewed portable C++ source libraries.
 
boostpython  1.70.0  Boost provides free peerreviewed portable C++ source libraries, including boost:python.
 
bowtie2  2.3.4.3  Bowtie 2 is an ultrafast and memoryefficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and pairedend alignment modes.
 
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.
 
cereal  1.2.2  A C++11 library for serialization
 
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.
 
chaiscript  6.1.0  Embedded Scripting Language Designed for C++
 
cmake  3.14.5 3.13.4  CMake, the crossplatform, opensource build system. CMake is a family of tools designed to build, test and package software.
 
ddd  3.3.12  GNU DDD is a graphical frontend for commandline debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb.
 
ddt  19.1 19.0.4  Parallel Debugging with DDT  DDT debugger and MAP profiler. DDT is a parallel debugger for C, C++, Fortran and python that supports threads, OpenMP, MPI, and CUDA. It is part of the 'ARM Forge' suite, which includes MAP, a parallel profiler.

doxygen  1.8.17  Doxygen is a documentation system for C++, C, Java, ObjectiveC, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
 
eigen  3.3.7  Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
 
fenics  2019.1.0  FEniCS is a computing platform for solving partial differential equations. FEniCS enables users to quickly translate scientific models into efficient finite element code. With the highlevel Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also powerful capabilities for more experienced programmers.
 
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.
 
freesurfer  6.0.0  FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
 
gcc  9.2.0 8.3.0  Niagara Quickstart  The GNU Compiler Collection for 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. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
 
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.
 
gitannex  2.8.1  gitannex allows managing files with git, without checking the file contents into git.
 
gmp  6.1.2  GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
 
gmt  6.0.0  Generic Mapping Tools is an open source collection of many commandline tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple xy plots via contour maps to artificially illuminated surfaces and 3D perspective views.
 
gnuparallel  20190322  Running Serial Jobs on Niagara  GNU parallel is a shell tool for executing (usually serial) jobs in parallel.

gnuplot  5.2.7  Portable interactive, function plotting utility
 
go  1.13~ 1.13  Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
 
graphviz  2.40.1  Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
 
gromacs  2018.6plumed2.5.1 2018.6  GROMACS  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.

gsl  2.5  The GNU Scientific Library (GSL) is a numerical library for C and C++. The library provides a wide range of mathematical routines such as random number generators, special functions and leastsquares fitting.
 
hdf5  1.8.21 1.10.5  HDF5  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.

intel  2019u5 2019u4 2019u3  Niagara Quickstart  Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries.

intelmpi  2019u5 2019u4 2019u3  Niagara Quickstart  Intel MPI library with compiler wrappers for C, C++, and Fortran. Compatible with MPICH.

intelpython2  2019u5 2019u4 2019u3  Python  Intel Python distribution for python 2, based on anaconda.

intelpython3  2019u5 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.
 
jags  4.3.0  JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
 
java  1.8.0_201  Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
 
jellyfish  2.3.0  Jellyfish is a tool for fast, memoryefficient counting of kmers in DNA.
 
julia  1.1.0  A highlevel, highperformance dynamic language for technical computing.
 
lammps  29Mar2019  The 'Largescale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation. LAMMPS has potentials for solidstate materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarsegrained 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.
 
libxc  4.3.4  Libxc is a library of exchangecorrelation functionals for densityfunctional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
 
lmdb  0.9.23  OpenLDAP's Lightning MemoryMapped Database (LMDB) library.
 
lsbrelease  versionless  Replacement for the true lsbrelease utility
 
mcr  R2019a  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.

mercurial  5.1  Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
 
meson  0.51.2  Meson is a crossplatform build system designed to be both as fast and as user friendly as possible.
 
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. The algorithms implemented in METIS are based on the multilevel recursivebisection, multilevel kway, and multiconstraint partitioning schemes.
 
mkl  2019u4 2019u3  Niagara Quickstart  Intel Math Kernel Library. This is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Provided by the 'intel' modules, but needs to be separately loaded when using GCC.

mothur  1.42.3  Mothur is a single piece of opensource, expandable software to fill the bioinformatics needs of the microbial ecology community.
 
mpfr  4.0.2  The MPFR library is a C library for multipleprecision floatingpoint computations with correct rounding.
 
mumps  5.2.1 5.1.2  A parallel sparse direct solver
 
namd  2.13  NAMD  NAMD is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems.

ncl  6.6.2  NCL is an interpreted language designed specifically for scientific data analysis and visualization.
 
nco  4.8.1  Python bindings for NCO
 
ncview  2.1.7  Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, pushbutton look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
 
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.
 
ninja  1.9.0  Ninja is a small build system with a focus on speed.
 
openblas  0.3.7  OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
 
openfoam  7broken 19.06  OpenFOAM is a free, open source CFD software package
 
openjpeg  2.3.1  OpenJPEG is an opensource JPEG 2000 codec, developed in order to promote the use of JPEG 2000, a stillimage compression standard from the Joint Photographic Experts Group (JPEG).
 
openmpi  4.0.1 3.1.3  Niagara Quickstart  The Open MPI Project is an open source MPI2 implementation.

orthofinder  2.3.3  Program for identifying orthologous protein sequence families. It is written in python and runs as a single command that takes as input a directory of FASTA files, one per species. It outputs a file containing the orthologous groups of genes from these species.
 
osumicrobenchmarks  5.6.1  OSU MicroBenchmarks
 
pandoc  2.7.3  If you need to convert files from one markup format into another, pandoc is your swissarmy knife
 
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. 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 kway graphpartitioning, adaptive repartitioning, and parallel multiconstrained partitioning schemes.
 
perl  5.28.1  Larry Wall's Practical Extraction and Report Language
 
petsc  3.9.3 3.11.3 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.
 
pixman  0.38.4  The Pixman library is a C library, part of the Cairo package, used for 2D graphics.
 
plumed  2.5.1  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. 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 Jarzynskiequation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
 
pnetcdf  1.11.2 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.

qbatch  2.1.5 2.1.4  qbatch is a tool for executing commands in parallel across a compute cluster. It takes as input a list of commands (shell command lines or executable scripts) in a file or piped to qbatch. The list of commands are divided into arbitrarily sized chunks which are submitted as jobs to the cluster either as individual submissions or an array. Each job runs the commands in its chunk in parallel according to cores. Commands can also be run locally on systems with no cluster capability via gnuparalel.
 
qt  5.12.4 4.8.7  Qt is a comprehensive crossplatform C++ application framework.
 
r  3.6.1 3.5.3  R is a free software environment for statistical computing and graphics.
 
rarray  2.1.1 2.0.0 1.2  Library for runtime multidimensional arrays in C++.
 
rsync  3.1.3  Data Management  Fast, versatile, remote filecopying tool

salmon  0.99.0beta2  Salmon is a tool for fast, accurate, and biasaware transcript quantification estimates from RNAseq data.
 
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.
 
scalapack  2.0.2  The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
 
scons  3.0.5  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.
 
siesta  master27Oct2019 4.1b4 4.0.2  Computer implementation of the SIESTA method to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
 
singularity  3.5.2  Singularity  Singularity is a portable application stack packaging and runtime utility.

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
 
subversion  1.10.4  Subversion is an open source version control system.
 
superlu  5.2.1  SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
 
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.
 
tbb  2019u9 2019u8  Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have futureproof scalability.
 
texlive  2019  Highquality typesetting programs TeX and LaTeX
 
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. A unique design feature of Trilinos is its focus on packages.
 
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  Introduction To Performance  Valgrind3.8.1: Debugging and profiling tools

vmd  1.9.4a38  Visualization  VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3D graphics and builtin scripting.

vtk  8.2.0  The Visualization Toolkit (VTK) is an opensource, 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.

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. ANTs is useful for managing, interpreting and visualizing multidimensional data.
 
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. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
 
arpackng  3.5.0  ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
 
aspect  2.1.0pre 2.1.0 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. 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.
 
bazel  0.15.0 0.11.1  Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
 
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. Tasks can be easily split by chromosome for distributing wholegenome analyses across a computational cluster.
 
bedtools  2.27.1  The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widelyused file formats: BED, GFF/GTF, VCF, and SAM/BAM.
 
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. CMake is a family of tools designed to build, test and package software.
 
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. 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 manybody potentials.
 
dakotampi  6.7.0  The Dakota project delivers both stateoftheart research and robust, usable software for optimization and Unicertainly Quantification.
 
ddt  19.1 19.0.4 18.2 18.1.2  Parallel Debugging with DDT  DDT debugger and MAP profiler. DDT is a parallel debugger for C, C++, Fortran and python that supports threads, OpenMP, MPI, and CUDA. It is part of the 'ARM Forge' suite, which includes MAP, a parallel 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. FEniCS enables users to quickly translate scientific models into efficient finite element code. With the highlevel Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also powerful capabilities for more experienced programmers.
 
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. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal 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.
 
gitannex  2.8.1  gitannex allows managing files with git, without checking the file contents into git.
 
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
 
go  1.13  Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
 
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.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

gsl  2.4  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 leastsquares fitting.
 
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. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hdf5mpi  1.8.20 1.10.2  HDF5  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.

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. Compatible with MPICH.

intelmpibenchmarks  2018.1  a set of elementary benchmarks that conform to MPI1, MPI2, and MPI3 standard. You can run all of the supported benchmarks, or a subset specified in the command line using one executable file. Use commandline parameters to specify various settings, such as time measurement, message lengths, and selection of communicators.
 
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. LAMMPS has potentials for solidstate materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarsegrained 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.
 
libatomic_ops  7.6.4  C/C++ Library for semiportable access to hardwareprovided atomic memory update operations on a number of architectures. In new code, please use C11 or C++14 standard atomics instead of this package.
 
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. Furthermore, libevent also support callbacks due to signals or regular timeouts.
 
libffi  3.2.1  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 runtime.
 
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. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
 
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 1.1 parser and emitter written in C.
 
lmdb  0.9.22  OpenLDAP's Lightning MemoryMapped Database (LMDB) library.
 
lsbrelease  versionless  Replacement for the true lsbrelease utility
 
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. It efficiently handles projects of any size and offers an easy and intuitive interface.
 
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. The algorithms implemented in METIS are based on the multilevel recursivebisection, multilevel kway, and multiconstraint partitioning schemes.
 
mkl  2018.3 2018.2 2017.7  Niagara Quickstart  Intel Math Kernel Library. This is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Provided by the 'intel' modules, but needs to be separately loaded when using GCC.

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. Typically you would use ncview to get a quick and easy, pushbutton look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
 
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 1.13 BSD version.
 
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. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
 
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. It is written in python and runs as a single command that takes as input a directory of FASTA files, one per species. It outputs a file containing the orthologous groups of genes from these species.
 
osumicrobenchmarks  5.4.3  OSU MicroBenchmarks
 
pandoc  2.7.3  If you need to convert files from one markup format into another, pandoc is your swissarmy knife
 
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. 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 kway graphpartitioning, adaptive repartitioning, and parallel multiconstrained partitioning schemes.
 
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. 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 Jarzynskiequation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
 
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  2.1.5 2.1.4 2.1  qbatch is a tool for executing commands in parallel across a compute cluster. It takes as input a list of commands (shell command lines or executable scripts) in a file or piped to qbatch. The list of commands are divided into arbitrarily sized chunks which are submitted as jobs to the cluster either as individual submissions or an array. Each job runs the commands in its chunk in parallel according to cores. Commands can also be run locally on systems with no cluster capability via gnuparalel.
 
qhull  2015.2  Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthestsite Delaunay triangulation, and furthestsite Voronoi diagram. The source code runs in 2d, 3d, 4d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
 
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. It is based on densityfunctional theory, plane waves, and pseudopotentials.
 
r  3.5.1 3.5.0  R is a free software environment for statistical computing and graphics.
 
rarray  2.1.1 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  3.5.2  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. Stacks was developed to work with restriction enzymebased data, such as RADseq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
 
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. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind.
 
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. A unique design feature of Trilinos is its focus on packages.
 
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  1.9.4a38 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. 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.
