Modules specific to Niagara

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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 open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
arpack-ng 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 widely-used 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 amino-acid sequences of different proteins or the nucleotides of DNA sequences.
blitz++ 1.0.1 
Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
boost 1.70.0  1.69.0 
Boost provides free peer-reviewed portable C++ source libraries.
boost-python 1.70.0 
Boost provides free peer-reviewed portable C++ source libraries, including boost:python.
bowtie2 2.3.4.3 
Bowtie 2 is an ultrafast and memory-efficient 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 paired-end alignment modes.
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.
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 cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
ddd 3.3.12 
GNU DDD is a graphical front-end for command-line 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, Objective-C, 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 high-level 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, 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.
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.
git-annex 2.8.1 
git-annex 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 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views.
gnu-parallel 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 2018.6-plumed-2.5.1  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 least-squares 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, memory-efficient counting of k-mers in DNA.
julia 1.1.0 
A high-level, high-performance dynamic language for technical computing.
lammps 29Mar2019 
The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs.
libxc 4.3.4 
Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
lmdb 0.9.23 
OpenLDAP's Lightning Memory-Mapped Database (LMDB) library.
lsb-release versionless 
Replacement for the true lsb-release 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 cross-platform 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 recursive-bisection, multilevel k-way, and multi-constraint 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 open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mpfr 4.0.2 
The MPFR library is a C library for multiple-precision floating-point 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 high-performance 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, push-button 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 machine-independent data formats that support the creation, access, and sharing of array-oriented 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 7-broken  19.06 
OpenFOAM is a free, open source CFD software package
openjpeg 2.3.1 
OpenJPEG is an open-source JPEG 2000 codec, developed in order to promote the use of JPEG 2000, a still-image 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 MPI-2 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.
osu-micro-benchmarks 5.6.1 
OSU Micro-Benchmarks
pandoc 2.7.3 
If you need to convert files from one markup format into another, pandoc is your swiss-army knife
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. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
perl 5.28.1 
Larry Wall's Practical Extraction and Report Language
petsc 3.9.3  3.11.3  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.
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 Jarzynski-equation 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 gnu-paralel.
qt 5.12.4  4.8.7 
Qt is a comprehensive cross-platform 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 multi-dimensional arrays in C++.
rsync 3.1.3  Data Management
Fast, versatile, remote file-copying tool
salmon 0.99.0-beta2 
Salmon is a tool for fast, accurate, and bias-aware transcript quantification estimates from RNA-seq 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 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 3.0.5 
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 master-27Oct2019  4.1-b4  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 high-level 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 future-proof scalability.
texlive 2019 
High-quality 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 object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
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  Introduction To Performance
Valgrind-3.8.1: Debugging and profiling tools
vmd 1.9.4a38  Visualization
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
vtk 8.2.0 
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

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. ANTs is useful for managing, interpreting and visualizing multidimensional data.
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. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
arpack-ng 3.5.0 
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
aspect 2.1.0-pre  2.1.0  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. 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 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. Tasks can be easily split by chromosome for distributing whole-genome 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 widely-used 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 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. 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 many-body potentials.
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  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 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. FEniCS enables users to quickly translate scientific models into efficient finite element code. With the high-level 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, 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. 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 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.
git-annex 2.8.1 
git-annex 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/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
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  2016.5-plumed-2.4.1  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 least-squares 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 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. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
hdf5-mpi 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 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. Compatible with MPICH.
intel-mpi-benchmarks 2018.1 
a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard. You can run all of the supported benchmarks, or a subset specified in the command line using one executable file. Use command-line 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 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. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs.
libatomic_ops 7.6.4 
C/C++ Library for semi-portable access to hardware-provided 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 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. 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 run-time.
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. 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 matrix-matrix 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 Memory-Mapped Database (LMDB) library.
lsb-release versionless 
Replacement for the true lsb-release utility
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. 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 recursive-bisection, multilevel k-way, and multi-constraint 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 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. Typically you would use ncview to get a quick and easy, push-button 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 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 1.13 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  5.0-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. 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.
osu-micro-benchmarks 5.4.3 
OSU Micro-Benchmarks
pandoc 2.7.3 
If you need to convert files from one markup format into another, pandoc is your swiss-army knife
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. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
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. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
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 gnu-paralel.
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. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
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. It is based on density-functional 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 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 3.5.2 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. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
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. 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
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. A unique design feature of Trilinos is its focus on packages.
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 1.9.4a38  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. 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.