Difference between revisions of "Modules specific to Niagara"

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{| class="wikitable sortable" style="width:85%"
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=== NiaEnv/2019b ===
 +
{| class="wikitable sortable" style="width:100%"
 
! style="width: 25%" align="center" | Module
 
! style="width: 25%" align="center" | Module
! style="width: 15%" align="center" | Versions
+
! style="width: 15%" align="center" | Version(s)
 
! style="width: 15%" align="center" | Documentation
 
! style="width: 15%" align="center" | Documentation
 
! align="center" | Description
 
! align="center" | Description
 
|-
 
|-
| align="center" | [https://www.continuum.io/anaconda-overview anaconda2]
+
| align="left"  | CCEnv
| align="center" | 5.1.0
+
| align="left"  |
 +
| align="center" | [[Using modules]]
 +
| <div> {{Alliance}} software modules. Must be loaded to see {{Alliance}} modules in 'module spider'. </div>
 +
|-
 +
| align="left"  | [https://www.antlr2.org/ antlr]
 +
| align="left"  |  2.7.7
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://stnava.github.io/ANTs/ ants]
 +
| align="left"  |  2.3.1
 +
| align="center" |
 +
| <div> ANTs extracts information from complex datasets that include imaging </div>
 +
|-
 +
| align="left"  | arm-forge
 +
| align="left"  |  21.0.3
 +
| align="center" | [[Parallel Debugging with DDT]]
 +
| <div> Arm Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. </div>
 +
|-
 +
| align="left"  | [https://arma.sourceforge.net/ armadillo]
 +
| align="left"  |  9.700.2
 +
| align="center" |
 +
| <div> Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use </div>
 +
|-
 +
| align="left"  | [https://github.com/opencollab/arpack-ng arpack-ng]
 +
| align="left"  |  3.7.0
 +
| align="center" |
 +
| <div> ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems </div>
 +
|-
 +
| align="left"  | [https://github.com/autodiff/autodiff autodiff]
 +
| align="left"  |  0.5.11
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://autotools.io autotools]
 +
| align="left"  |  2018b&nbsp; 2018
 +
| align="center" |
 +
| <div> The standard GNU build tools: autoconf, automake and libtool </div>
 +
|-
 +
| align="left"  | [https://www.htslib.org/ bcftools]
 +
| align="left"  |  1.8&nbsp; 1.12(E)&nbsp; 1.13(E)
 +
| align="center" |
 +
| <div> SAMtools is a suite of programs for interacting with high-throughput sequencing data </div>
 +
|-
 +
| align="left"  | [https://github.com/arq5x/bedtools2 bedtools]
 +
| align="left"  |  2.29.0&nbsp; 2.30.0
 +
| align="center" |
 +
| <div> The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage </div>
 +
|-
 +
| align="left"  | [https://blast.ncbi.nlm.nih.gov/ blast+]
 +
| align="left"  |  2.9.0
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://github.com/blitzpp/blitz/ blitz++]
 +
| align="left"  |  1.0.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.boost.org/ boost]
 +
| align="left"  |  1.69.0&nbsp; 1.70.0&nbsp; 1.73.0&nbsp; 1.78.0
 +
| align="center" |
 +
| <div> Boost provides free peer-reviewed portable C++ source libraries </div>
 +
|-
 +
| align="left"  | [https://www.boost.org/ boost-python]
 +
| align="left"  | 1.69.0 1.70.0 1.75.0 
 +
| align="center" |
 +
| <div> Boost provides free peer-reviewed portable C++ source libraries, including boost:python </div>
 +
|-
 +
| align="left"  | [https://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
 +
| align="left"  |  2.3.4.3&nbsp; 2.4.4
 +
| align="center" |
 +
| <div> Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences </div>
 +
|-
 +
| align="left"  | [https://bio-bwa.sourceforge.net/ bwa]
 +
| align="left"  |  0.7.17
 +
| align="center" |
 +
| <div> Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome </div>
 +
|-
 +
| align="left"  | bwa-mem2
 +
| align="left"  |  2.0
 +
| align="center" |
 +
| <div> Bwa-mem2 is the next version of the bwa-mem algorithm in bwa </div>
 +
|-
 +
| align="left"  | [https://cairographics.org cairo]
 +
| align="left"  |  1.17.2
 +
| align="center" |
 +
| <div> Cairo is a 2D graphics library with support for multiple output devices </div>
 +
|-
 +
| align="left"  | [https://cairographics.org cairo]
 +
| align="left"  |  1.17.2
 +
| align="center" |
 +
| <div> Cairo is a 2D graphics library with support for multiple output devices </div>
 +
|-
 +
| align="left"  | [https://uscilab.github.io/cereal/ cereal]
 +
| align="left"  |  1.2.2
 +
| align="center" |
 +
| <div> A C++11 library for serialization </div>
 +
|-
 +
| align="left"  | [https://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]
 +
| align="left"  |  3.450
 +
| align="center" |
 +
| <div> CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format </div>
 +
|-
 +
| align="left"  | [https://www.cgal.org/ cgal]
 +
| align="left"  |  5.1
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://cget.readthedocs.io/en/latest/index.html cget]
 +
| align="left"  |  0.1.9
 +
| align="center" |
 +
| <div> Cmake package retrieval </div>
 +
|-
 +
| align="left"  | [https://chaiscript.com/ chaiscript]
 +
| align="left"  |  6.1.0
 +
| align="center" |
 +
| <div> Embedded Scripting Language Designed for C++ </div>
 +
|-
 +
| align="left"  | [https://www.cmake.org cmake]
 +
| align="left"  |  3.13.4&nbsp; 3.14.5&nbsp; 3.17.3&nbsp; 3.21.4
 +
| align="center" |
 +
| <div> CMake, the cross-platform, open-source build system </div>
 +
|-
 +
| align="left"  | [https://www.cp2k.org/ cp2k]
 +
| align="left"  |  6.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://cole-trapnell-lab.github.io/cufflinks/ cufflinks]
 +
| align="left"  |  2.2.1
 +
| align="center" |
 +
| <div> Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples </div>
 +
|-
 +
| align="left"  | [https://cole-trapnell-lab.github.io/cufflinks/ cufflinks]
 +
| align="left"  |  2.2.1
 +
| align="center" |
 +
| <div> Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples </div>
 +
|-
 +
| align="left"  | [https://opensource.scilifelab.se/projects/cutadapt/ cutadapt]
 +
| align="left"  |  2.10
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/ddd ddd]
 +
| align="left"  |  3.3.12
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.arm.com/products/development-tools/server-and-hpc/forge/ddt arm-forge]
 +
| align="left"  |  22.0.2
 +
| align="center" | [[Parallel Debugging with DDT]]
 +
| <div> DDT debugger and MAP profiler </div>
 +
|-
 +
| align="left"  | [https://www.dealii.org/ dealii]
 +
| align="left"  |  9.2.0
 +
| align="center" |
 +
| <div> deal </div>
 +
|-
 +
| align="left"  | [https://www.doxygen.org doxygen]
 +
| align="left"  |  1.8.17
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://eigen.tuxfamily.org eigen]
 +
| align="left"  |  3.3.7
 +
| align="center" |
 +
| <div> Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms </div>
 +
|-
 +
| align="left"  | [https://elpa.mpcdf.mpg.de elpa]
 +
| align="left"  |  2017.05.003&nbsp; 2020.05.001
 +
| align="center" |
 +
| <div> Eigenvalue SoLvers for Petaflop-Applications </div>
 +
|-
 +
| align="left"  | [https://core.tcl.tk/expect/index expect]
 +
| align="left"  |  5.45.4
 +
| align="center" |
 +
| <div> Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. </div>
 +
|-
 +
| align="left"  | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
 +
| align="left"  |  0.11.9
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://fenicsproject.org fenics]
 +
| align="left"  |  2019.1.0
 +
| align="center" |
 +
| <div> FEniCS is a computing platform for solving partial differential equations </div>
 +
|-
 +
| align="left"  | [https://www.ffmpeg.org ffmpeg]
 +
| align="left"  |  3.4.2
 +
| align="center" |
 +
| <div> A complete, cross-platform solution to record, convert and stream audio and video </div>
 +
|-
 +
| align="left"  | [https://www.fftw.org fftw]
 +
| align="left"  |  3.3.8
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://fmtlib.net fmt]
 +
| align="left"  |  4.1.0
 +
| align="center" |
 +
| <div> fmt (formerly cppformat) is an open-source formatting library </div>
 +
|-
 +
| align="left"  | [https://freesurfer.net freesurfer]
 +
| align="left"  |  6.0.0&nbsp; 7.1.0
 +
| align="center" |
 +
| <div> FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data </div>
 +
|-
 +
| align="left"  | [https://www.fmrib.ox.ac.uk/fsl fsl]
 +
| align="left"  |  6.0.4
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.broadinstitute.org/gatk gatk]
 +
| align="left"  |  4.1.7.0
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://gcc.gnu.org gcc]
 +
| align="left"  |  8.3.0&nbsp; 9.2.0&nbsp; 9.4.0
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> The GNU Compiler Collection C, C++, and Fortran </div>
 +
|-
 +
| align="left"  | [https://www.gdal.org gdal]
 +
| align="left"  |  2.4.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://trac.osgeo.org/geos geos]
 +
| align="left"  |  3.7.1
 +
| align="center" |
 +
| <div> GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) </div>
 +
|-
 +
| align="left"  | [https://git-scm.com/ git]
 +
| align="left"  |  2.21.0&nbsp; 2.30.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://git-annex.branchable.com/ git-annex]
 +
| align="left"  |  2.8.1&nbsp; 8.20200618
 +
| align="center" |
 +
| <div> git-annex allows managing files with git, without checking the file contents into git </div>
 +
|-
 +
| align="left"  | [https://git-lfs.github.com git-lfs]
 +
| align="left"  |  2.13.2
 +
| align="center" |
 +
| <div> Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub </div>
 +
|-
 +
| align="left"  | [https://www.gtk.org/ glib]
 +
| align="left"  |  2.48.2
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://gmplib.org/ gmp]
 +
| align="left"  |  6.1.2&nbsp; 6.2.0
 +
| align="center" |
 +
| <div> GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers </div>
 +
|-
 +
| align="left"  | [https://gmt.soest.hawaii.edu/ gmt]
 +
| align="left"  |  6.0.0
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/parallel gnu-parallel]
 +
| align="left"  |  20190322&nbsp; 20191122
 +
| align="center" | [[Running Serial Jobs on Niagara]]
 +
| <div> GNU parallel is a shell tool for executing (usually serial) jobs in parallel </div>
 +
|-
 +
| align="left"  | [https://gnuplot.sourceforge.net/ gnuplot]
 +
| align="left"  |  5.2.7
 +
| align="center" |
 +
| <div> Portable interactive, function plotting utility </div>
 +
|-
 +
| align="left"  | [https://www.golang.org go]
 +
| align="left"  |  1.13
 +
| align="center" |
 +
| <div> Go is an open source programming language that makes it easy to build simple, reliable, and efficient software </div>
 +
|-
 +
| align="left"  | [https://github.com/google/googletest googletest]
 +
| align="left"  |  1.10.0
 +
| align="center" |
 +
| <div> Google's C++ test framework </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/gperf/ gperf]
 +
| align="left"  |  3.1
 +
| align="center" |
 +
| <div> GNU gperf is a perfect hash function generator </div>
 +
|-
 +
| align="left"  | [https://www.graphviz.org/ graphviz]
 +
| align="left"  |  2.40.1
 +
| align="center" |
 +
| <div> Graphviz is open source graph visualization software </div>
 +
|-
 +
| align="left"  | [https://www.gromacs.org gromacs]
 +
| align="left"  |  2018.6-plumed-2.5.1&nbsp; 2018.6
 +
| align="center" | [[GROMACS]]
 +
| <div> GROMACS is a versatile package to perform molecular dynamics, i </div>
 +
|-
 +
| align="left"  | gromacs-ls
 +
| align="left"  |  2016.3
 +
| align="center" |
 +
| <div> GROMACS-LS is a custom version of GROMACS developed for local stress calculations from molecular simulations. </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/gsl/ gsl]
 +
| align="left"  |  2.5&nbsp; 2.7
 +
| align="center" |
 +
| <div> The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers </div>
 +
|-
 +
| align="left"  | [https://portal.hdfgroup.org/display/support hdf5]
 +
| align="left"  |  1.8.21&nbsp; 1.10.5&nbsp; 1.10.7
 +
| align="center" | [[HDF5]]
 +
| <div> HDF5 is a data model, library, and file format for storing and managing data </div>
 +
|-
 +
| align="left"  | [https://github.com/soedinglab/hh-suite hh-suite]
 +
| align="left"  |  3.3.0
 +
| align="center" |
 +
| <div> The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs) </div>
 +
|-
 +
| align="left"  | highfive
 +
| align="left"  |  2.3
 +
| align="center" |
 +
| <div> HighFive is a modern header-only C++11 friendly interface for libhdf5. </div>
 +
|-
 +
| align="left"  | [https://www.htslib.org/ htslib]
 +
| align="left"  |  1.12(E)&nbsp; 1.13(E)
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://icu-project.org/ icu]
 +
| align="left"  |  68.1
 +
| align="center" |
 +
| <div> International Components for Unicode </div>
 +
|-
 +
| align="left"  | [https://www.imagemagick.org/ imagemagick]
 +
| align="left"  |  6
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain intel]
 +
| align="left"  | 2019u3 2019u4 2019u5 2020u2 2020u4 
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/mpi-library intelmpi]
 +
| align="left"  | 2019u3 2019u4 2019u5 2020u2 2020u4 
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/distribution-for-python intelpython2]
 +
| align="left"  | 2019u3 2019u4 2019u5 
 +
| align="center" | [[Python]]
 +
| <div> Intel Python distribution for python 2, based on anaconda </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/distribution-for-python intelpython3]
 +
| align="left"  | 2019u3 2019u4 2019u5 
 +
| align="center" | [[Python]]
 +
| <div> Intel Python distribution for python 3, based on anaconda </div>
 +
|-
 +
| align="left"  | inteltools
 +
| align="left"  |  2019u4
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://itk.org itk]
 +
| align="left"  |  4.13.2
 +
| align="center" |
 +
| <div> Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data </div>
 +
|-
 +
| align="left"  | [https://mcmc-jags.sourceforge.net/ jags]
 +
| align="left"  |  4.3.0
 +
| align="center" |
 +
| <div> JAGS is Just Another Gibbs Sampler </div>
 +
|-
 +
| align="left"  | [https://java.com/ java]
 +
| align="left"  |  1.8.0_201
 +
| align="center" |
 +
| <div> Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers </div>
 +
|-
 +
| align="left"  | [https://www.genome.umd.edu/jellyfish.html jellyfish]
 +
| align="left"  |  2.3.0
 +
| align="center" |
 +
| <div> Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA </div>
 +
|-
 +
| align="left"  | [https://julialang.org julia]
 +
| align="left"  |  1.1.0&nbsp; 1.5.3&nbsp; 1.6.1&nbsp; 1.7.2
 +
| align="center" |
 +
| <div> A high-level, high-performance dynamic language for technical computing </div>
 +
|-
 +
| align="left"  | [https://julialang.org julia]
 +
| align="left"  |  1.1.0&nbsp; 1.5.3&nbsp; 1.6.1&nbsp; 1.7.2
 +
| align="center" |
 +
| <div> A high-level, high-performance dynamic language for technical computing </div>
 +
|-
 +
| align="left"  | [https://lammps.sandia.gov/ lammps]
 +
| align="left"  |  20Nov2019&nbsp; 29Mar2019
 +
| align="center" |
 +
| <div> The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation </div>
 +
|-
 +
| align="left"  | [https://libgit2.org/ libgit2]
 +
| align="left"  |  1.1.0
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://github.com/evaleev/libint libint]
 +
| align="left"  |  1.1.5&nbsp; 2.6-shared&nbsp; 2.6.0
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://doc.libsodium.org/ libsodium]
 +
| align="left"  |  1.0.18
 +
| align="center" |
 +
| <div> Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more </div>
 +
|-
 +
| align="left"  | [https://www.tddft.org/programs/libxc libxc]
 +
| align="left"  |  4.0.5&nbsp; 4.3.4&nbsp; 5.0.0
 +
| align="center" |
 +
| <div> Libxc is a library of exchange-correlation functionals for density-functional theory </div>
 +
|-
 +
| align="left"  | [https://xmlsoft.org/ libxslt]
 +
| align="left"  |  1.1.34
 +
| align="center" |
 +
| <div> Libxslt is the XSLT C library developed for the GNOME project </div>
 +
|-
 +
| align="left"  | [https://symas.com/lmdb lmdb]
 +
| align="left"  |  0.9.23
 +
| align="center" |
 +
| <div> OpenLDAP's Lightning Memory-Mapped Database (LMDB) library </div>
 +
|-
 +
| align="left"  | lsb-release
 +
| align="left"  |  versionless
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.mathworks.com/products/compiler/mcr/ mcr]
 +
| align="left"  |  R2019a
 +
| align="center" | [[MATLAB]]
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.mercurial-scm.org mercurial]
 +
| align="left"  |  5.1
 +
| align="center" |
 +
| <div> Mercurial is a free, distributed source control management tool </div>
 +
|-
 +
| align="left"  | [https://mesonbuild.com meson]
 +
| align="left"  |  0.51.2
 +
| align="center" |
 +
| <div> Meson is a cross-platform build system designed to be both as fast and as user friendly as possible </div>
 +
|-
 +
| align="left"  | [https://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis]
 +
| align="left"  |  5.1.0-shared&nbsp; 5.1.0
 +
| align="center" |
 +
| <div> METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices </div>
 +
|-
 +
| align="left"  | mii
 +
| align="left"  |  1.1.1
 +
| align="center" |
 +
| <div> A smart search engine for module environments. </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/mkl mkl]
 +
| align="left"  |  2019u3&nbsp; 2019u4
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> Intel Math Kernel Library </div>
 +
|-
 +
| align="left"  | [https://www.mothur.org/ mothur]  
 +
| align="left"  |  1.42.3
 +
| align="center" |  
 +
| <div> Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community </div>
 +
|-
 +
| align="left"  | [https://www.mpfr.org mpfr]
 +
| align="left"  |  4.0.2&nbsp; 4.1.0
 +
| align="center" |
 +
| <div> The MPFR library is a C library for multiple-precision floating-point computations with correct rounding </div>
 +
|-
 +
| align="left"  | [https://mrbayes.csit.fsu.edu mrbayes]
 +
| align="left"  |  3.2.7
 +
| align="center" |
 +
| <div> MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models </div>
 +
|-
 +
| align="left"  | [https://www.brain.org.au/software/index.html#mrtrix mrtrix]
 +
| align="left"  |  3.0.0
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://graal.ens-lyon.fr/MUMPS/ mumps]
 +
| align="left"  |  5.1.2&nbsp; 5.2.1
 +
| align="center" |
 +
| <div> A parallel sparse direct solver </div>
 +
|-
 +
| align="left"  | [https://drive5.com/muscle/ muscle]
 +
| align="left"  |  3.8.31
 +
| align="center" |
 +
| <div> MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW </div>
 +
|-
 +
| align="left"  | [https://www.ks.uiuc.edu/Research/namd/ namd]
 +
| align="left"  |  2.14
 +
| align="center" | [[NAMD]]
 +
| <div> NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems </div>
 +
|-
 +
| align="left"  | [https://www.ncl.ucar.edu ncl]
 +
| align="left"  |  6.6.2
 +
| align="center" |
 +
| <div> NCL is an interpreted language designed specifically for scientific data analysis and visualization </div>
 +
|-
 +
| align="left"  | [https://nco.sourceforge.net nco]
 +
| align="left"  |  4.8.1
 +
| align="center" |
 +
| <div> Python bindings for NCO </div>
 +
|-
 +
| align="left"  | [https://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
 +
| align="left"  |  2.1.7
 +
| align="center" |
 +
| <div> Ncview is a visual browser for netCDF format files </div>
 +
|-
 +
| align="left"  | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
 +
| align="left"  |  4.6.3
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://ninja-build.org/ ninja]
 +
| align="left"  |  1.9.0
 +
| align="center" |
 +
| <div> Ninja is a small build system with a focus on speed </div>
 +
|-
 +
| align="left"  | numdiff
 +
| align="left"  |  5.9.0
 +
| align="center" |
 +
| <div> numdiff can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/octave/ octave]
 +
| align="left"  |  5.2.0
 +
| align="center" | [[Octave]]
 +
| <div> GNU Octave is a high-level interpreted language, primarily intended for numerical computations </div>
 +
|-
 +
| align="left"  | [https://xianyi.github.com/OpenBLAS/ openblas]
 +
| align="left"  |  0.3.7
 +
| align="center" |
 +
| <div> OpenBLAS is an optimized BLAS library based on GotoBLAS2 1 </div>
 +
|-
 +
| align="left"  | [https://opencv.org/ opencv]
 +
| align="left"  |  4.5.0
 +
| align="center" |
 +
| <div> OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library </div>
 +
|-
 +
| align="left"  | [https://www.openfoam.com/ openfoam]
 +
| align="left"  | 7-broken 19.06 20.06 20.12 
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.openjpeg.org/ openjpeg]
 +
| align="left"  |  2.3.1
 +
| align="center" |
 +
| <div> 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) </div>
 +
|-
 +
| align="left"  | [https://www.open-mpi.org/ openmpi]
 +
| align="left"  |  3.1.3&nbsp; 4.0.1&nbsp; 4.0.3&nbsp; 4.1.1
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> The Open MPI Project is an open source MPI-2 implementation </div>
 +
|-
 +
| align="left"  | [https://github.com/davidemms/OrthoFinder orthofinder]
 +
| align="left"  |  2.3.3
 +
| align="center" |
 +
| <div> Program for identifying orthologous protein sequence families </div>
 +
|-
 +
| align="left"  | [https://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
 +
| align="left"  | 5.6.1 5.7.1 
 +
| align="center" |
 +
| <div> OSU Micro-Benchmarks </div>
 +
|-
 +
| align="left"  | [https://pandoc.org/ pandoc]
 +
| align="left"  |  2.7.3
 +
| align="center" |
 +
| <div> If you need to convert files from one markup format into another, pandoc is your swiss-army knife </div>
 +
|-
 +
| align="left"  | [https://icl.cs.utk.edu/projects/papi/ papi]
 +
| align="left"  |  6.0.0.1
 +
| align="center" |
 +
| <div> Performace Application Programming Interface </div>
 +
|-
 +
| align="left"  | [https://www.paraview.org paraview-offscreen]
 +
| align="left"  |  5.9.1
 +
| align="center" | [[Visualization]]
 +
| <div> Off-screen rendering with ParaView, a scientific parallel visualizer </div>
 +
|-
 +
| align="left"  | [https://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview parmetis]
 +
| align="left"  |  4.0.3
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | pcre2
 +
| align="left"  |  10.35
 +
| align="center" |
 +
| <div> A set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5 </div>
 +
|-
 +
| align="left"  | [https://www.perl.org/ perl]
 +
| align="left"  |  5.28.1&nbsp; 5.30.3&nbsp; 5.34.0
 +
| align="center" |
 +
| <div> Larry Wall's Practical Extraction and Report Language </div>
 +
|-
 +
| align="left"  | [https://www.mcs.anl.gov/petsc petsc]
 +
| align="left"  |  3.9.3&nbsp; 3.10.5&nbsp; 3.11.3&nbsp; 3.13.5
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.astro.caltech.edu/~tjp/pgplot/ pgplot]
 +
| align="left"  |  5.2.2
 +
| align="center" |
 +
| <div> Graphics subroutine library for C/C++ and Fortran </div>
 +
|-
 +
| align="left"  | [https://www.pixman.org/ pixman]
 +
| align="left"  |  0.38.4
 +
| align="center" |
 +
| <div> The Pixman library is a C library, part of the Cairo package, used for 2D graphics </div>
 +
|-
 +
| align="left"  | [https://zzz.bwh.harvard.edu/plink/dist plink]
 +
| align="left"  |  1.90b6
 +
| align="center" |
 +
| <div> PLINK is a whole-genome association analysis toolset, version 1 </div>
 +
|-
 +
| align="left"  | plink2
 +
| align="left"  |  2.00a3
 +
| align="center" |
 +
| <div> PLINK is a whole-genome association analysis toolset, version 2 </div>
 +
|-
 +
| align="left"  | [https://www.plumed-code.org plumed]
 +
| align="left"  |  2.5.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
 +
| align="left"  |  1.11.0&nbsp; 1.11.2
 +
| align="center" |
 +
| <div> Parallel netCDF: A Parallel I/O Library for NetCDF File Access </div>
 +
|-
 +
| align="left"  | postgresql
 +
| align="left"  |  14.1
 +
| align="center" |
 +
| <div> PostgreSQL is a powerful, open source object-relational database system with over 30 years of active development that has earned it a strong reputation for reliability, feature robustness, and performance. </div>
 +
|-
 +
| align="left"  | [https://proj.org proj]
 +
| align="left"  |  4.9.3&nbsp; 6.0.0
 +
| align="center" |
 +
| <div> Cartographic projections and coordinate transformations library </div>
 +
|-
 +
| align="left"  | [https://python.org/ python]
 +
| align="left"  | 2.7.15 3.6.8 3.7.9 3.8.5 3.9.8 
 +
| align="center" | [[Python]]
 +
| <div> Python is a programming language that lets you work more quickly and integrate your systems more effectively </div>
 +
|-
 +
| align="left"  | [https://github.com/pipitone/qbatch qbatch]
 +
| align="left"  |  2.1.4&nbsp; 2.1.5&nbsp; 2.2.1&nbsp; 2.3.0
 +
| align="center" |
 +
| <div> qbatch is a tool for executing commands in parallel across a compute cluster </div>
 +
|-
 +
| align="left"  | [https://www.qhull.org qhull]
 +
| align="left"  |  2020.2
 +
| align="center" |
 +
| <div> Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram </div>
 +
|-
 +
| align="left"  | [https://qt.io/ qt]
 +
| align="left"  |  4.8.7&nbsp; 5.12.4
 +
| align="center" |
 +
| <div> Qt is a comprehensive cross-platform C++ application framework </div>
 +
|-
 +
| align="left"  | [https://www.quantum-espresso.org quantum-espresso]
 +
| align="left"  | 6.4.1 6.5-perturbo 6.5-w90-perturbo 
 +
| align="center" |
 +
| <div> An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale </div>
 +
|-
 +
| align="left"  | [https://github.com/request/request/ r]
 +
| align="left"  |  3.5.3&nbsp; 3.6.1&nbsp; 3.6.3&nbsp; 4.0.3&nbsp; 4.1.2
 +
| align="center" |
 +
| <div> R is a free software environment for statistical computing and graphics </div>
 +
|-
 +
| align="left"  | [https://github.com/request/request/ r]
 +
| align="left"  |  3.5.3&nbsp; 3.6.1&nbsp; 3.6.3&nbsp; 4.0.3&nbsp; 4.1.2
 +
| align="center" |
 +
| <div> R is a free software environment for statistical computing and graphics </div>
 +
|-
 +
| align="left"  | [https://github.com/vanzonr/rarray rarray]
 +
| align="left"  |  1.2&nbsp; 2.0.0&nbsp; 2.1.1&nbsp; 2.3.0
 +
| align="center" |
 +
| <div> Library for runtime multi-dimensional arrays in C++ </div>
 +
|-
 +
| align="left"  | [https://www.rosettacommons.org rosetta]
 +
| align="left"  |  3.13
 +
| align="center" |
 +
| <div> Rosetta is the premier software suite for modeling macromolecular structures </div>
 +
|-
 +
| align="left"  | [https://rsync.samba.org/ rsync]
 +
| align="left"  |  3.1.3
 +
| align="center" | [[Data Management]]
 +
| <div> Fast, versatile, remote file-copying tool </div>
 +
|-
 +
| align="left"  | [https://www.rust-lang.org rust]
 +
| align="left"  |  1.47.0
 +
| align="center" |
 +
| <div> Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety </div>
 +
|-
 +
| align="left"  | [https://github.com/COMBINE-lab/salmon salmon]
 +
| align="left"  |  0.14.2&nbsp; 0.99.0-beta2
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://lomereiter.github.io/sambamba/ sambamba]
 +
| align="left"  |  0.7.1
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.htslib.org/ samtools]
 +
| align="left"  |  1.9&nbsp; 1.11&nbsp; 1.12&nbsp; 1.13
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform  that empowers companies to adopt a modern open data science analytics architecture. <br />Homepage: https://www.continuum.io/anaconda-overview </div>
+
| <div> SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format </div>
 
|-
 
|-
| align="center" | [https://www.continuum.io/anaconda-overview anaconda3]
+
| align="left"   | [https://www.netlib.org/scalapack/ scalapack]  
| align="center" | 5.1.0
+
| align="left"   | 2.0.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform  that empowers companies to adopt a modern open data science analytics architecture. <br />Homepage: https://www.continuum.io/anaconda-overview </div>
+
| <div> The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers </div>
 
|-
 
|-
| align="center" | [http://arma.sourceforge.net/ armadillo]
+
| align="left"   | [https://www.scons.org/ scons]  
| align="center" | 8.500.1
+
| align="left"   | 3.0.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards  a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,  as well as a subset of trigonometric and statistics functions.<br />Homepage: http://arma.sourceforge.net/ </div>
+
| <div> SCons is a software construction tool </div>
 
|-
 
|-
| align="center" | [ arpack-ng]
+
| align="left"   | [https://gforge.inria.fr/projects/scotch/ scotch]  
| align="center" | 3.5.0
+
| align="left"   | 6.0.6
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning </div>
 
|-
 
|-
| align="center" | [ aspect]
+
| align="left"   | [https://www.shengbte.org/ shengbte]  
| align="center" | 2.0.0 2.0.1
+
| align="left"   | 1.1.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Software package for solving the Boltzmann Transport Equation for phonons </div>
 
|-
 
|-
| align="center" | [http://autotools.io autotools]
+
| align="left"   | [https://departments.icmab.es/leem/siesta siesta]  
| align="center" | 2017
+
| align="left"   | master-27Oct2019 4.0.2 4.1-b4-transiesta-netcdf4 4.1-b4-transiesta 4.1-b4 4.1.5-util 4.1.5 
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This bundle collect the standard GNU build tools: Autoconf, Automake and libtool<br />Homepage: http://autotools.io </div>
+
| <div> Computer implementation of the SIESTA method to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids </div>
 +
|-
 +
| align="left"  | [https://www.sylabs.io/docs singularity]
 +
| align="left"  | 3.8.0
 +
| align="center" | [[Singularity]]
 +
| <div> Singularity is a portable application stack packaging and runtime utility </div>
 
|-
 
|-
| align="center" | [http://bazel.io/ bazel]
+
| align="left"   | [https://sourceforge.net/projects/sox sox]  
| align="center" | 0.11.1 0.15.0
+
| align="left"   | 14.4.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bazel is a build tool that builds code quickly and reliably.  It is used to build the majority of Google's software.<br />Homepage: http://bazel.io/ </div>
+
| <div> SoX, the Swiss Army knife of sound processing programs. </div>
 
|-
 
|-
| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast+]
+
| align="left"   | [https://spglib.github.io/spglib/ spglib]  
| align="center" | 2.7.1
+
| align="left"   | 1.10.3
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm  for comparing primary biological sequence information, such as the amino-acid  sequences of different proteins or the nucleotides of DNA sequences.<br />Homepage: http://blast.ncbi.nlm.nih.gov/ </div>
+
| <div> Spglib is a C library for finding and handling crystal symmetries </div>
 
|-
 
|-
| align="center" | [http://www.boost.org/ boost]
+
| align="left"   | [https://www.sqlite.org/ sqlite]  
| align="center" | 1.63.0 1.66.0 1.67.0
+
| align="left"   | 3.23.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries.<br />Homepage: http://www.boost.org/ </div>
+
| <div> SQLite: SQL Database Engine in a C Library </div>
 
|-
 
|-
| align="center" | [http://www.boost.org/ boost-mpi]
+
| align="left"   | [https://creskolab.uoregon.edu/stacks/ stacks]  
| align="center" | 1.67.0
+
| align="left"   | 2.55
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries.<br />Homepage: http://www.boost.org/ </div>
+
| <div> Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform </div>
 
|-
 
|-
| align="center" | [https://code.zmaw.de/projects/cdo cdo]
+
| align="left"   | [https://subversion.apache.org/ subversion]  
| align="center" | 1.9.4
+
| align="left"   | 1.10.4
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.<br />Homepage: https://code.zmaw.de/projects/cdo </div>
+
| <div> Subversion is an open source version control system </div>
 
|-
 
|-
| align="center" | [http://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]
+
| align="left"   | [https://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse]  
| align="center" | 3.430
+
| align="left"   | 5.8.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.<br />Homepage: http://heasarc.gsfc.nasa.gov/fitsio/ </div>
+
| <div> SuiteSparse is a suite of sparse matrix software </div>
 
|-
 
|-
| align="center" | [ cmake]
+
| align="left"   | [https://computation.llnl.gov/projects/sundials sundials]  
| align="center" | 3.10.3 3.11.0 3.11.1
+
| align="left"   | 5.3.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:   CMake, the cross-platform, open-source build system.  CMake is a family of tools designed to build, test and package software. <br />Homepage:  </div>
+
| <div> SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers </div>
 
|-
 
|-
| align="center" | [http://www.cp2k.org/ cp2k]
+
| align="left"   | [https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]  
| align="center" | 5.1
+
| align="left"   | 5.2.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular  simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different  methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and  classical pair and many-body potentials. <br />Homepage: http://www.cp2k.org/ </div>
+
| <div> SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines </div>
 
|-
 
|-
| align="center" | [ dakota-mpi]
+
| align="left"   | [https://www.swig.org/ swig]  
| align="center" | 6.7.0
+
| align="left"   | 3.0.12&nbsp; 4.0.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages </div>
 
|-
 
|-
| align="center" | [https://www.arm.com/products/development-tools/hpc-tools/cross-platform/forge ddt]
+
| align="left"   | [https://github.com/oneapi-src/oneTBB tbb]  
| align="center" | 18.1.2 18.2
+
| align="left"   | 2019u8&nbsp; 2019u9
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ARM's HPC development tools: Distributed Debugging Tool and MAP Profiler<br />Homepage: https://www.arm.com/products/development-tools/hpc-tools/cross-platform/forge </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://eigen.tuxfamily.org/index.php?title=Main_Page eigen]
+
| align="left"   | [https://tug.org texlive]  
| align="center" | 3.3.4
+
| align="left"   | 2019
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra:  matrices, vectors, numerical solvers, and related algorithms.<br />Homepage: http://eigen.tuxfamily.org/index.php?title=Main_Page </div>
+
| <div> High-quality typesetting programs TeX and LaTeX </div>
 
|-
 
|-
| align="center" | [http://elpa.rzg.mpg.de elpa]
+
| align="left"   | [http://www.shengbte.org/ thirdorder]  
| align="center" | 2016.05.003 2017.05.003 2018.05.001
+
| align="left"   | 1.1.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications .<br />Homepage: http://elpa.rzg.mpg.de </div>
+
| <div> Set of scripts to help users of ShengBTE and almaBTE create FORCE_CONSTANTS_3RD files in an efficient and convenient manner </div>
 
|-
 
|-
| align="center" | [https://fenicsproject.org/ fenics]
+
| align="left"   | tmux
| align="center" | 2017.2.0
+
| align="left"   | 3.2a
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FEniCS Project is a collection of free and open-source software components with the common goal to enable automated solution of differential equations. The components provide scientific computing tools for working with computational meshes, finite-element variational formulations of ordinary and partial differential equations, and numerical linear algebra.<br />Homepage: https://fenicsproject.org/</div>
+
| <div> tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached. </div>
 
|-
 
|-
| align="center" | [ fetk]
+
| align="left"   | [https://trilinos.sandia.gov/ trilinos]  
| align="center" | 1.5
+
| align="left"   | 12.12.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [https://www.ffmpeg.org/ ffmpeg]
+
| align="left"   | trimgalore
| align="center" | 3.4.2
+
| align="left"   | 0.6.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A complete, cross-platform solution to record, convert and stream audio and video.<br />Homepage: https://www.ffmpeg.org/ </div>
+
| <div> </div>
 
|-
 
|-
| align="center" | [http://www.fftw.org fftw]
+
| align="left"   | [https://github.com/trinityrnaseq/trinityrnaseq trinityrnaseq]  
| align="center" | 3.3.7
+
| align="left"   | 2.8.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)  in one or more dimensions, of arbitrary input size, and of both real and complex data.<br />Homepage: http://www.fftw.org </div>
+
| <div> Trinity RNA-Seq de novo transcriptome assembly </div>
 
|-
 
|-
| align="center" | [http://www.fftw.org fftw-mpi]
+
| align="left"   | [https://www.unidata.ucar.edu/software/udunits/ udunits]  
| align="center" | 3.3.7
+
| align="left"   | 2.2.26
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)  in one or more dimensions, of arbitrary input size, and of both real and complex data.<br />Homepage: http://www.fftw.org </div>
+
| <div> UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement </div>
 +
|-
 +
| align="left"  | [https://valgrind.org valgrind]
 +
| align="left"  |  3.14.0
 +
| align="center" | [[Introduction To Performance]]
 +
| <div> Valgrind-3 </div>
 
|-
 
|-
| align="center" | [http://fmtlib.net/ fmt]
+
| align="left"   | [https://vcftools.github.io vcftools]  
| align="center" | 3.0.2 4.1.0
+
| align="left"   | 0.1.16
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library.<br />Homepage: http://fmtlib.net/ </div>
+
| <div> A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project </div>
 
|-
 
|-
| align="center" | [ foam-extend]
+
| align="left"  | [https://wci.llnl.gov/simulation/computer-codes/visit visit]
| align="center" | 4.0
+
| align="left"  |  3.2.1&nbsp; 3.2.2
 +
| align="center" | [[Visualization]]
 +
| <div> Open Source, interactive, scalable, visualization, animation and analysis tool. </div>
 +
|-
 +
| align="left"  | [https://www.ks.uiuc.edu/Research/vmd vmd]  
 +
| align="left"  |  1.9.4a38
 +
| align="center" | [[Visualization]]
 +
| <div> VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting </div>
 +
|-
 +
| align="left"  | [https://github.com/torognes/vsearch vsearch]
 +
| align="left"  |  2.14.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting </div>
 
|-
 
|-
| align="center" | [http://hboehm.info/gc/ gc]
+
| align="left"   | [https://www.vtk.org vtk]  
| align="center" | 7.6.6
+
| align="left"   | 8.1.0&nbsp; 8.2.0&nbsp; 9.0.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting  replacement for C malloc or C++ new.<br />Homepage: http://hboehm.info/gc/ </div>
+
| <div> The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization </div>
 
|-
 
|-
| align="center" | [http://gcc.gnu.org/ gcc]
+
| align="left"   | [https://www.zlib.net/ zlib]  
| align="center" | 7.3.0
+
| align="left"   | 1.2.11
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,  as well as libraries for these languages (libstdc++, libgcj,...).<br />Homepage: http://gcc.gnu.org/ </div>
+
| <div> zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system </div>
 
|-
 
|-
| align="center" | [http://www.gnu.org/software/gdb/gdb.html gdb]
+
| align="left"   | [https://www.zlib.net/ zlib]  
| align="center" | 8.1
+
| align="left"   | 1.2.11
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Project Debugger<br />Homepage: http://www.gnu.org/software/gdb/gdb.html </div>
+
| <div> zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system </div>
 +
|}
 +
 
 +
=== NiaEnv/2018a ===
 +
{| class="wikitable sortable" style="width:100%"
 +
! style="width: 25%" align="center" | Module
 +
! style="width: 15%" align="center" | Version(s)
 +
! style="width: 15%" align="center" | Documentation
 +
! align="center" | Description
 +
|-
 +
| align="left"  | CCEnv
 +
| align="left"  |
 +
| align="center" | [[Using modules]]
 +
| <div> {{Alliance}} software modules. Must be loaded to see {{Alliance}} modules in 'module spider'.  </div>
 +
|-
 +
| align="left"  | [https://www.anaconda.com anaconda2]
 +
| align="left"  |  5.1.0
 +
| align="center" | [[Python]]
 +
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://git-scm.com/ git]
+
| align="left"  | [https://www.anaconda.com anaconda3]
| align="center" | 2.16.3
+
| align="left"  |  5.1.0&nbsp; 5.2.0&nbsp; 2018.12
 +
| align="center" | [[Python]]
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.antlr2.org/ antlr]  
 +
| align="left"   | 2.7.7
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.<br />Homepage: http://git-scm.com/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.gtk.org/ glib]
+
| align="left"   | [https://stnava.github.io/ANTs/ ants]  
| align="center" | 1.10.3 2.22.5
+
| align="left"   | 2.3.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLib is one of the base libraries of the GTK+ project<br />Homepage: http://www.gtk.org/ </div>
+
| <div> ANTs extracts information from complex datasets that include imaging </div>
 
|-
 
|-
| align="center" | [ g_mmpbsa]
+
| align="left"   | [https://arma.sourceforge.net/ armadillo]  
| align="center" | 5.1.2
+
| align="left"   | 8.500.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use </div>
 
|-
 
|-
| align="center" | [http://gmplib.org/ gmp]
+
| align="left"   | [https://github.com/opencollab/arpack-ng arpack-ng]  
| align="center" | 6.1.2
+
| align="left"   | 3.5.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMP is a free library for arbitrary precision arithmetic,  operating on signed integers, rational numbers, and floating point numbers. <br />Homepage: http://gmplib.org/ </div>
+
| <div> ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems </div>
 
|-
 
|-
| align="center" | [https://www.gnu.org/software/parallel/ gnu-parallel]
+
| align="left"   | [https://aspect.geodynamics.org/ aspect]  
| align="center" | 20180322
+
| align="left"   | 2.0.0&nbsp; 2.0.1&nbsp; 2.1.0-pre&nbsp; 2.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tools for running commands in parallel on one or more nodes.<br />Homepage: https://www.gnu.org/software/parallel/ </div>
+
| <div> Finite element parallel code to simulate problems in thermal convection in both 2D and 3D models </div>
 
|-
 
|-
| align="center" | [http://gnuplot.sourceforge.net/ gnuplot]
+
| align="left"   | aspera-client
| align="center" | 5.2.2
+
| align="left"   | 3.8.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Portable interactive, function plotting utility<br />Homepage: http://gnuplot.sourceforge.net/ </div>
+
| <div> Command-line interface for Aspera, a data transport and streaming technology </div>
 
|-
 
|-
| align="center" | [https://github.com/google/googletest googletest]
+
| align="left"   | [https://autotools.io autotools]  
| align="center" | 1.8.0
+
| align="left"   | 2017
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:   Welcome to Google Test, Google-s C++ test framework!  Please see the project page for more information as well as the mailing list for questions, discussions, and development. There is also an IRC channel on OFTC.  Getting started information for Google Test is available in the Google Test Primer documentation.  Google Mock is an extension to Google Test for writing and using C++ mock classes. See the separate Google Mock documentation.  More detailed documentation for googletest (including build instructions) are in its interior googletest/README.md file. <br />Homepage: https://github.com/google/googletest </div>
+
| <div> The standard GNU build tools: autoconf, automake and libtool </div>
 
|-
 
|-
| align="center" | [http://www.gromacs.org gromacs]
+
| align="left"   | [https://www.evolution.reading.ac.uk/BayesTraitsV1.html bayestraits]  
| align="center" | 2016.5 2016.5-plumed-2.4.1
+
| align="left"   | 3.0.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:  GROMACS is a versatile package to perform molecular dynamics,  i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is CPU only build, containing both MPI and threadMPI builds. <br />Homepage: http://www.gromacs.org </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.gnu.org/software/gsl/ gsl]
+
| align="left"   | [https://bazel.io/ bazel]  
| align="center" | 2.4
+
| align="left"   | 0.11.1&nbsp; 0.15.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.  The library provides a wide range of mathematical routines such as random number generators, special functions  and least-squares fitting.<br />Homepage: http://www.gnu.org/software/gsl/ </div>
+
| <div> Bazel is a build tool that builds code quickly and reliably </div>
 
|-
 
|-
| align="center" | [http://www.gnu.org/software/guile guile]
+
| align="left"   | [https://bedops.readthedocs.io/en/latest/index.html bedops]  
| align="center" | 2.2.3
+
| align="left"   | 2.4.35
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.<br />Homepage: http://www.gnu.org/software/guile </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/Harminv harminv]
+
| align="left"   | [https://github.com/arq5x/bedtools2 bedtools]  
| align="center" | 1.4.1
+
| align="left"   | 2.27.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion -  given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially  decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those  sinusoids.<br />Homepage: http://ab-initio.mit.edu/wiki/index.php/Harminv </div>
+
| <div> The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage </div>
 
|-
 
|-
| align="center" | [https://support.hdfgroup.org/HDF5/ hdf5]
+
| align="left"   | [https://blast.ncbi.nlm.nih.gov/ blast+]  
| align="center" | 1.10.2 1.8.20
+
| align="left"   | 2.7.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data.  It supports an unlimited variety of datatypes, and is designed for flexible  and efficient I/O and for high volume and complex data.<br />Homepage: https://support.hdfgroup.org/HDF5/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [https://support.hdfgroup.org/HDF5/ hdf5-mpi]
+
| align="left"   | [https://www.boost.org/ boost]  
| align="center" | 1.10.2 1.8.20
+
| align="left"   | 1.63.0&nbsp; 1.66.0&nbsp; 1.67.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data.  It supports an unlimited variety of datatypes, and is designed for flexible  and efficient I/O and for high volume and complex data.<br />Homepage: https://support.hdfgroup.org/HDF5/ </div>
+
| <div> Boost provides free peer-reviewed portable C++ source libraries </div>
 
|-
 
|-
| align="center" | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]
+
| align="left"   | [https://www.boost.org/ boost-mpi]  
| align="center" | 2.1.0
+
| align="left"   | 1.67.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads  (both DNA and RNA) against the general human population (as well as against a single reference genome).<br />Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml </div>
+
| <div> Boost provides free peer-reviewed portable C++ source libraries </div>
 
|-
 
|-
| align="center" | [ hpn-ssh]
+
| align="left"   | [https://bio-bwa.sourceforge.net/ bwa]  
| align="center" | 7.7p1-14v15
+
| align="left"   | 0.7.17
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome </div>
 
|-
 
|-
| align="center" | [http://www.x.org/ imake]
+
| align="left"   | [https://code.zmaw.de/projects/cdo cdo]  
| align="center" | 1.0.7
+
| align="left"   | 1.9.4
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: imake is a Makefile-generator that is intended to make it easier to develop software  portably for multiple systems.<br />Homepage: http://www.x.org/ </div>
+
| <div> CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data </div>
 
|-
 
|-
| align="center" | [https://software.intel.com/en-us/intel-parallel-studio-xe intel]
+
| align="left"   | [https://uscilab.github.io/cereal/ cereal]  
| align="center" | 2017.7 2018.2 2018.3
+
| align="left"   | 1.2.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Compiler toolchain including Intel compilers and Intel Math Kernel Library (MKL).<br />Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe </div>
+
| <div> A C++11 library for serialization </div>
 
|-
 
|-
| align="center" | [https://software.intel.com/en-us/intel-parallel-studio-xe intelmpi]
+
| align="left"   | [https://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]  
| align="center" | 2017.7 2018.2 2018.3
+
| align="left"   | 3.430
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel's (MPICH-based) MPI implementation.<br />Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe </div>
+
| <div> CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format </div>
 
|-
 
|-
| align="center" | [ intelpython2]
+
| align="left"   | [https://chaiscript.com/ chaiscript]  
| align="center" | 2018.2
+
| align="left"   | 6.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Embedded Scripting Language Designed for C++ </div>
 
|-
 
|-
| align="center" | [ intelpython3]
+
| align="left"   | [https://www.cmake.org cmake]  
| align="center" | 2018.2
+
| align="left"   | 3.10.3&nbsp; 3.11.0&nbsp; 3.11.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> CMake, the cross-platform, open-source build system </div>
 
|-
 
|-
| align="center" | [http://java.com/ java]
+
| align="left"   | [https://www.cp2k.org/ cp2k]  
| align="center" | 1.8.0_162
+
| align="left"   | 6.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy  Java applications on desktops and servers.<br />Homepage: http://java.com/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://lammps.sandia.gov/ lammps]
+
| align="left"   | [https://dakota.sandia.gov dakota-mpi]  
| align="center" | 11May2018 22Sep2017
+
| align="left"   | 6.7.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:  LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is  a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials  (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or  mesoscopic systems. It can be used to model atoms or, more generically, as a parallel  particle simulator at the atomic, meso, or continuum scale. It can be coupled to various  programs. The following packages are not included within this version:  -KIM, -MSCG, -KOKKOS, -USER-QUIP, -USER-INTEL, -USER-VTK<br />Homepage: http://lammps.sandia.gov/ </div>
+
| <div> The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and Unicertainly Quantification </div>
 
|-
 
|-
| align="center" | [ libatomic_ops]
+
| align="left"   | [https://github.com/rordenlab/dcm2niix dcm2niix]  
| align="center" | 7.6.4
+
| align="left"   | 1.0.20200331
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format </div>
 
|-
 
|-
| align="center" | [http://www.hyperrealm.com/libconfig/ libconfig]
+
| align="left"   | [https://www.arm.com/products/development-tools/server-and-hpc/forge/ddt arm-forge]  
| align="center" | 1.7.2
+
| align="left"  |  22.0.2
 +
| align="center" | [[Parallel Debugging with DDT]]
 +
| <div> DDT debugger and MAP profiler </div>
 +
|-
 +
| align="left"  | [https://github.com/bbuchfink/diamond diamond]
 +
| align="left"  |  0.9.23
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libconfig is a simple library for processing structured configuration files<br />Homepage: http://www.hyperrealm.com/libconfig/ </div>
+
| <div> Accelerated BLAST compatible local sequence aligner </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/libctl libctl]
+
| align="left"   | [https://eigen.tuxfamily.org eigen]  
| align="center" | 4.0.1
+
| align="left"   | 3.3.4
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations.<br />Homepage: http://ab-initio.mit.edu/libctl </div>
+
| <div> Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms </div>
 
|-
 
|-
| align="center" | [http://sourceware.org/libffi/ libffi]
+
| align="left"   | [https://elpa.mpcdf.mpg.de elpa]  
| align="center" | 3.2.1
+
| align="left"   | 2016.05.003&nbsp; 2017.05.003&nbsp; 2018.05.001
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.<br />Homepage: http://sourceware.org/libffi/ </div>
+
| <div> Eigenvalue SoLvers for Petaflop-Applications </div>
 
|-
 
|-
| align="center" | [https://sourceforge.net/p/libint/ libint]
+
| align="left"   | [https://sourceforge.net/projects/esmf esmf]  
| align="center" | 1.1.5 1.1.6
+
| align="left"   | 7.1.0r
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body  matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.<br />Homepage: https://sourceforge.net/p/libint/ </div>
+
| <div> The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models </div>
 
|-
 
|-
| align="center" | [http://www.gnu.org/software/libunistring/ libunistring]
+
| align="left"   | [https://www.atgc-montpellier.fr/fastme/ fastme]  
| align="center" | 0.9.9
+
| align="left"   | 2.1.6.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This library provides functions for manipulating Unicode strings and for manipulating C strings  according to the Unicode standard.<br />Homepage: http://www.gnu.org/software/libunistring/ </div>
+
| <div> FastME: a comprehensive, accurate and fast distance-based phylogeny inference program </div>
 
|-
 
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc]
+
| align="left"   | [https://fenicsproject.org fenics]  
| align="center" | 3.0.0 4.0.3 4.0.5
+
| align="left"   | 2017.2.0&nbsp; 2018.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory.  The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.<br />Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc </div>
+
| <div> FEniCS is a computing platform for solving partial differential equations </div>
 
|-
 
|-
| align="center" | [http://xmlsoft.org/ libxslt]
+
| align="left"   | [http://www.fetk.org fetk]  
| align="center" | 1.1.32
+
| align="left"   | 1.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxslt is the XSLT C library developed for the GNOME project  (but usable outside of the Gnome platform).<br />Homepage: http://xmlsoft.org/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [ libyaml]
+
| align="left"   | [https://www.ffmpeg.org ffmpeg]  
| align="center" | 0.1.7
+
| align="left"   | 3.4.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LibYAML is a YAML parser and emitter written in C.<br />Homepage:  </div>
+
| <div> A complete, cross-platform solution to record, convert and stream audio and video </div>
 
|-
 
|-
| align="center" | [https://symas.com/lmdb lmdb]
+
| align="left"   | [https://www.fftw.org fftw]  
| align="center" | 0.9.22
+
| align="left"   | 3.3.7
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance  of a pure in-memory database while retaining the persistence of standard disk-based databases.<br />Homepage: https://symas.com/lmdb </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html makedepend]
+
| align="left"   | [https://www.fftw.org fftw-mpi]  
| align="center" | 1.0.5
+
| align="left"   | 3.3.7
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.<br />Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr]
+
| align="left"   | [https://fmtlib.net fmt]  
| align="center" | R2018a
+
| align="left"   | 3.0.2&nbsp; 4.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries  that enables the execution of compiled MATLAB applications  or components on computers that do not have MATLAB installed.<br />Homepage: http://www.mathworks.com/products/compiler/mcr/ </div>
+
| <div> fmt (formerly cppformat) is an open-source formatting library </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/Meep meep]
+
| align="left"   | [https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-4.0 foam-extend]  
| align="center" | 1.4.3
+
| align="left"   | 4.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package  developed at MIT to model electromagnetic systems.<br />Homepage: http://ab-initio.mit.edu/wiki/index.php/Meep </div>
+
| <div> The foam-extend project is a fork of the OpenFOAM open source library for Computational Fluid Dynamics </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/Meep meep-mpi]
+
| align="left"   | [https://freesurfer.net freesurfer]  
| align="center" | 1.4.3
+
| align="left"   | 5.3.0&nbsp; 6.0.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package  developed at MIT to model electromagnetic systems.<br />Homepage: http://ab-initio.mit.edu/wiki/index.php/Meep </div>
+
| <div> FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data </div>
 
|-
 
|-
| align="center" | [http://mercurial.selenic.com/ mercurial]
+
| align="left"   | [https://rashmikumari.github.io/g_mmpbsa g_mmpbsa]  
| align="center" | 4.6
+
| align="left"   | 5.1.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. <br />Homepage: http://mercurial.selenic.com/ </div>
+
| <div> Molecular mechanics/Poisson-Bolzmann surface area method for GROMACS </div>
 
|-
 
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis]
+
| align="left"   | [https://www.msg.chem.iastate.edu/GAMESS gamess]
| align="center" | 5.1.0
+
| align="left"  |  14Feb2018
 +
| align="center" | [[GAMESS]]
 +
| <div> General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package </div>
 +
|-
 +
| align="left"  | [https://hboehm.info/gc gc]  
 +
| align="left"   | 7.6.6
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.<br />Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview </div>
+
| <div> The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new </div>
 
|-
 
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ mkl]
+
| align="left"  | [https://gcc.gnu.org gcc]
| align="center" | 2017.7 2018.2 2018.2.lua 2018.3
+
| align="left"  |  4.9.4&nbsp; 7.3.0
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> The GNU Compiler Collection C, C++, and Fortran </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/gdb/gdb.html gdb]
 +
| align="left"  |  8.1
 +
| align="center" | [[Performance And Debugging Tools: Niagara]]
 +
| <div> The GNU Project Debugger </div>
 +
|-
 +
| align="left"  | [https://git-scm.com/ git]  
 +
| align="left"   | 2.16.3
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel's Math Kernel Library, for use with gcc modules (the intel modules include mkl already).<br />Homepage: http://software.intel.com/en-us/intel-mkl/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/MPB mpb]
+
| align="left"   | [https://git-annex.branchable.com/ git-annex]  
| align="center" | 1.6.2
+
| align="left"   | 2.8.1&nbsp; 8.20200618
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPB is a free and open-source software package for computing electromagnetic band structures and modes.<br />Homepage: http://ab-initio.mit.edu/wiki/index.php/MPB</div>
+
| <div> git-annex allows managing files with git, without checking the file contents into git </div>
 
|-
 
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/MPB mpb-mpi]
+
| align="left"   | [https://git-lfs.github.com git-lfs]  
| align="center" | 1.6.2
+
| align="left"   | 2.13.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPB is a free and open-source software package for computing electromagnetic band structures and modes.<br />Homepage:  http://ab-initio.mit.edu/wiki/index.php/MPB</div>
+
| <div> Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub </div>
 
|-
 
|-
| align="center" | [http://www.mpfr.org mpfr]
+
| align="left"   | [https://www.gtk.org/ glib]  
| align="center" | 4.0.1
+
| align="left"   | 2.22.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MPFR library is a C library for multiple-precision  floating-point computations with correct rounding.<br />Homepage: http://www.mpfr.org </div>
+
| <div> GLib is one of the base libraries of the GTK+ project </div>
 
|-
 
|-
| align="center" | [http://www.ncl.ucar.edu ncl]
+
| align="left"   | [https://gmplib.org/ gmp]  
| align="center" | 6.4.0
+
| align="left"   | 6.1.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization.<br />Homepage: http://www.ncl.ucar.edu </div>
+
| <div> GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/parallel gnu-parallel]
 +
| align="left"  |  20180322
 +
| align="center" | [[Running Serial Jobs on Niagara]]
 +
| <div> GNU parallel is a shell tool for executing (usually serial) jobs in parallel </div>
 
|-
 
|-
| align="center" | [https://github.com/nco/pynco nco]
+
| align="left"   | [https://gnuplot.sourceforge.net/ gnuplot]  
| align="center" | 4.7.4
+
| align="left"   | 5.2.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python bindings for NCO<br />Homepage: https://github.com/nco/pynco </div>
+
| <div> Portable interactive, function plotting utility </div>
 
|-
 
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf]
+
| align="left"   | [https://www.golang.org go]  
| align="center" | 1.9.0 4.6.1
+
| align="left"   | 1.13
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries  and machine-independent data formats that support the creation, access, and sharing of array-oriented  scientific data.<br />Homepage: http://www.unidata.ucar.edu/software/netcdf/ </div>
+
| <div> Go is an open source programming language that makes it easy to build simple, reliable, and efficient software </div>
 
|-
 
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi]
+
| align="left"   | [https://github.com/google/googletest googletest]  
| align="center" | 4.6.1
+
| align="left"   | 1.8.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries  and machine-independent data formats that support the creation, access, and sharing of array-oriented  scientific data.<br />Homepage: http://www.unidata.ucar.edu/software/netcdf/ </div>
+
| <div> Google's C++ test framework </div>
 +
|-
 +
| align="left"   | [https://www.gromacs.org gromacs]
 +
| align="left"  | 5.1.4 2016.5-plumed-2.4.1 2016.5 2019.1 
 +
| align="center" | [[GROMACS]]
 +
| <div> GROMACS is a versatile package to perform molecular dynamics, i </div>
 
|-
 
|-
| align="center" | [http://www.gnu.org/software/octave/ octave]
+
| align="left"   | [https://www.gnu.org/software/gsl/ gsl]  
| align="center" | 4.4.0
+
| align="left"   | 2.4
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations.<br />Homepage: http://www.gnu.org/software/octave/ </div>
+
| <div> The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers </div>
 
|-
 
|-
| align="center" | [http://xianyi.github.com/OpenBLAS/ openblas]
+
| align="left"   | [https://www.gnu.org/software/guile/ guile]  
| align="center" | 0.2.20
+
| align="left"   | 2.2.3
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.<br />Homepage: http://xianyi.github.com/OpenBLAS/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.openfoam.com/ openfoam]
+
| align="left"   | [https://github.com/stevengj/harminv harminv]  
| align="center" | 17.12 4.1 5.0 5.0-debug
+
| align="left"   | 1.4.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package.  OpenFOAM has an extensive range of features to solve anything from complex fluid flows  involving chemical reactions, turbulence and heat transfer,   to solid dynamics and electromagnetics.<br />Homepage: http://www.openfoam.com/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.open-mpi.org/ openmpi]
+
| align="left"   | [https://github.com/stevengj/harminv harminv]  
| align="center" | 1.10.7 2.1.3 3.0.1 3.0.2 3.1.0 3.1.0rc3 3.1.0rc4 3.1.1
+
| align="left"   | 1.4.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-2 implementation.<br />Homepage: http://www.open-mpi.org/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.paraview.org paraview]
+
| align="left"  | [https://portal.hdfgroup.org/display/support hdf5]
| align="center" | 5.5.0
+
| align="left"  |  1.8.20&nbsp; 1.10.2
 +
| align="center" | [[HDF5]]
 +
| <div> HDF5 is a data model, library, and file format for storing and managing data </div>
 +
|-
 +
| align="left"  | [https://portal.hdfgroup.org/display/support hdf5-mpi]  
 +
| align="left"  |  1.8.20&nbsp; 1.10.2
 +
| align="center" | [[HDF5]]
 +
| <div> HDF5 is a data model, library, and file format for storing and managing data </div>
 +
|-
 +
| align="left"  | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]
 +
| align="left"  |  2.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer.<br />Homepage: http://www.paraview.org </div>
+
| <div> 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) </div>
 
|-
 
|-
| align="center" | [ perf-reports]
+
| align="left"   | [https://www.psc.edu/hpn-ssh hpn-ssh]  
| align="center" | 18.2
+
| align="left"   | 7.7p1-14v15
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Optimized ssh protocol </div>
 
|-
 
|-
| align="center" | [http://www.perl.org/ perl]
+
| align="left"   | [https://github.com/simon-anders/htseq htseq]  
| align="center" | 5.20.3 5.26.1
+
| align="left"   | 0.11.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language<br />Homepage: http://www.perl.org/ </div>
+
| <div> A framework to process and analyze data from high-throughput sequencing (HTS) assays </div>
 
|-
 
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc]
+
| align="left"   | [https://www.x.org/ imake]  
| align="center" | 3.8.4 3.8.4-debug 3.9.2
+
| align="left"   | 1.0.7
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the  scalable (parallel) solution of scientific applications modeled by partial differential equations.<br />Homepage: http://www.mcs.anl.gov/petsc </div>
+
| <div> imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems </div>
 
|-
 
|-
| align="center" | [http://www.astro.caltech.edu/~tjp/pgplot/ pgplot]
+
| align="left"   | [https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain intel]  
| align="center" | 5.2.2 5.2.2-x
+
| align="left"   | 2017.7&nbsp; 2018.1&nbsp; 2018.2&nbsp; 2018.3
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries </div>
 +
|-
 +
| align="left"  | [https://github.com/intel/mpi-benchmarks intel-mpi-benchmarks]
 +
| align="left"  |  2018.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.<br />Homepage: http://www.astro.caltech.edu/~tjp/pgplot/ </div>
+
| <div> a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard </div>
 
|-
 
|-
| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink]
+
| align="left"  | [https://software.intel.com/en-us/mpi-library intelmpi]
| align="center" | 1.07
+
| align="left"  | 2017.7 2018.1 2018.2 2018.3 
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> Intel MPI library with compiler wrappers for C, C++, and Fortran </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/distribution-for-python intelpython2]
 +
| align="left"  |  2018.2
 +
| align="center" | [[Python]]
 +
| <div> Intel Python distribution for python 2, based on anaconda </div>
 +
|-
 +
| align="left"  | [https://software.intel.com/en-us/distribution-for-python intelpython3]
 +
| align="left"  |  2018.2
 +
| align="center" | [[Python]]
 +
| <div> Intel Python distribution for python 3, based on anaconda </div>
 +
|-
 +
| align="left"  | [https://itk.org itk]
 +
| align="left"  |  4.13.0
 +
| align="center" |
 +
| <div> Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data </div>
 +
|-
 +
| align="left"  | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]  
 +
| align="left"   | 2.0.14
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset<br />Homepage: https://www.cog-genomics.org/plink/1.9/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.plumed-code.org plumed]
+
| align="left"   | [https://java.com/ java]  
| align="center" | 2.4.1
+
| align="left"   | 1.8.0_162
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which  works together with some of the most popular molecular dynamics engines. Free energy calculations can be  performed as a function of many order parameters with a particular  focus on biological problems, using  state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.  The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. <br />Homepage: http://www.plumed-code.org </div>
+
| <div> Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers </div>
 
|-
 
|-
| align="center" | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
+
| align="left"   | [https://julialang.org julia]  
| align="center" | 1.9.0
+
| align="left"   | 1.0.0&nbsp; 1.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Parallel netCDF: A Parallel I/O Library for NetCDF File Access<br />Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf </div>
+
| <div> A high-level, high-performance dynamic language for technical computing </div>
 
|-
 
|-
| align="center" | [http://python.org/ python]
+
| align="left"   | [https://julialang.org julia]  
| align="center" | 2.7.14 3.6.5
+
| align="left"   | 1.0.0&nbsp; 1.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python is a programming language that lets you work more quickly and integrate your systems  more effectively.<br />Homepage: http://python.org/ </div>
+
| <div> A high-level, high-performance dynamic language for technical computing </div>
 
|-
 
|-
| align="center" | [ qhull]
+
| align="left"   | [https://lammps.sandia.gov/ lammps]  
| align="center" | 2015.2
+
| align="left"   | 11May2018&nbsp; 22Sep2017
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:  Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram,  halfspace intersection about a point, furthest-site Delaunay triangulation,  and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and  higher dimensions. Qhull implements the Quickhull algorithm for computing the  convex hull. <br />Homepage:  </div>
+
| <div> The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation </div>
 
|-
 
|-
| align="center" | [ quantum-espresso]
+
| align="left"   | [https://github.com/ivmai/libatomic_ops libatomic_ops]  
| align="center" | 6.2.1
+
| align="left"   | 7.6.4
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> C/C++ Library for semi-portable access to hardware-provided atomic memory update operations on a number of architectures </div>
 
|-
 
|-
| align="center" | [http://www.r-project.org/ r]
+
| align="left"   | [https://hyperrealm.github.io/libconfig libconfig]  
| align="center" | 1.1.1 3.5.0 4.0.1 R2018a
+
| align="left"   | 1.7.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics.<br />Homepage: http://www.r-project.org/ </div>
+
| <div> Libconfig is a simple library for processing structured configuration files </div>
 
|-
 
|-
| align="center" | [ rarray]
+
| align="left"   | [https://libctl.readthedocs.io/en/latest/ libctl]  
| align="center" | 1.2
+
| align="left"   | 4.0.1&nbsp; 4.1.2
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> libctl is a free Guile-based library implementing flexible control files for scientific simulations </div>
 
|-
 
|-
| align="center" | [https://rsync.samba.org/ rsync]
+
| align="left"   | [https://libevent.org/ libevent]  
| align="center" | 3.1.3
+
| align="left"   | 2.1.8
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Utility that provides fast incremental file transfer; this module provides a newer version than is present in the operating system.<br />Homepage: https://rsync.samba.org/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [https://www.rust-lang.org rust]
+
| align="left"   | [https://sourceware.org/libffi/ libffi]  
| align="center" | 1.26.1
+
| align="left"   | 3.2.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults,  and guarantees thread safety.<br />Homepage: https://www.rust-lang.org </div>
+
| <div> The libffi library provides a portable, high level programming interface to various calling conventions </div>
 
|-
 
|-
| align="center" | [http://www.htslib.org/ samtools]
+
| align="left"   | [https://github.com/evaleev/libint libint]  
| align="center" | 1.8
+
| align="left"   | 1.1.5&nbsp; 1.1.6
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format,  including sorting, merging, indexing and generating alignments in a per-position format.<br />Homepage: http://www.htslib.org/ </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.netlib.org/scalapack/ scalapack]
+
| align="left"   | [https://doc.libsodium.org/ libsodium]  
| align="center" | 2.0.2
+
| align="left"   | 1.0.18
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines  redesigned for distributed memory MIMD parallel computers.<br />Homepage: http://www.netlib.org/scalapack/ </div>
+
| <div> Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more </div>
 
|-
 
|-
| align="center" | [http://www.scons.org/ scons]
+
| align="left"   | [https://www.remotesensing.org/libtiff/ libtiff]  
| align="center" | 3.0.1
+
| align="left"   | 4.0.9
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SCons is a software construction tool.<br />Homepage: http://www.scons.org/ </div>
+
| <div> tiff: Library and tools for reading and writing TIFF data files </div>
 
|-
 
|-
| align="center" | [http://www.shengbte.org/ shengbte]
+
| align="left"   | [https://www.gnu.org/software/libunistring/ libunistring]  
| align="center" | 1.1.1
+
| align="left"   | 0.9.9
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.  Also installed is the 'thirdorder' package of Python scripts.<br />Homepage: http://www.shengbte.org/ </div>
+
| <div> This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard </div>
 
|-
 
|-
| align="center" | [https://wci.llnl.gov/codes/silo/ silo]
+
| align="left"   | [https://www.tddft.org/programs/libxc libxc]  
| align="center" | 4.10.2-bsd
+
| align="left"   | 3.0.0&nbsp; 4.0.3&nbsp; 4.0.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Silo is a library for reading and writing a wide variety of scientific data to binary, disk files<br />Homepage: https://wci.llnl.gov/codes/silo/ </div>
+
| <div> Libxc is a library of exchange-correlation functionals for density-functional theory </div>
 
|-
 
|-
| align="center" | [http://singularity.lbl.gov singularity]
+
| align="left"   | [https://xmlsoft.org/ libxslt]  
| align="center" | 2.5.2
+
| align="left"   | 1.1.32
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Singularity is a portable application stack packaging and runtime utility.<br />Homepage: http://singularity.lbl.gov </div>
+
| <div> Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform) </div>
 
|-
 
|-
| align="center" | [http://spglib.sourceforge.net/ spglib]
+
| align="left"   | [https://github.com/hfp/libxsmm libxsmm]  
| align="center" | 1.10.3
+
| align="left"   | 1.9
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spglib is a C library for finding and handling crystal symmetries.<br />Homepage: http://spglib.sourceforge.net/ </div>
+
| <div> LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86) </div>
 
|-
 
|-
| align="center" | [ sqlite]
+
| align="left"   | [https://pyyaml.org/wiki/LibYAML libyaml]  
| align="center" | 3.23.0
+
| align="left"   | 0.1.7
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SQLite: SQL Database Engine in a C Library<br />Homepage:  </div>
+
| <div> LibYAML is a YAML 1 </div>
 
|-
 
|-
| align="center" | [http://su2.stanford.edu su2]
+
| align="left"   | [https://symas.com/lmdb lmdb]  
| align="center" | 5.0.0 6.0.0
+
| align="left"   | 0.9.22
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind.<br />Homepage: http://su2.stanford.edu </div>
+
| <div> OpenLDAP's Lightning Memory-Mapped Database (LMDB) library </div>
 
|-
 
|-
| align="center" | [http://subversion.apache.org/ subversion]
+
| align="left"   | lsb-release
| align="center" | 1.9.7
+
| align="left"   | versionless
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description:  Subversion is an open source version control system.<br />Homepage: http://subversion.apache.org/ </div>
+
| <div> </div>
 
|-
 
|-
| align="center" | [http://computation.llnl.gov/projects/sundials sundials]
+
| align="left"   | [https://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html makedepend]  
| align="center" | 2.6.0 2.7.0 3.1.0
+
| align="left"   | 1.0.5
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers<br />Homepage: http://computation.llnl.gov/projects/sundials </div>
+
| <div> The makedepend package contains a C-preprocessor like utility to determine build-time dependencies </div>
 
|-
 
|-
| align="center" | [http://computation.llnl.gov/projects/sundials sundials-mpi]
+
| align="left"   | [https://micans.org/mcl/ mcl]  
| align="center" | 3.1.0
+
| align="left"   | 14-137
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers<br />Homepage: http://computation.llnl.gov/projects/sundials </div>
+
| <div> 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 </div>
 
|-
 
|-
| align="center" | [http://www.swig.org/ swig]
+
| align="left"   | [https://www.mathworks.com/products/compiler/mcr/ mcr]  
| align="center" | 3.0.12
+
| align="left"  |  R2018a
 +
| align="center" | [[MATLAB]]
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://meep.readthedocs.io/en/latest/ meep]
 +
| align="left"  |  1.4.3&nbsp; 1.5.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SWIG is a software development tool that connects programs written in C and C++ with  a variety of high-level programming languages.<br />Homepage: http://www.swig.org/ </div>
+
| <div> Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems </div>
 
|-
 
|-
| align="center" | [ thirdorder]
+
| align="left"   | [https://meep.readthedocs.io/en/latest/ meep-mpi]  
| align="center" | 1.1.1
+
| align="left"   | 1.4.3&nbsp; 1.5.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: <br />Homepage:  </div>
+
| <div> Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems </div>
 
|-
 
|-
| align="center" | [http://trilinos.sandia.gov/ trilinos]
+
| align="left"   | [https://www.mercurial-scm.org mercurial]  
| align="center" | 12.12.1
+
| align="left"   | 4.6
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Trilinos Project is an effort to develop algorithms and enabling technologies  within an object-oriented software framework for the solution of large-scale, complex multi-physics  engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.<br />Homepage: http://trilinos.sandia.gov/ </div>
+
| <div> Mercurial is a free, distributed source control management tool </div>
 
|-
 
|-
| align="center" | [http://valgrind.org valgrind]
+
| align="left"   | [https://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis]  
| align="center" | 3.13.0
+
| align="left"   | 5.1.0
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools<br />Homepage: http://valgrind.org </div>
+
| <div> METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices </div>
 
|-
 
|-
| align="center" | [https://wci.llnl.gov/simulation/computer-codes/visit visit]
+
| align="left"   | [https://software.intel.com/en-us/mkl mkl]  
| align="center" | 2.13.1
+
| align="left"   | 2017.7&nbsp; 2018.1&nbsp; 2018.2&nbsp; 2018.3
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> Intel Math Kernel Library </div>
 +
|-
 +
| align="left"  | [https://mmseqs.com mmseqs2]
 +
| align="left"  |  7-4e23d
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />DescriptionVisIt is an Open Source, interactive, scalable,     visualization, animation and analysis tool.<br />Homepage: https://wci.llnl.gov/simulation/computer-codes/visit </div>
+
| <div> MMseqs2: ultra fast and sensitive search and clustering suite </div>
 +
|-
 +
| align="left"  | [https://mosh.org mosh]
 +
| align="left"  |  1.3.2
 +
| align="center" |
 +
| <div> Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes </div>
 +
|-
 +
| align="left"  | [https://mpb.readthedocs.io/en/latest/ mpb]
 +
| align="left"  |  1.6.2
 +
| align="center" |
 +
| <div> MIT Photonic-Bands: computation of photonic band structures in periodic media </div>
 +
|-
 +
| align="left"  | [https://mpb.readthedocs.io/en/latest mpb-mpi]
 +
| align="left"  |  1.6.2
 +
| align="center" |
 +
| <div> MIT Photonic-Bands: computation of photonic band structures in periodic media </div>
 +
|-
 +
| align="left"  | [https://www.mpfr.org mpfr]
 +
| align="left"  |  4.0.1
 +
| align="center" |
 +
| <div> The MPFR library is a C library for multiple-precision floating-point computations with correct rounding </div>
 +
|-
 +
| align="left"  | [https://www.brain.org.au/software/index.html#mrtrix mrtrix]
 +
| align="left"  |  3.0.0
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://graal.ens-lyon.fr/MUMPS/ mumps]
 +
| align="left"  |  5.1.2
 +
| align="center" |
 +
| <div> A parallel sparse direct solver </div>
 +
|-
 +
| align="left"  | [https://www.mysql.com/ mysql]
 +
| align="left"  |  8.0.13
 +
| align="center" |
 +
| <div> MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS) </div>
 +
|-
 +
| align="left"  | [https://www.ks.uiuc.edu/Research/namd/ namd]
 +
| align="left"  |  2.13
 +
| align="center" | [[NAMD]]
 +
| <div> NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems </div>
 +
|-
 +
| align="left"  | [https://www.ncl.ucar.edu ncl]
 +
| align="left"  |  6.4.0
 +
| align="center" |
 +
| <div> NCL is an interpreted language designed specifically for scientific data analysis and visualization </div>
 +
|-
 +
| align="left"  | [https://nco.sourceforge.net nco]
 +
| align="left"  |  4.7.4&nbsp; 4.7.6
 +
| align="center" |
 +
| <div> Python bindings for NCO </div>
 +
|-
 +
| align="left"  | [https://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
 +
| align="left"  |  2.1.7
 +
| align="center" |
 +
| <div> Ncview is a visual browser for netCDF format files </div>
 +
|-
 +
| align="left"  | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
 +
| align="left"  |  4.6.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi]
 +
| align="left"  |  4.6.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.neuron.yale.edu/neuron neuron]
 +
| align="left"  |  7.6.2
 +
| align="center" |
 +
| <div> Empirically-based simulations of neurons and networks of neurons </div>
 +
|-
 +
| align="left"  | [https://www.gnu.org/software/octave/ octave]
 +
| align="left"  |  4.4.0
 +
| align="center" | [[Octave]]
 +
| <div> GNU Octave is a high-level interpreted language, primarily intended for numerical computations </div>
 +
|-
 +
| align="left"  | [https://xianyi.github.com/OpenBLAS/ openblas]
 +
| align="left"  | 0.2.20
 +
| align="center" |
 +
| <div> OpenBLAS is an optimized BLAS library based on GotoBLAS2 1 </div>
 +
|-
 +
| align="left"  | [https://opencv.org/ opencv]
 +
| align="left"  |  2.4.13.6&nbsp; 4.1.0
 +
| align="center" |
 +
| <div> OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library </div>
 +
|-
 +
| align="left"  | [https://www.openfoam.com/ openfoam]
 +
| align="left"  | 4.1 5.0-debug 5.0 6 17.12 18.06 18.12 
 +
| align="center" |
 +
| <div> OpenFOAM is a free, open source CFD software package </div>
 +
|-
 +
| align="left"  | [https://www.open-mpi.org/ openmpi]
 +
| align="left"  | 1.10.7 2.1.3 2.1.4 3.0.1 3.0.2 3.1.0rc3 3.1.0rc4 3.1.0 3.1.1 
 +
| align="center" | [[Niagara Quickstart]]
 +
| <div> The Open MPI Project is an open source MPI-2 implementation </div>
 +
|-
 +
| align="left"  | [https://github.com/davidemms/OrthoFinder orthofinder]
 +
| align="left"  |  2.2.7
 +
| align="center" |
 +
| <div> Program for identifying orthologous protein sequence families </div>
 +
|-
 +
| align="left"  | [https://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
 +
| align="left"  |  5.4.3
 +
| align="center" |
 +
| <div> OSU Micro-Benchmarks </div>
 +
|-
 +
| align="left"  | [https://pandoc.org/ pandoc]
 +
| align="left"  |  2.7.3
 +
| align="center" |
 +
| <div> If you need to convert files from one markup format into another, pandoc is your swiss-army knife </div>
 +
|-
 +
| align="left"  | [https://www.paraview.org paraview]
 +
| align="left"  |  5.5.0
 +
| align="center" | [[Visualization]]
 +
| <div> ParaView is a scientific parallel visualizer </div>
 +
|-
 +
| align="left"  | [https://www.paraview.org paraview-offscreen]
 +
| align="left"  |  5.6.0
 +
| align="center" | [[Visualization]]
 +
| <div> Off-screen rendering with ParaView, a scientific parallel visualizer </div>
 +
|-
 +
| align="left"  | [https://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview parmetis]
 +
| align="left"  |  4.0.3
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://nixos.org/patchelf.html patchelf]
 +
| align="left"  |  0.10
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://developer.arm.com/tools-and-software/server-and-hpc/arm-architecture-tools/arm-performance-reports perf-reports]
 +
| align="left"  |  18.2
 +
| align="center" |
 +
| <div> ARM performance reports </div>
 +
|-
 +
| align="left"  | [https://www.perl.org/ perl]
 +
| align="left"  |  5.20.3&nbsp; 5.26.1
 +
| align="center" |
 +
| <div> Larry Wall's Practical Extraction and Report Language </div>
 +
|-
 +
| align="left"  | [https://www.mcs.anl.gov/petsc petsc]
 +
| align="left"  |  3.8.4-debug&nbsp; 3.8.4&nbsp; 3.9.2
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://www.astro.caltech.edu/~tjp/pgplot/ pgplot]
 +
| align="left"  |  5.2.2-x&nbsp; 5.2.2
 +
| align="center" |
 +
| <div> Graphics subroutine library for C/C++ and Fortran </div>
 +
|-
 +
| align="left"  | [http://www.pism-docs.org pism]
 +
| align="left"  |  1.0
 +
| align="center" |
 +
| <div> Parallel Ice Sheet Model is open source and capable of high resolution </div>
 +
|-
 +
| align="left"  | [https://zzz.bwh.harvard.edu/plink/dist plink]
 +
| align="left"  |  1.07&nbsp; 1.90b6
 +
| align="center" |
 +
| <div> </div>
 +
|-
 +
| align="left"  | [https://www.plumed-code.org plumed]
 +
| align="left"  |  2.4.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
 +
| align="left"  |  1.9.0
 +
| align="center" |
 +
| <div> Parallel netCDF: A Parallel I/O Library for NetCDF File Access </div>
 +
|-
 +
| align="left"  | [https://github.com/google/protobuf/ protobuf]
 +
| align="left"  |  3.6.1
 +
| align="center" |
 +
| <div> Google Protocol Buffers </div>
 +
|-
 +
| align="left"  | [https://python.org/ python]
 +
| align="left"  | 2.7.14-anaconda5.1.0 2.7.14 2.7.15 3.6.4-anaconda5.1.0 3.6.5 
 +
| align="center" | [[Python]]
 +
| <div> Python is a programming language that lets you work more quickly and integrate your systems more effectively </div>
 +
|-
 +
| align="left"  | [https://github.com/pipitone/qbatch qbatch]
 +
| align="left"  |  2.1&nbsp; 2.1.4&nbsp; 2.1.5
 +
| align="center" |
 +
| <div> qbatch is a tool for executing commands in parallel across a compute cluster </div>
 +
|-
 +
| align="left"  | [https://www.qhull.org qhull]
 +
| align="left"  |  2015.2
 +
| align="center" |
 +
| <div> Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram </div>
 +
|-
 +
| align="left"  | [https://qt.io/ qt]
 +
| align="left"  |  5.11.1
 +
| align="center" |
 +
| <div> Qt is a comprehensive cross-platform C++ application framework </div>
 +
|-
 +
| align="left"  | [https://www.quantum-espresso.org quantum-espresso]
 +
| align="left"  |  6.2.1&nbsp; 6.3
 +
| align="center" |
 +
| <div> An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale </div>
 +
|-
 +
| align="left"  | [https://github.com/request/request/ r]
 +
| align="left"  |  3.4.3-anaconda5.1.0&nbsp; 3.5.0&nbsp; 3.5.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://github.com/vanzonr/rarray rarray]
 +
| align="left"  |  1.2&nbsp; 2.1.1
 +
| align="center" |
 +
| <div> Library for runtime multi-dimensional arrays in C++ </div>
 +
|-
 +
| align="left"  | [https://rsync.samba.org/ rsync]
 +
| align="left"  |  3.1.3
 +
| align="center" | [[Data Management]]
 +
| <div> Fast, versatile, remote file-copying tool </div>
 +
|-
 +
| align="left"  | [https://itk.org rtk]
 +
| align="left"  |  1.4.0
 +
| align="center" |
 +
| <div> An open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit </div>
 +
|-
 +
| align="left"  | [https://www.rust-lang.org rust]
 +
| align="left"  |  1.26.1&nbsp; 1.28.0
 +
| align="center" |
 +
| <div> Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety </div>
 +
|-
 +
| align="left"  | [https://www.htslib.org/ samtools]
 +
| align="left"  |  1.8
 +
| align="center" |
 +
| <div> SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format </div>
 +
|-
 +
| align="left"  | [https://www.netlib.org/scalapack/ scalapack]
 +
| align="left"  |  2.0.2
 +
| align="center" |
 +
| <div> The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers </div>
 +
|-
 +
| align="left"  | [https://www.scons.org/ scons]
 +
| align="left"  |  3.0.1
 +
| align="center" |
 +
| <div> SCons is a software construction tool </div>
 +
|-
 +
| align="left"  | [https://gforge.inria.fr/projects/scotch/ scotch]
 +
| align="left"  |  6.0.6
 +
| align="center" |
 +
| <div> Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning </div>
 +
|-
 +
| align="left"  | [https://www.shengbte.org/ shengbte]
 +
| align="left"  |  1.1.1
 +
| align="center" |
 +
| <div> Software package for solving the Boltzmann Transport Equation for phonons </div>
 +
|-
 +
| align="left"  | [https://wci.llnl.gov/codes/silo silo]
 +
| align="left"  |  4.10.2-bsd
 +
| align="center" |
 +
| <div> Silo is a library for reading and writing a wide variety of scientific data to binary, disk files </div>
 +
|-
 +
| align="left"  | [https://www.sylabs.io/docs singularity]
 +
| align="left"  | 3.5.3
 +
| align="center" | [[Singularity]]
 +
| <div> Singularity is a portable application stack packaging and runtime utility </div>
 +
|-
 +
| align="left"  | [https://cab.spbu.ru/software/spades/ spades]
 +
| align="left"  |  3.13.0
 +
| align="center" |
 +
| <div> Genome assembler for single-cell and isolates data sets </div>
 +
|-
 +
| align="left"  | [https://spglib.github.io/spglib/ spglib]
 +
| align="left"  |  1.10.3
 +
| align="center" |
 +
| <div> Spglib is a C library for finding and handling crystal symmetries </div>
 +
|-
 +
| align="left"  | [https://www.sqlite.org/ sqlite]
 +
| align="left"  |  3.23.0
 +
| align="center" |
 +
| <div> SQLite: SQL Database Engine in a C Library </div>
 +
|-
 +
| align="left"  | [https://creskolab.uoregon.edu/stacks/ stacks]
 +
| align="left"  |  2.2
 +
| align="center" |
 +
| <div> Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform </div>
 +
|-
 +
| align="left"  | [https://github.com/alexdobin/STAR star]
 +
| align="left"  |  2.6.1b
 +
| align="center" |
 +
| <div> STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays </div>
 +
|-
 +
| align="left"  | [https://ccb.jhu.edu/software/stringtie/ stringtie]
 +
| align="left"  |  1.3.5
 +
| align="center" |
 +
| <div> StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts </div>
 +
|-
 +
| align="left"  | [https://su2.stanford.edu su2]
 +
| align="left"  |  5.0.0&nbsp; 6.0.0&nbsp; 6.1.0
 +
| align="center" |
 +
| <div> An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems </div>
 +
|-
 +
| align="left"  | [https://subversion.apache.org/ subversion]
 +
| align="left"  |  1.9.7
 +
| align="center" |
 +
| <div> Subversion is an open source version control system </div>
 +
|-
 +
| align="left"  | [https://computation.llnl.gov/projects/sundials sundials]
 +
| align="left"  |  2.6.0&nbsp; 2.7.0&nbsp; 3.1.0
 +
| align="center" |
 +
| <div> SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers </div>
 +
|-
 +
| align="left"  | [https://computation.llnl.gov/projects/sundials sundials-mpi]
 +
| align="left"  |  3.1.0
 +
| align="center" |
 +
| <div> SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers </div>
 +
|-
 +
| align="left"  | [https://www.swig.org/ swig]
 +
| align="left"  |  3.0.12
 +
| align="center" |
 +
| <div> SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages </div>
 +
|-
 +
| align="left"  | [https://tug.org texlive]
 +
| align="left"  |  2019
 +
| align="center" |
 +
| <div> High-quality typesetting programs TeX and LaTeX </div>
 +
|-
 +
| align="left"  | [http://www.shengbte.org/ thirdorder]
 +
| align="left"  |  1.1.1
 +
| align="center" |
 +
| <div> Set of scripts to help users of ShengBTE and almaBTE create FORCE_CONSTANTS_3RD files in an efficient and convenient manner </div>
 +
|-
 +
| align="left"  | [https://trilinos.sandia.gov/ trilinos]
 +
| align="left"  |  12.12.1
 +
| align="center" |
 +
| <div> 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 </div>
 +
|-
 +
| align="left"  | [https://github.com/trinityrnaseq/trinityrnaseq trinityrnaseq]
 +
| align="left"  |  2.8.1
 +
| align="center" |
 +
| <div> Trinity RNA-Seq de novo transcriptome assembly </div>
 +
|-
 +
| align="left"  | [https://www.unidata.ucar.edu/software/udunits/ udunits]
 +
| align="left"  |  2.2.26
 +
| align="center" |
 +
| <div> UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement </div>
 +
|-
 +
| align="left"  | [https://valgrind.org valgrind]
 +
| align="left"  |  3.13.0&nbsp; 3.14.0
 +
| align="center" | [[Introduction To Performance]]
 +
| <div> Valgrind provides debugging and profiling tools </div>
 +
|-
 +
| align="left"  | [https://wci.llnl.gov/simulation/computer-codes/visit visit]
 +
| align="left"  |  2.13.1
 +
| align="center" | [[Visualization]]
 +
| <div> An open-source, interactive, scalable, visualization, animation and analysis tool </div>
 +
|-
 +
| align="left"  | [https://www.ks.uiuc.edu/Research/vmd vmd]
 +
| align="left"  |  1.9.4a12&nbsp; 1.9.4a38
 +
| align="center" | [[Visualization]]
 +
| <div> VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting </div>
 
|-
 
|-
| align="center" | [http://www.ks.uiuc.edu/Research/vmd vmd]
+
| align="left"   | [https://www.vtk.org vtk]  
| align="center" | 1.9.4a12
+
| align="left"   | 8.1.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular    systems using 3-D graphics and built-in scripting.<br />Homepage: http://www.ks.uiuc.edu/Research/vmd </div>
+
| <div> The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization </div>
 
|-
 
|-
| align="center" | [http://www.vtk.org vtk]
+
| align="left"   | [https://www.mmm.ucar.edu/weather-research-and-forecasting-model wrf]  
| align="center" | 8.1.1
+
| align="left"   | 3.9.1.1
 
| align="center" |  
 
| align="center" |  
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for  3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several  interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization  algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques  such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.<br />Homepage: http://www.vtk.org </div>
+
| <div> </div>
 
|}
 
|}

Latest revision as of 17:49, 10 June 2022

NiaEnv/2019b

Module Version(s) Documentation Description
CCEnv Using modules
Alliance (formerly Compute Canada) software modules. Must be loaded to see Alliance (formerly Compute Canada) modules in 'module spider'.
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
arm-forge 21.0.3 Parallel Debugging with DDT
Arm Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
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
arpack-ng 3.7.0
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
autodiff 0.5.11
autotools 2018b  2018
The standard GNU build tools: autoconf, automake and libtool
bcftools 1.8  1.12(E)  1.13(E)
SAMtools is a suite of programs for interacting with high-throughput sequencing data
bedtools 2.29.0  2.30.0
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage
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 1.69.0  1.70.0  1.73.0  1.78.0
Boost provides free peer-reviewed portable C++ source libraries
boost-python 1.69.0 1.70.0 1.75.0
Boost provides free peer-reviewed portable C++ source libraries, including boost:python
bowtie2 2.3.4.3  2.4.4
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
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
bwa-mem2 2.0
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa
cairo 1.17.2
Cairo is a 2D graphics library with support for multiple output devices
cairo 1.17.2
Cairo is a 2D graphics library with support for multiple output devices
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
cgal 5.1
cget 0.1.9
Cmake package retrieval
chaiscript 6.1.0
Embedded Scripting Language Designed for C++
cmake 3.13.4  3.14.5  3.17.3  3.21.4
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
cufflinks 2.2.1
Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
cufflinks 2.2.1
Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
cutadapt 2.10
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
arm-forge 22.0.2 Parallel Debugging with DDT
DDT debugger and MAP profiler
dealii 9.2.0
deal
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
elpa 2017.05.003  2020.05.001
Eigenvalue SoLvers for Petaflop-Applications
expect 5.45.4
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.
fastqc 0.11.9
fenics 2019.1.0
FEniCS is a computing platform for solving partial differential equations
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
fmt 4.1.0
fmt (formerly cppformat) is an open-source formatting library
freesurfer 6.0.0  7.1.0
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
fsl 6.0.4
gatk 4.1.7.0
gcc 8.3.0  9.2.0  9.4.0 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  2.30.1
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  8.20200618
git-annex allows managing files with git, without checking the file contents into git
git-lfs 2.13.2
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub
glib 2.48.2
gmp 6.1.2  6.2.0
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
gnu-parallel 20190322  20191122 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
Go is an open source programming language that makes it easy to build simple, reliable, and efficient software
googletest 1.10.0
Google's C++ test framework
gperf 3.1
GNU gperf is a perfect hash function generator
graphviz 2.40.1
Graphviz is open source graph visualization software
gromacs 2018.6-plumed-2.5.1  2018.6 GROMACS
GROMACS is a versatile package to perform molecular dynamics, i
gromacs-ls 2016.3
GROMACS-LS is a custom version of GROMACS developed for local stress calculations from molecular simulations.
gsl 2.5  2.7
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
hdf5 1.8.21  1.10.5  1.10.7 HDF5
HDF5 is a data model, library, and file format for storing and managing data
hh-suite 3.3.0
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)
highfive 2.3
HighFive is a modern header-only C++11 friendly interface for libhdf5.
htslib 1.12(E)  1.13(E)
icu 68.1
International Components for Unicode
imagemagick 6
intel 2019u3 2019u4 2019u5 2020u2 2020u4 Niagara Quickstart
Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries
intelmpi 2019u3 2019u4 2019u5 2020u2 2020u4 Niagara Quickstart
intelpython2 2019u3 2019u4 2019u5 Python
Intel Python distribution for python 2, based on anaconda
intelpython3 2019u3 2019u4 2019u5 Python
Intel Python distribution for python 3, based on anaconda
inteltools 2019u4
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
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  1.5.3  1.6.1  1.7.2
A high-level, high-performance dynamic language for technical computing
julia 1.1.0  1.5.3  1.6.1  1.7.2
A high-level, high-performance dynamic language for technical computing
lammps 20Nov2019  29Mar2019
The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
libgit2 1.1.0
libint 1.1.5  2.6-shared  2.6.0
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
libsodium 1.0.18
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more
libxc 4.0.5  4.3.4  5.0.0
Libxc is a library of exchange-correlation functionals for density-functional theory
libxslt 1.1.34
Libxslt is the XSLT C library developed for the GNOME project
lmdb 0.9.23
OpenLDAP's Lightning Memory-Mapped Database (LMDB) library
lsb-release versionless
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
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-shared  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
mii 1.1.1
A smart search engine for module environments.
mkl 2019u3  2019u4 Niagara Quickstart
Intel Math Kernel Library
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  4.1.0
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding
mrbayes 3.2.7
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
mrtrix 3.0.0
mumps 5.1.2  5.2.1
A parallel sparse direct solver
muscle 3.8.31
MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW
namd 2.14 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
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
numdiff 5.9.0
numdiff can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats
octave 5.2.0 Octave
GNU Octave is a high-level interpreted language, primarily intended for numerical computations
openblas 0.3.7
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1
opencv 4.5.0
OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library
openfoam 7-broken 19.06 20.06 20.12
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 3.1.3  4.0.1  4.0.3  4.1.1 Niagara Quickstart
The Open MPI Project is an open source MPI-2 implementation
orthofinder 2.3.3
Program for identifying orthologous protein sequence families
osu-micro-benchmarks 5.6.1 5.7.1
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
papi 6.0.0.1
Performace Application Programming Interface
paraview-offscreen 5.9.1 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
pcre2 10.35
A set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5
perl 5.28.1  5.30.3  5.34.0
Larry Wall's Practical Extraction and Report Language
petsc 3.9.3  3.10.5  3.11.3  3.13.5
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
plink 1.90b6
PLINK is a whole-genome association analysis toolset, version 1
plink2 2.00a3
PLINK is a whole-genome association analysis toolset, version 2
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
pnetcdf 1.11.0  1.11.2
Parallel netCDF: A Parallel I/O Library for NetCDF File Access
postgresql 14.1
PostgreSQL is a powerful, open source object-relational database system with over 30 years of active development that has earned it a strong reputation for reliability, feature robustness, and performance.
proj 4.9.3  6.0.0
Cartographic projections and coordinate transformations library
python 2.7.15 3.6.8 3.7.9 3.8.5 3.9.8 Python
Python is a programming language that lets you work more quickly and integrate your systems more effectively
qbatch 2.1.4  2.1.5  2.2.1  2.3.0
qbatch is a tool for executing commands in parallel across a compute cluster
qhull 2020.2
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
qt 4.8.7  5.12.4
Qt is a comprehensive cross-platform C++ application framework
quantum-espresso 6.4.1 6.5-perturbo 6.5-w90-perturbo
An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
r 3.5.3  3.6.1  3.6.3  4.0.3  4.1.2
R is a free software environment for statistical computing and graphics
r 3.5.3  3.6.1  3.6.3  4.0.3  4.1.2
R is a free software environment for statistical computing and graphics
rarray 1.2  2.0.0  2.1.1  2.3.0
Library for runtime multi-dimensional arrays in C++
rosetta 3.13
Rosetta is the premier software suite for modeling macromolecular structures
rsync 3.1.3 Data Management
Fast, versatile, remote file-copying tool
rust 1.47.0
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety
salmon 0.14.2  0.99.0-beta2
sambamba 0.7.1
samtools 1.9  1.11  1.12  1.13
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 4.0.2 4.1-b4-transiesta-netcdf4 4.1-b4-transiesta 4.1-b4 4.1.5-util 4.1.5
Computer implementation of the SIESTA method to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
singularity 3.8.0 Singularity
Singularity is a portable application stack packaging and runtime utility
sox 14.4.2
SoX, the Swiss Army knife of sound processing programs.
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 2.55
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform
subversion 1.10.4
Subversion is an open source version control system
suitesparse 5.8.1
SuiteSparse is a suite of sparse matrix software
sundials 5.3.0
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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  4.0.1
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages
tbb 2019u8  2019u9
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
tmux 3.2a
tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
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
trimgalore 0.6.5
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
vcftools 0.1.16
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project
visit 3.2.1  3.2.2 Visualization
Open Source, interactive, scalable, visualization, animation and analysis tool.
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
vsearch 2.14.2
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting
vtk 8.1.0  8.2.0  9.0.1
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
zlib 1.2.11
zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system
zlib 1.2.11
zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system

NiaEnv/2018a

Module Version(s) Documentation Description
CCEnv Using modules
Alliance (formerly Compute Canada) software modules. Must be loaded to see Alliance (formerly Compute Canada) modules in 'module spider'.
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 5.1.0  5.2.0  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 2.0.0  2.0.1  2.1.0-pre  2.1.0
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 0.11.1  0.15.0
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 1.63.0  1.66.0  1.67.0
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 3.10.3  3.11.0  3.11.1
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
dcm2niix 1.0.20200331
dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format
arm-forge 22.0.2 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 2016.05.003  2017.05.003  2018.05.001
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 2017.2.0  2018.1.0
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 3.0.2  4.1.0
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 5.3.0  6.0.0
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
g_mmpbsa 5.1.2
Molecular mechanics/Poisson-Bolzmann surface area method for GROMACS
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 4.9.4  7.3.0 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  8.20200618
git-annex allows managing files with git, without checking the file contents into git
git-lfs 2.13.2
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub
glib 2.22.5
GLib is one of the base libraries of the GTK+ project
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 2016.5-plumed-2.4.1 2016.5 2019.1 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
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)
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 2017.7  2018.1  2018.2  2018.3 Niagara Quickstart
Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries
intel-mpi-benchmarks 2018.1
a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard
intelmpi 2017.7 2018.1 2018.2 2018.3 Niagara Quickstart
Intel MPI library with compiler wrappers for C, C++, and Fortran
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 1.0.0  1.1.0
A high-level, high-performance dynamic language for technical computing
julia 1.0.0  1.1.0
A high-level, high-performance dynamic language for technical computing
lammps 11May2018  22Sep2017
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 4.0.1  4.1.2
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 1.1.5  1.1.6
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
libsodium 1.0.18
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more
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 3.0.0  4.0.3  4.0.5
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
lsb-release versionless
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 1.4.3  1.5.0
Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems
meep-mpi 1.4.3  1.5.0
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 2017.7  2018.1  2018.2  2018.3 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
mrtrix 3.0.0
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 4.7.4  4.7.6
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 2.4.13.6  4.1.0
OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library
openfoam 4.1 5.0-debug 5.0 6 17.12 18.06 18.12
OpenFOAM is a free, open source CFD software package
openmpi 1.10.7 2.1.3 2.1.4 3.0.1 3.0.2 3.1.0rc3 3.1.0rc4 3.1.0 3.1.1 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
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
patchelf 0.10
perf-reports 18.2
ARM performance reports
perl 5.20.3  5.26.1
Larry Wall's Practical Extraction and Report Language
petsc 3.8.4-debug  3.8.4  3.9.2
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  1.90b6
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 2.7.14-anaconda5.1.0 2.7.14 2.7.15 3.6.4-anaconda5.1.0 3.6.5 Python
Python is a programming language that lets you work more quickly and integrate your systems more effectively
qbatch 2.1  2.1.4  2.1.5
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 6.2.1  6.3
An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
r 3.4.3-anaconda5.1.0  3.5.0  3.5.1
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
rarray 1.2  2.1.1
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 1.26.1  1.28.0
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 3.5.3 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 5.0.0  6.0.0  6.1.0
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 2.6.0  2.7.0  3.1.0
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
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
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 3.13.0  3.14.0 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  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 8.1.1
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
wrf 3.9.1.1