ABINIT: ABINIT/9.6.2
ABINIT is a package whose main program allows one to find the total energy, charge density
and electronic structure of systems made of electrons and nuclei (molecules and periodic
solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or
wavelet basis.
ANSYS_CFD: ANSYS_CFD/2021R1, ANSYS_CFD/2022R2
ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with
confidence, the impact of fluid flows on your product throughout design and manufacturing as
well as during end use. ANSYS renowned CFD analysis tools include the widely used and
well-validated ANSYS Fluent and ANSYS CFX.
ANTLR: ANTLR/2.7.7-Java-11
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.
ASE: ASE/3.22.1
ASE is a python package providing an open source Atomic Simulation Environment in the Python
scripting language. From version 3.20.1 we also include the ase-ext package, it contains
optional reimplementations in C of functions in ASE. ASE uses it automatically when
installed.
ATK: ATK/2.36.0, ATK/2.38.0
ATK provides the set of accessibility interfaces that are implemented by other toolkits and
applications. Using the ATK interfaces, accessibility tools have full access to view and
control running applications.
AmberTools: AmberTools/21, AmberTools/22.3
AmberTools consists of several independently developed packages that work well by themselves,
and with Amber itself. The suite can also be used to carry out complete molecular dynamics
simulations, with either explicit water or generalized Born solvent models.
Anaconda3: Anaconda3/2022.05
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.
Arrow: Arrow/6.0.0, Arrow/8.0.0
Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for
in-memory data.
ArviZ: ArviZ/0.11.4, ArviZ/0.12.1
Exploratory analysis of Bayesian models with Python
Autoconf: Autoconf/2.69, Autoconf/2.71
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically
configure software source code packages. These scripts can adapt the packages to many kinds
of UNIX-like systems without manual user intervention. Autoconf creates a configuration
script for a package from a template file that lists the operating system features that the
package can use, in the form of M4 macro calls.
Automake: Automake/1.16.1, Automake/1.16.4, Automake/1.16.5
Automake: GNU Standards-compliant Makefile generator
Autotools: Autotools/20180311, Autotools/20210726, Autotools/20220317
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BDBag: BDBag/1.6.3
The bdbag utilities are a collection of software programs for working with BagIt packages
that conform to the Bagit and Bagit/RO profiles.
BEDTools: BEDTools/2.30.0
BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to
address common genomics tasks such as finding feature overlaps and computing coverage. The
utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
BLIS: BLIS/0.8.1, BLIS/0.9.0
BLIS is a portable software framework for instantiating high-performance BLAS-like dense
linear algebra libraries.
BamTools: BamTools/2.5.2
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
Bambi: Bambi/0.7.1, Bambi/0.10.0
Bambi is a high-level Bayesian model-building interface written in Python. It works with the
probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit
Bayesian mixed-effects models common in biology, social sciences and other disciplines.
Bazel: Bazel/4.2.2, Bazel/5.1.1
Bazel is a build tool that builds code quickly and reliably. It is used to build the majority
of Google's software.
BeautifulSoup: BeautifulSoup/4.10.0
Beautiful Soup is a Python library designed for quick turnaround projects like
screen-scraping.
Biopython: Biopython/1.79
Biopython is a set of freely available tools for biological computation written in Python by
an international team of developers. It is a distributed collaborative effort to develop
Python libraries and applications which address the needs of current and future work in
bioinformatics.
Bison: Bison/3.5.3, Bison/3.7.6, Bison/3.8.2
Bison is a general-purpose parser generator that converts an annotated context-free grammar
into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
Boost: Boost/1.77.0, Boost/1.79.0
Boost provides free peer-reviewed portable C++ source libraries.
Brotli: Brotli/1.0.9
Brotli is a generic-purpose lossless compression algorithm that compresses data using a
combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context
modeling, with a compression ratio comparable to the best currently available general-purpose
compression methods. It is similar in speed with deflate but offers more dense compression.
The specification of the Brotli Compressed Data Format is defined in RFC 7932.
CGAL: CGAL/4.14.3
The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable
geometric algorithms in the form of a C++ library.
CMake: CMake/3.16.4, CMake/3.21.1, CMake/3.22.1, CMake/3.23.1, CMake/3.24.3
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to
build, test and package software.
CP2K: CP2K/8.2
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.
CapnProto: CapnProto/0.9.1
Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.
CheMPS2: CheMPS2/1.8.11, CheMPS2/1.8.12
CheMPS2 is a scientific library which contains a spin-adapted implementation of the density
matrix renormalization group (DMRG) for ab initio quantum chemistry.
CubeLib: CubeLib/4.4.4, CubeLib/4.8
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic
tool for displaying a multi-dimensional performance space consisting of the dimensions (i)
performance metric, (ii) call path, and (iii) system resource. Each dimension can be
represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to
achieve the desired level of granularity. This module provides the Cube general purpose C++
library component and command-line tools.
CubeWriter: CubeWriter/4.4.3, CubeWriter/4.8
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic
tool for displaying a multi-dimensional performance space consisting of the dimensions (i)
performance metric, (ii) call path, and (iii) system resource. Each dimension can be
represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to
achieve the desired level of granularity. This module provides the Cube high-performance C
writer library component.
DB: DB/18.1.32, DB/18.1.40
Berkeley DB enables the development of custom data management solutions, without the overhead
traditionally associated with such custom projects.
DBus: DBus/1.13.18, DBus/1.14.0
D-Bus is a message bus system, a simple way for applications to talk to one another. In
addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it
simple and reliable to code a "single instance" application or daemon, and to launch
applications and daemons on demand when their services are needed.
DFT-D3: DFT-D3/3.2.0
DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and
semi-empirical quantum chemical methods.
Dalton: Dalton/2020.0
The Dalton code is a powerful tool for a wide range of molecular properties at different
levels of theory. Any published work arising from use of one of the Dalton2016 programs must
acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html.
DendroPy: DendroPy/4.5.2
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation,
processing and manipulation of phylogenetic trees (phylogenies) and characters.
Doxygen: Doxygen/1.8.17, Doxygen/1.9.1, Doxygen/1.9.4
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.
ELPA: ELPA/2021.05.001, ELPA/2021.11.001
Eigenvalue SoLvers for Petaflop-Applications .
ESMF: ESMF/8.2.0, ESMF/8.3.0
The Earth System Modeling Framework (ESMF) is a suite of software tools for developing
high-performance, multi-component Earth science modeling applications.
Eigen: Eigen/3.3.9, Eigen/3.4.0
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and
related algorithms.
FDS: FDS/6.7.7, FDS/6.7.9
Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with
an emphasis on smoke and heat transport from fires.
FFTW: FFTW/3.3.8, FFTW/3.3.10
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: FFTW.MPI/3.3.10
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.
FFmpeg: FFmpeg/4.3.2, FFmpeg/4.4.2
A complete, cross-platform solution to record, convert and stream audio and video.
FLAC: FLAC/1.3.3, FLAC/1.3.4
FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless,
meaning that audio is compressed in FLAC without any loss in quality.
FMS: FMS/2022.02
The Flexible Modeling System (FMS) is a software framework for supporting the efficient
development, construction, execution, and scientific interpretation of atmospheric, oceanic,
and climate system models.
FastANI: FastANI/1.33
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide
Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared
between two microbial genomes. FastANI supports pairwise comparison of both complete and
draft genome assemblies.
FastQC: FastQC/0.11.9-Java-11
FastQC is a quality control application for high throughput sequence data. It reads in
sequence data in a variety of formats and can either provide an interactive application to
review the results of several different QC checks, or create an HTML based report which can
be integrated into a pipeline.
FastTree: FastTree/2.1.11
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of
nucleotide or protein sequences. FastTree can handle alignments with up to a million of
sequences in a reasonable amount of time and memory.
Flask: Flask/2.0.2, Flask/2.2.2
Flask is a lightweight WSGI web application framework. It is designed to make getting started
quick and easy, with the ability to scale up to complex applications. This module includes
the Flask extensions: Flask-Cors
FlexiBLAS: FlexiBLAS/3.0.4, FlexiBLAS/3.2.0
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK
implementation used by a program without recompiling or relinking it.
Flye: Flye/2.9, Flye/2.9.1
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and
Oxford Nanopore Technologies.
FriBidi: FriBidi/1.0.10, FriBidi/1.0.12
The Free Implementation of the Unicode Bidirectional Algorithm.
GATK: GATK/4.2.6.1-Java-11
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to
analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a
primary focus on variant discovery and genotyping as well as strong emphasis on data quality
assurance. Its robust architecture, powerful processing engine and high-performance computing
features make it capable of taking on projects of any size.
GCC: GCC/9.3.0, GCC/11.2.0, GCC/11.3.0
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,...).
GCCcore: GCCcore/9.3.0, GCCcore/11.2.0, GCCcore/11.3.0
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,...).
GDAL: GDAL/3.3.2, GDAL/3.5.0
GDAL is a translator library for raster geospatial data formats that is released under an
X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it
presents a single abstract data model to the calling application for all supported formats.
It also comes with a variety of useful commandline utilities for data translation and
processing.
GEOS: GEOS/3.9.1, GEOS/3.10.3
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GLPK: GLPK/5.0
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear
programming (LP), mixed integer programming (MIP), and other related problems. It is a set of
routines written in ANSI C and organized in the form of a callable library.
GLib: GLib/2.69.1, GLib/2.72.1
GLib is one of the base libraries of the GTK+ project
GMP: GMP/6.2.0, GMP/6.2.1
GMP is a free library for arbitrary precision arithmetic, operating on signed integers,
rational numbers, and floating point numbers.
GObject-Introspection: GObject-Introspection/1.68.0, GObject-Introspection/1.72.0
GObject introspection is a middleware layer between C libraries (using GObject) and language
bindings. The C library can be scanned at compile time and generate a metadata file, in
addition to the actual native C library. Then at runtime, language bindings can read this
metadata and automatically provide bindings to call into the C library.
GPAW: GPAW/22.8.0
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave
(PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids
and multigrid methods or atom-centered basis-functions.
GPAW-setups: GPAW-setups/0.9.20000
PAW setup for the GPAW Density Functional Theory package. Users can install setups manually
using 'gpaw install-data' or use setups from this package. The versions of GPAW and
GPAW-setups can be intermixed.
GROMACS: GROMACS/2021.5-PLUMED-2.8.0, GROMACS/2021.5-PLUMED-2.8.1, GROMACS/2021.5
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 a CPU only
build, containing both MPI and threadMPI builds for both single and double precision. It also
contains the gmxapi extension for the single precision MPI build next to PLUMED.
GSL: GSL/2.7
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.
GST-plugins-bad: GST-plugins-bad/1.20.2
GStreamer is a library for constructing graphs of media-handling components. The applications
it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing.
GST-plugins-base: GST-plugins-base/1.20.2
GStreamer is a library for constructing graphs of media-handling components. The applications
it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing.
GStreamer: GStreamer/1.20.2
GStreamer is a library for constructing graphs of media-handling components. The applications
it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing.
GTDB-Tk: GTDB-Tk/2.0.0
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal
genomes.
GTK2: GTK2/2.24.33
The GTK+ 2 package contains libraries used for creating graphical user interfaces for
applications.
GTK3: GTK3/3.24.31
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the
user interface controls, or widgets, used in a common graphical application. Its
object-oriented API allows you to construct user interfaces without dealing with the
low-level details of drawing and device interaction.
GTK4: GTK4/4.7.0
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the
user interface controls, or widgets, used in a common graphical application. Its
object-oriented API allows you to construct user interfaces without dealing with the
low-level details of drawing and device interaction.
Gdk-Pixbuf: Gdk-Pixbuf/2.42.6, Gdk-Pixbuf/2.42.8
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by
GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of
GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
Ghostscript: Ghostscript/9.54.0, Ghostscript/9.56.1
Ghostscript is a versatile processor for PostScript data with the ability to render
PostScript to different targets. It used to be part of the cups printing stack, but is no
longer used for that.
GitPython: GitPython/3.1.24, GitPython/3.1.27
GitPython is a python library used to interact with Git repositories
GlobalArrays: GlobalArrays/5.8.1
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
Graphene: Graphene/1.10.8
Graphene is a thin layer of types for graphic libraries
HDF: HDF/4.2.15
HDF (also known as HDF4) is a library and multi-object file format for storing and managing
data between machines.
HDF5: HDF5/1.10.6, HDF5/1.12.1, HDF5/1.12.2
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.
HMMER: HMMER/3.3.2
HMMER is used for searching sequence databases for homologs of protein sequences, and for
making protein sequence alignments. It implements methods using probabilistic models called
profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence
alignment and database search tools based on older scoring methodology, HMMER aims to be
significantly more accurate and more able to detect remote homologs because of the strength
of its underlying mathematical models. In the past, this strength came at significant
computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as
BLAST.
HPL: HPL/2.3
HPL is a software package that solves a (random) dense linear system in double precision (64
bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as
well as freely available implementation of the High Performance Computing Linpack Benchmark.
HarfBuzz: HarfBuzz/2.8.2, HarfBuzz/4.2.1
HarfBuzz is an OpenType text shaping engine.
Hypre: Hypre/2.24.0, Hypre/2.25.0
Hypre is a library for solving large, sparse linear systems of equations on massively
parallel computers. The problems of interest arise in the simulation codes being developed at
LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and
biological sciences.
ICU: ICU/69.1, ICU/71.1
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and
Globalization support for software applications.
IMB: IMB/2021.3
The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and
global communication operations for a range of message sizes
IPython: IPython/7.26.0, IPython/8.5.0
IPython provides a rich architecture for interactive computing with: Powerful interactive
shells (terminal and Qt-based). A browser-based notebook with support for code, text,
mathematical expressions, inline plots and other rich media. Support for interactive data
visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your
own projects. Easy to use, high performance tools for parallel computing.
ISA-L: ISA-L/2.30.0
Intelligent Storage Acceleration Library
ImageMagick: ImageMagick/7.1.0-4, ImageMagick/7.1.0-37
ImageMagick is a software suite to create, edit, compose, or convert bitmap images
Imath: Imath/3.1.5
Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for
computer graphics
JasPer: JasPer/2.0.33
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: Java/11.0.16
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on
desktops and servers.
JsonCpp: JsonCpp/1.9.4, JsonCpp/1.9.5
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and
deserialization to and from strings. It can also preserve existing comment in
unserialization/serialization steps, making it a convenient format to store user input files.
Julia: Julia/1.8.5-linux-x86_64
Julia is a high-level, high-performance dynamic programming language for numerical computing
KaHIP: KaHIP/3.14
The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.
LAME: LAME/3.100
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LAMMPS: LAMMPS/23Jun2022-kokkos
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
Atomic/Molecular Massively Parallel Simulator. 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. LAMMPS runs on single
processors or in parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
LAPACK: LAPACK/3.10.1
LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous
linear equations, least-squares solutions of linear systems of equations, eigenvalue
problems, and singular value problems.
LLVM: LLVM/12.0.1, LLVM/14.0.3
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with
code generation support for many popular CPUs (as well as some less common ones!) These
libraries are built around a well specified code representation known as the LLVM
intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it
is particularly easy to invent your own language (or port an existing compiler) to use LLVM
as an optimizer and code generator.
LMDB: LMDB/0.9.29
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.
LMfit: LMfit/1.0.3
Lmfit provides a high-level interface to non-linear optimization and curve fitting problems
for Python
LibTIFF: LibTIFF/4.3.0
tiff: Library and tools for reading and writing TIFF data files
Libint: Libint/2.6.0-lmax-6-cp2k
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.
LittleCMS: LittleCMS/2.12, LittleCMS/2.13.1
Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special
focus on accuracy and performance.
Lua: Lua/5.4.3, Lua/5.4.4
Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple
procedural syntax with powerful data description constructs based on associative arrays and
extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a
register-based virtual machine, and has automatic memory management with incremental garbage
collection, making it ideal for configuration, scripting, and rapid prototyping.
M4: M4/1.4.18, M4/1.4.19
GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4
compatible although it has some extensions (for example, handling more than 9 positional
parameters to macros). GNU M4 also has built-in functions for including files, running shell
commands, doing arithmetic, etc.
MDAnalysis: MDAnalysis/2.0.0, MDAnalysis/2.2.0
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular
dynamics (MD) simulations in many popular formats.
MDTraj: MDTraj/1.9.7
Read, write and analyze MD trajectories with only a few lines of Python code.
METIS: METIS/5.1.0
METIS is a set of serial programs for partitioning graphs, partitioning finite element
meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented
in METIS are based on the multilevel recursive-bisection, multilevel k-way, and
multi-constraint partitioning schemes.
MPFR: MPFR/4.1.0
The MPFR library is a C library for multiple-precision floating-point computations with
correct rounding.
MPICH: MPICH/3.4.2
MPICH is a high-performance and widely portable implementation of the Message Passing
Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).
MUMPS: MUMPS/5.4.1-metis, MUMPS/5.5.1-metis
A parallel sparse direct solver
Mako: Mako/1.1.4, Mako/1.2.0
A super-fast templating language that borrows the best ideas from the existing templating
languages
Mash: Mash/2.3
Fast genome and metagenome distance estimation using MinHash
Mesa: Mesa/21.1.7, Mesa/22.0.3
Mesa is an open-source implementation of the OpenGL specification - a system for rendering
interactive 3D graphics.
Meson: Meson/0.55.1-Python-3.8.2, Meson/0.58.2, Meson/0.62.1
Meson is a cross-platform build system designed to be both as fast and as user friendly as
possible.
MultiQC: MultiQC/1.12
Aggregate results from bioinformatics analyses across many samples into a single report.
MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a
general use tool, perfect for summarising the output from numerous bioinformatics tools.
NASM: NASM/2.15.05
NASM: General-purpose x86 assembler
NCO: NCO/5.0.3, NCO/5.1.0
The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including
DAP, HDF4, and HDF5.
NLopt: NLopt/2.7.0, NLopt/2.7.1
NLopt is a free/open-source library for nonlinear optimization, providing a common interface
for a number of different free optimization routines available online as well as original
implementations of various other algorithms.
NSPR: NSPR/4.32, NSPR/4.34
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and
libc-like functions.
NSS: NSS/3.69, NSS/3.79
Network Security Services (NSS) is a set of libraries designed to support cross-platform
development of security-enabled client and server applications.
NWChem: NWChem/7.0.2
NWChem aims to provide its users with computational chemistry tools that are scalable both in
their ability to treat large scientific computational chemistry problems efficiently, and in
their use of available parallel computing resources from high-performance parallel
supercomputers to conventional workstation clusters. NWChem software can handle:
biomolecules, nanostructures, and solid-state; from quantum to classical, and all
combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of
processors; properties and relativity.
Ninja: Ninja/1.10.0, Ninja/1.10.2
Ninja is a small build system with a focus on speed.
OPARI2: OPARI2/2.0.5, OPARI2/2.0.7
OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source
instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime
library calls with calls to the POMP2 measurement interface.
ORCA: ORCA/5.0.3
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with
specific emphasis on spectroscopic properties of open-shell molecules. It features a wide
variety of standard quantum chemical methods ranging from semiempirical methods to DFT to
single- and multireference correlated ab initio methods. It can also treat environmental and
relativistic effects.
OSU-Micro-Benchmarks: OSU-Micro-Benchmarks/5.6.3, OSU-Micro-Benchmarks/5.7.1, ...
OSU Micro-Benchmarks
OTF2: OTF2/2.2, OTF2/3.0.2
The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus
support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is
open for other tools.
OpenBLAS: OpenBLAS/0.3.9, OpenBLAS/0.3.18, OpenBLAS/0.3.20
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenCV: OpenCV/4.5.5-contrib, OpenCV/4.6.0-contrib
OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine
learning software library. OpenCV was built to provide a common infrastructure for computer
vision applications and to accelerate the use of machine perception in the commercial
products. Includes extra modules for OpenCV from the contrib repository.
OpenEXR: OpenEXR/3.1.1, OpenEXR/3.1.5
OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic
for use in computer imaging applications
OpenFOAM: OpenFOAM/v2112, OpenFOAM/v2206
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.
OpenJPEG: OpenJPEG/2.5.0
OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in
order to promote the use of JPEG 2000, a still-image compression standard from the Joint
Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and
ITU-T as a JPEG 2000 Reference Software.
OpenMPI: OpenMPI/4.0.3, OpenMPI/4.1.1, OpenMPI/4.1.4, OpenMPI/4.1.5
The Open MPI Project is an open source MPI-3 implementation.
OpenMolcas: OpenMolcas/22.10
OpenMolcas is a quantum chemistry software package.
OpenPGM: OpenPGM/5.2.122
OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM)
specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast
protocol that enables receivers to detect loss, request retransmission of lost data, or
notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means
the receiver is responsible for ensuring all data is received, absolving the sender of
reception responsibility.
OpenSSL: OpenSSL/1.1
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade,
full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3)
and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose
cryptography library.
PAPI: PAPI/6.0.0, PAPI/7.0.0
PAPI provides the tool designer and application engineer with a consistent interface and
methodology for use of the performance counter hardware found in most major microprocessors.
PAPI enables software engineers to see, in near real time, the relation between software
performance and processor events. In addition Component PAPI provides access to a collection
of components that expose performance measurement opportunites across the hardware and
software stack.
PCRE: PCRE/8.45
The PCRE library is a set of functions that implement regular expression pattern matching
using the same syntax and semantics as Perl 5.
PCRE2: PCRE2/10.37, PCRE2/10.40
The PCRE library is a set of functions that implement regular expression pattern matching
using the same syntax and semantics as Perl 5.
PDT: PDT/3.25.1
Program Database Toolkit (PDT) is a framework for analyzing source code written in several
programming languages and for making rich program knowledge accessible to developers of
static and dynamic analysis tools. PDT implements a standard program representation, the
program database (PDB), that can be accessed in a uniform way through a class library
supporting common PDB operations.
PLUMED: PLUMED/2.8.0, PLUMED/2.8.1
PLUMED is an open source library for free energy calculations in molecular systems which
works together with some of the most popular molecular dynamics engines. Free energy
calculations can be performed as a function of many order parameters with a particular focus
on biological problems, using state of the art methods such as metadynamics, umbrella
sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily
interfaced with both fortran and C/C++ codes.
PMIx: PMIx/3.1.5, PMIx/4.1.0, PMIx/4.1.2
Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to
provide an extended version of the PMI standard specifically designed to support clusters up
to and including exascale sizes. The overall objective of the project is not to branch the
existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing
PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some
current restrictions that impact scalability, and (b) provide a reference implementation of
the PMI-server that demonstrates the desired level of scalability.
PROJ: PROJ/8.1.0, PROJ/9.0.0
Program proj is a standard Unix filter function which converts geographic longitude and
latitude coordinates into cartesian coordinates
PSolver: PSolver/1.8.3
Interpolating scaling function Poisson Solver Library
Pango: Pango/1.48.8, Pango/1.50.7
Pango is a library for laying out and rendering of text, with an emphasis on
internationalization. Pango can be used anywhere that text layout is needed, though most of
the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms
the core of text and font handling for GTK+-2.x.
ParMETIS: ParMETIS/4.0.3
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for
partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse
matrices. ParMETIS extends the functionality provided by METIS and includes routines that are
especially suited for parallel AMR computations and large scale numerical simulations. The
algorithms implemented in ParMETIS are based on the parallel multilevel k-way
graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning
schemes.
ParaView: ParaView/5.9.1-mpi, ParaView/5.10.1-mpi
ParaView is a scientific parallel visualizer.
Perl: Perl/5.30.2-minimal, Perl/5.30.2, Perl/5.34.0-minimal, Perl/5.34.0, Perl/5.34.1-minimal, ...
Larry Wall's Practical Extraction and Report Language This is a minimal build without any
modules. Should only be used for build dependencies.
Pillow: Pillow/8.3.2, Pillow/9.1.1
Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging
Library by Fredrik Lundh and Contributors.
Pillow-SIMD: Pillow-SIMD/9.2.0
Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging
Library by Fredrik Lundh and Contributors.
PnetCDF: PnetCDF/1.12.1, PnetCDF/1.12.3
Parallel netCDF: A Parallel I/O Library for NetCDF File Access
PyCairo: PyCairo/1.21.0
Python bindings for the cairo library
PyGObject: PyGObject/3.42.1
PyGObject is a Python package which provides bindings for GObject based libraries such as
GTK, GStreamer, WebKitGTK, GLib, GIO and many more.
PyMC3: PyMC3/3.11.1
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning
with Theano
PyTorch: PyTorch/1.12.1
Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep
learning framework that puts Python first.
PyYAML: PyYAML/5.4.1, PyYAML/6.0
PyYAML is a YAML parser and emitter for the Python programming language.
Pysam: Pysam/0.17.0, Pysam/0.19.1
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of
the samtools C-API. Pysam also includes an interface for tabix.
Python: Python/2.7.18-bare, Python/3.8.2, Python/3.9.6-bare, Python/3.9.6, Python/3.10.4-bare, ...
Python is a programming language that lets you work more quickly and integrate your systems
more effectively.
Qhull: 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. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the
Quickhull algorithm for computing the convex hull.
Qt5: Qt5/5.15.2, Qt5/5.15.5
Qt is a comprehensive cross-platform C++ application framework.
QuantumESPRESSO: QuantumESPRESSO/7.0, QuantumESPRESSO/7.1
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure
calculations and materials modeling at the nanoscale. It is based on density-functional
theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
R: R/4.2.0, R/4.2.1
R is a free software environment for statistical computing and graphics.
R-bundle-Bioconductor: R-bundle-Bioconductor/3.15-R-4.2.0, R-bundle-Bioconductor/3.15-R-4.2.1
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic
data.
RE2: RE2/2022-02-01, RE2/2022-06-01
RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines
like those used in PCRE, Perl, and Python. It is a C++ library.
RapidJSON: RapidJSON/1.1.0
A fast JSON parser/generator for C++ with both SAX/DOM style API
Rust: Rust/1.54.0, Rust/1.60.0
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and
guarantees thread safety.
SAMtools: SAMtools/1.16.1
SAM Tools provide various utilities for manipulating alignments in the SAM format, including
sorting, merging, indexing and generating alignments in a per-position format.
SCOTCH: SCOTCH/6.0.9, SCOTCH/6.1.2, SCOTCH/7.0.1
Software package and libraries for sequential and parallel graph partitioning, static
mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SIONlib: SIONlib/1.7.6-tools, SIONlib/1.7.7-tools
SIONlib is a scalable I/O library for parallel access to task-local files. The library not
only supports writing and reading binary data to or from several thousands of processors into
a single or a small number of physical files, but also provides global open and close
functions to access SIONlib files in parallel. This package provides a stripped-down
installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols
to avoid conflicts when an application using SIONlib itself is linked against a tool
requiring a different SIONlib version.
SISSO: SISSO/3.1-20220324
A data-driven method combining symbolic regression and compressed sensing toward accurate &
interpretable models.
SPOTPY: SPOTPY/1.5.14
SPOTPY is a Python framework that enables the use of Computational optimization techniques
for calibration, uncertainty and sensitivity analysis techniques of almost every
(environmental-) model.
SQLite: SQLite/3.31.1, SQLite/3.36, SQLite/3.38.3
SQLite: SQL Database Engine in a C Library
STAR: STAR/2.7.9a
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
SUNDIALS: SUNDIALS/6.3.0
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
ScaFaCoS: ScaFaCoS/1.0.1
ScaFaCoS is a library of scalable fast coulomb solvers.
ScaLAPACK: ScaLAPACK/2.1.0-fb, ScaLAPACK/2.1.0, ScaLAPACK/2.2.0-fb
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned
for distributed memory MIMD parallel computers.
SciPy-bundle: SciPy-bundle/2021.10, SciPy-bundle/2022.05
Bundle of Python packages for scientific software
Score-P: Score-P/6.0, Score-P/8.0
The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for
profiling, event tracing, and online analysis of HPC applications.
Siesta: Siesta/4.1.5
SIESTA is both a method and its computer program implementation, to perform efficient
electronic structure calculations and ab initio molecular dynamics simulations of molecules
and solids.
SimPEG: SimPEG/0.18.1
An open source Python package for simulation and gradient based parameter estimation in
geophysical applications.
SuiteSparse: SuiteSparse/5.10.1-METIS-5.1.0, SuiteSparse/5.13.0-METIS-5.1.0
SuiteSparse is a collection of libraries manipulate sparse matrices.
SuperLU: SuperLU/5.3.0
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric
systems of linear equations on high performance machines.
Szip: Szip/2.1.1
Szip compression software, providing lossless compression of scientific data
TELEMAC-MASCARET: TELEMAC-MASCARET/8p3r1
TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow.
Having been used in the context of many studies throughout the world, it has become one of
the major standards in its field.
Tcl: Tcl/8.6.10, Tcl/8.6.11, Tcl/8.6.12
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming
language, suitable for a very wide range of uses, including web and desktop applications,
networking, administration, testing and many more.
TensorFlow: TensorFlow/2.8.4
An open-source software library for Machine Intelligence
Theano: Theano/1.1.2-PyMC
Theano is a Python library that allows you to define, optimize, and evaluate mathematical
expressions involving multi-dimensional arrays efficiently.
Tk: Tk/8.6.11, Tk/8.6.12
Tk is an open source, cross-platform widget toolchain that provides a library of basic
elements for building a graphical user interface (GUI) in many different programming
languages.
Tkinter: Tkinter/3.9.6, Tkinter/3.10.4
Tkinter module, built with the Python buildsystem
Togl: Togl/2.0
A Tcl/Tk widget for OpenGL rendering.
UCC: UCC/1.0.0
UCC (Unified Collective Communication) is a collective communication operations API and
library that is flexible, complete, and feature-rich for current and emerging programming
models and runtimes.
UCX: UCX/1.8.0, UCX/1.11.2, UCX/1.12.1
Unified Communication X An open-source production grade communication framework for data
centric and high-performance applications
UDUNITS: UDUNITS/2.2.26, UDUNITS/2.2.28
UDUNITS supports conversion of unit specifications between formatted and binary forms,
arithmetic manipulation of units, and conversion of values between compatible scales of
measurement.
UnZip: UnZip/6.0
UnZip is an extraction utility for archives compressed in .zip format (also called
"zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for
MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and
non-MSDOS functionality.
VTK: VTK/9.1.0, VTK/9.2.2
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.
Valgrind: Valgrind/3.16.1, Valgrind/3.18.1, Valgrind/3.20.0
Valgrind: Debugging and profiling tools
Voro++: Voro++/0.4.6
Voro++ is a software library for carrying out three-dimensional computations of the Voronoi
tessellation. A distinguishing feature of the Voro++ library is that it carries out
cell-based calculations, computing the Voronoi cell for each particle individually. It is
particularly well-suited for applications that rely on cell-based statistics, where features
of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of
particles.
Wannier90: Wannier90/3.1.0
A tool for obtaining maximally-localised Wannier functions
Wayland: Wayland/1.20.0
Wayland is a project to define a protocol for a compositor to talk to its clients as well as
a library implementation of the protocol. The compositor can be a standalone display server
running on Linux kernel modesetting and evdev input devices, an X application, or a wayland
client itself. The clients can be traditional applications, X servers (rootless or
fullscreen) or other display servers.
X11: X11/20200222, X11/20210802, X11/20220504
The X Window System (X11) is a windowing system for bitmap displays
XCrySDen: XCrySDen/1.6.2
XCrySDen is a crystalline and molecular structure visualisation program aiming at display of
isosurfaces and contours, which can be superimposed on crystalline structures and
interactively rotated and manipulated. It also possesses some tools for analysis of
properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone
for the band-structure plots, and visualisation of Fermi surfaces.
XZ: XZ/5.2.5
xz: XZ utilities
Xvfb: Xvfb/1.20.13, Xvfb/21.1.3
Xvfb is an X server that can run on machines with no display hardware and no physical input
devices. It emulates a dumb framebuffer using virtual memory.
YAXT: YAXT/0.9.2
Yet Another eXchange Tool
Yasm: Yasm/1.3.0
Yasm: Complete rewrite of the NASM assembler with BSD license
ZeroMQ: ZeroMQ/4.3.4
ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It
gives you sockets that carry atomic messages across various transports like in-process,
inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout,
pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for
clustered products. Its asynchronous I/O model gives you scalable multicore applications,
built as asynchronous message-processing tasks. It has a score of language APIs and runs on
most operating systems.
Zip: Zip/3.0
Zip is a compression and file packaging/archive utility. Although highly compatible both with
PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary
objectives have been portability and other-than-MSDOS functionality
ant: ant/1.10.11-Java-11, ant/1.10.12-Java-11
Apache Ant is a Java library and command-line tool whose mission is to drive processes
described in build files as targets and extension points dependent upon each other. The main
known usage of Ant is the build of Java applications.
archspec: archspec/0.1.3, archspec/0.1.4
A library for detecting, labeling, and reasoning about microarchitectures
arpack-ng: arpack-ng/3.8.0
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue
problems.
arrow-R: arrow-R/6.0.0.2-R-4.2.0, arrow-R/8.0.0-R-4.2.1
R interface to the Apache Arrow C++ library
astropy: astropy/5.0.4, astropy/5.1.1
The Astropy Project is a community effort to develop a single core package for Astronomy in
Python and foster interoperability between Python astronomy packages.
at-spi2-atk: at-spi2-atk/2.38.0
AT-SPI 2 toolkit bridge
at-spi2-core: at-spi2-core/2.40.3, at-spi2-core/2.44.1
Assistive Technology Service Provider Interface.
attr: attr/2.5.1
Commands for Manipulating Filesystem Extended Attributes
binutils: binutils/2.34, binutils/2.37, binutils/2.38
binutils: GNU binary utilities
buildenv: buildenv/default
This module sets a group of environment variables for compilers, linkers, maths libraries,
etc., that you can use to easily transition between toolchains when building your software.
To query the variables being set please use: module show <this module name>
bwidget: bwidget/1.9.15
The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x
namespaces.
bzip2: bzip2/1.0.8
bzip2 is a freely available, patent free, high-quality data compressor. It typically
compresses files to within 10% to 15% of the best available techniques (the PPM family of
statistical compressors), whilst being around twice as fast at compression and six times
faster at decompression.
cURL: cURL/7.69.1, cURL/7.78.0, cURL/7.83.0
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE,
FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP,
SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP
uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic,
Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
cairo: cairo/1.16.0, cairo/1.17.4
Cairo is a 2D graphics library with support for multiple output devices. Currently supported
output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image
buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS,
OS/2, and DirectFB
cppy: cppy/1.1.0, cppy/1.2.1
A small C++ header library which makes it easier to write Python extension modules. The
primary feature is a PyObject smart pointer which automatically handles reference counting
and provides convenience methods for performing common object operations.
cutadapt: cutadapt/3.5
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of
unwanted sequence from your high-throughput sequencing reads.
dill: dill/0.3.4
dill extends python's pickle module for serializing and de-serializing python objects to the
majority of the built-in python types. Serialization is the process of converting an object
to a byte stream, and the inverse of which is converting a byte stream back to on python
object hierarchy.
double-conversion: double-conversion/3.1.5, double-conversion/3.2.0
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
ecCodes: ecCodes/2.24.2, ecCodes/2.27.0
ecCodes is a package developed by ECMWF which provides an application programming interface
and a set of tools for decoding and encoding messages in the following formats: WMO FM-92
GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated
header (only decoding).
elfutils: elfutils/0.187
The elfutils project provides libraries and tools for ELF files and DWARF data.
expat: expat/2.2.9, expat/2.4.1, expat/2.4.8
Expat is an XML parser library written in C. It is a stream-oriented parser in which an
application registers handlers for things the parser might find in the XML document (like
start tags)
expecttest: expecttest/0.1.3
This library implements expect tests (also known as "golden" tests). Expect tests are a
method of writing tests where instead of hard-coding the expected output of a test, you run
the test to get the output, and the test framework automatically populates the expected
output. If the output of the test changes, you can rerun the test with the environment
variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.
flatbuffers: flatbuffers/2.0.0
FlatBuffers: Memory Efficient Serialization Library
flatbuffers-python: flatbuffers-python/2.0
Python Flatbuffers runtime library.
flex: flex/2.6.4
Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a
tokenizer, is a program which recognizes lexical patterns in text.
fontconfig: fontconfig/2.13.92, fontconfig/2.13.94, fontconfig/2.14.0
Fontconfig is a library designed to provide system-wide font configuration, customization and
application access.
foss: foss/2020a, foss/2021b, foss/2022a
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support,
OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
freetype: freetype/2.10.1, freetype/2.11.0, freetype/2.12.1
FreeType 2 is a software font engine that is designed to be small, efficient, highly
customizable, and portable while capable of producing high-quality output (glyph images). It
can be used in graphics libraries, display servers, font conversion tools, text image
generation tools, and many other products as well.
futile: futile/1.8.3
The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is
a set of modules and wrapper that encapsulate the most common low-level operations of a
Fortran code.
gettext: gettext/0.20.1, gettext/0.21
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on
which we may build many other steps. This package offers to programmers, translators, and
even users, a well integrated set of tools and documentation
giflib: giflib/5.2.1
giflib is a library for reading and writing gif images. It is API and ABI compatible with
libungif which was in wide use while the LZW compression algorithm was patented.
git: git/2.23.0-nodocs, git/2.33.1-nodocs, git/2.36.0-nodocs
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.
gnuplot: gnuplot/5.4.2, gnuplot/5.4.4
Portable interactive, function plotting utility
gompi: gompi/2020a, gompi/2021b, gompi/2022a
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
googletest: googletest/1.11.0
Google's framework for writing C++ tests on a variety of platforms
gperf: gperf/3.1
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a
hash function and hash table, in form of C or C++ code, for looking up a value depending on
the input string. The hash function is perfect, which means that the hash table has no
collisions, and the hash table lookup needs a single string comparison only.
graphite2: graphite2/1.3.14
Graphite is a "smart font" system developed specifically to handle the complexities of
lesser-known languages of the world.
groff: groff/1.22.4
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting
commands and produces formatted output.
gzip: gzip/1.10, gzip/1.12
gzip (GNU zip) is a popular data compression program as a replacement for compress
h5py: h5py/3.6.0, h5py/3.7.0
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format
library, version 5. HDF5 is a versatile, mature scientific software library designed for the
fast, flexible storage of enormous amounts of data.
help2man: help2man/1.47.12, help2man/1.48.3, help2man/1.49.2
help2man produces simple manual pages from the '--help' and '--version' output of other
commands.
hwloc: hwloc/2.2.0, hwloc/2.5.0, hwloc/2.7.1
The Portable Hardware Locality (hwloc) software package provides a portable abstraction
(across OS, versions, architectures, ...) of the hierarchical topology of modern
architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous
multithreading. It also gathers various system attributes such as cache and memory
information as well as the locality of I/O devices such as network interfaces, InfiniBand
HCAs or GPUs. It primarily aims at helping applications with gathering information about
modern computing hardware so as to exploit it accordingly and efficiently.
hypothesis: hypothesis/6.14.6, hypothesis/6.46.7
Hypothesis is an advanced testing library for Python. It lets you write tests which are
parametrized by a source of examples, and then generates simple and comprehensible examples
that make your tests fail. This lets you find more bugs in your code with less work.
iimpi: iimpi/2021b, iimpi/2022a
Intel C/C++ and Fortran compilers, alongside Intel MPI.
imkl: imkl/2021.4.0, imkl/2022.1.0
Intel oneAPI Math Kernel Library
imkl-FFTW: imkl-FFTW/2021.4.0, imkl-FFTW/2022.1.0
FFTW interfaces using Intel oneAPI Math Kernel Library
impi: impi/2021.4.0, impi/2021.6.0
Intel MPI Library, compatible with MPICH ABI
intel: intel/2021b, intel/2022a
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
intel-compilers: intel-compilers/2021.4.0, intel-compilers/2022.1.0
Intel C, C++ & Fortran compilers (classic and oneAPI)
intltool: intltool/0.51.0
intltool is a set of tools to centralize translation of many different file formats using GNU
gettext-compatible PO files.
iompi: iompi/2021b
Intel C/C++ and Fortran compilers, alongside Open MPI.
jbigkit: jbigkit/2.1
JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82),
which was designed for bi-level image data, such as scanned documents.
kim-api: kim-api/2.3.0
Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of
interatomic models (potentials) for atomistic simulations. This is a library that can be used
by simulation programs to get access to the models in the OpenKIM database. This EasyBuild
only installs the API, the models can be installed with the package openkim-models, or the
user can install them manually by running kim-api-collections-management install user
MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
libGLU: libGLU/9.0.2
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libGridXC: libGridXC/0.9.6
A library to compute the exchange and correlation energy and potential in spherical (i.e.
atoms) or periodic systems.
libaec: libaec/1.0.6
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers
(samples). The library achieves best results for low entropy data as often encountered in
space imaging instrument data or numerical model output from weather or climate simulations.
While floating point representations are not directly supported, they can also be efficiently
coded by grouping exponents and mantissa.
libarchive: libarchive/3.5.1, libarchive/3.6.1
Multi-format archive and compression library
libcerf: libcerf/1.17, libcerf/2.1
libcerf is a self-contained numeric library that provides an efficient and accurate
implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
libdap: libdap/3.20.8, libdap/3.20.11
A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client-
and Server-side support classes.
libdeflate: libdeflate/1.10
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
libdrm: libdrm/2.4.107, libdrm/2.4.110
Direct Rendering Manager runtime library.
libepoxy: libepoxy/1.5.8, libepoxy/1.5.10
Epoxy is a library for handling OpenGL function pointer management for you
libevent: libevent/2.1.11, libevent/2.1.12
The libevent API provides a mechanism to execute a callback function when a specific event
occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also
support callbacks due to signals or regular timeouts.
libfabric: libfabric/1.11.0, libfabric/1.13.2, libfabric/1.15.1
Libfabric is a core component of OFI. It is the library that defines and exports the
user-space API of OFI, and is typically the only software that applications deal with
directly. It works in conjunction with provider libraries, which are often integrated
directly into libfabric.
libffi: libffi/3.3, libffi/3.4.2
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.
libgd: libgd/2.3.3
GD is an open source code library for the dynamic creation of images by programmers.
libgeotiff: libgeotiff/1.7.0, libgeotiff/1.7.1
Library for reading and writing coordinate system information from/to GeoTIFF files
libgit2: libgit2/1.1.1, libgit2/1.4.3
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant
linkable library with a solid API, allowing you to write native speed custom Git applications
in any language which supports C bindings.
libglvnd: libglvnd/1.3.3, libglvnd/1.4.0
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple
vendors.
libiconv: libiconv/1.16, libiconv/1.17
Libiconv converts from one character encoding to another through Unicode conversion
libjpeg-turbo: libjpeg-turbo/2.0.6, libjpeg-turbo/2.1.3
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline
JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding,
decoding and transcoding.
libogg: libogg/1.3.5
Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
multimedia codecs.
libopus: libopus/1.3.1
Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for
interactive speech and music transmission over the Internet, but is also intended for storage
and streaming applications. It is standardized by the Internet Engineering Task Force (IETF)
as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT
codec.
libpciaccess: libpciaccess/0.16
Generic PCI access library.
libpng: libpng/1.6.37
libpng is the official PNG reference library
libreadline: libreadline/8.0, libreadline/8.1, libreadline/8.1.2
The GNU Readline library provides a set of functions for use by applications that allow users
to edit command lines as they are typed in. Both Emacs and vi editing modes are available.
The Readline library includes additional functions to maintain a list of previously-entered
command lines, to recall and perhaps reedit those lines, and perform csh-like history
expansion on previous commands.
libsndfile: libsndfile/1.0.31, libsndfile/1.1.0
Libsndfile is a C library for reading and writing files containing sampled sound (such as MS
Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
libsodium: libsodium/1.0.18
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures,
password hashing and more.
libtirpc: libtirpc/1.3.2
Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
libtool: libtool/2.4.6, libtool/2.4.7
GNU libtool is a generic library support script. Libtool hides the complexity of using shared
libraries behind a consistent, portable interface.
libunwind: libunwind/1.3.1, libunwind/1.5.0, libunwind/1.6.2
The primary goal of libunwind is to define a portable and efficient C programming interface
(API) to determine the call-chain of a program. The API additionally provides the means to
manipulate the preserved (callee-saved) state of each call-frame and to resume execution at
any point in the call-chain (non-local goto). The API supports both local (same-process) and
remote (across-process) operation. As such, the API is useful in a number of applications
libvdwxc: libvdwxc/0.4.0
libvdwxc is a general library for evaluating energy and potential for exchange-correlation
(XC) functionals from the vdW-DF family that can be used with various of density functional
theory (DFT) codes.
libvorbis: libvorbis/1.3.7
Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose
compressed audio format
libwebp: libwebp/1.2.0, libwebp/1.2.4
WebP is a modern image format that provides superior lossless and lossy compression for
images on the web. Using WebP, webmasters and web developers can create smaller, richer
images that make the web faster.
libxc: libxc/4.3.4, libxc/5.1.6, libxc/5.2.3
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.
libxml2: libxml2/2.9.10, libxml2/2.9.13
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside
of the Gnome platform).
libxslt: libxslt/1.1.34
Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the
Gnome platform).
libxsmm: libxsmm/1.17
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting
Intel Architecture (x86).
libyaml: libyaml/0.2.5
LibYAML is a YAML parser and emitter written in C.
lmod: lmod
Lmod: An Environment Module System
loompy: loompy/3.0.7
Python implementation of the Loom file format, an efficient file format for large omics
datasets
lxml: lxml/4.9.1
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
lz4: lz4/1.9.3
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It
features an extremely fast decoder, with speed in multiple GB/s per core.
make: make/4.3
GNU version of make utility
makeinfo: makeinfo/6.7-minimal
makeinfo is part of the Texinfo project, the official documentation format of the GNU
project. This is a minimal build with very basic functionality. Should only be used for build
dependencies.
matplotlib: matplotlib/3.4.3, matplotlib/3.5.2
matplotlib is a python 2D plotting library which produces publication quality figures in a
variety of hardcopy formats and interactive environments across platforms. matplotlib can be
used in python scripts, the python and ipython shell, web application servers, and six
graphical user interface toolkits.
mkl-service: mkl-service/2.3.0
Python hooks for Intel(R) Math Kernel Library runtime control settings.
ncurses: ncurses/6.1, ncurses/6.2, ncurses/6.3
The Ncurses (new curses) library is a free software emulation of curses in System V Release
4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and
forms characters and function-key mapping, and has all the other SYSV-curses enhancements
over BSD Curses.
ncview: ncview/2.1.8
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a
quick and easy, push-button look at your netCDF files. You can view simple movies of the
data, view along various dimensions, take a look at the actual data values, change color
maps, invert the data, etc.
netCDF: netCDF/4.7.4, netCDF/4.8.1, netCDF/4.9.0
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-C++4: netCDF-C++4/4.3.1
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-Fortran: netCDF-Fortran/4.5.2, netCDF-Fortran/4.5.3, netCDF-Fortran/4.6.0
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.
netcdf4-python: netcdf4-python/1.5.7, netcdf4-python/1.6.1
Python/numpy interface to netCDF.
nettle: nettle/3.7.3, nettle/3.8
Nettle is a cryptographic library that is designed to fit easily in more or less any context:
In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications
like LSH or GNUPG, or even in kernel space.
networkx: networkx/2.6.3, networkx/2.8.4
NetworkX is a Python package for the creation, manipulation, and study of the structure,
dynamics, and functions of complex networks.
nlohmann_json: nlohmann_json/3.10.5
JSON for Modern C++
nodejs: nodejs/14.17.6, nodejs/16.15.1
Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable
network applications. Node.js uses an event-driven, non-blocking I/O model that makes it
lightweight and efficient, perfect for data-intensive real-time applications that run across
distributed devices.
nsync: nsync/1.24.0, nsync/1.25.0
nsync is a C library that exports various synchronization primitives, such as mutexes
numactl: numactl/2.0.13, numactl/2.0.14
The numactl program allows you to run your application program on specific cpu's and memory
nodes. It does this by supplying a NUMA memory policy to the operating system before running
your program. The libnuma library provides convenient ways for you to add NUMA memory
policies into your own program.
numba: numba/0.54.1, numba/0.56.4
Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum
Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax
to machine code.
pigz: pigz/2.6
pigz, which stands for parallel implementation of gzip, is a fully functional replacement for
gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
pigz was written by Mark Adler, and uses the zlib and pthread libraries.
pixman: pixman/0.40.0
Pixman is a low-level software library for pixel manipulation, providing features such as
image compositing and trapezoid rasterization. Important users of pixman are the cairo
graphics library and the X server.
pkg-config: pkg-config/0.29.2
pkg-config is a helper tool used when compiling applications and libraries. It helps you
insert the correct compiler options on the command line so an application can use gcc -o test
test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on
where to find glib (or other libraries).
pkgconf: pkgconf/1.8.0
pkgconf is a program which helps to configure compiler and linker flags for development
libraries. It is similar to pkg-config from freedesktop.org.
pkgconfig: pkgconfig/1.5.5-python
pkgconfig is a Python module to interface with the pkg-config command line tool
pmi: pmi/pmix-x86_64
pplacer: pplacer/1.1.alpha19
Pplacer places query sequences on a fixed reference phylogenetic tree to maximize
phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer
is designed to be fast, to give useful information about uncertainty, and to offer advanced
visualization and downstream analysis.
prodigal: prodigal/2.6.3
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial
and archaeal) gene finding program developed at Oak Ridge National Laboratory and the
University of Tennessee.
protobuf: protobuf/3.17.3, protobuf/3.19.4
Google Protocol Buffers
protobuf-python: protobuf-python/3.17.3, protobuf-python/3.19.4
Python Protocol Buffers runtime library.
pybedtools: pybedtools/0.8.2, pybedtools/0.9.0
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within
Python.
pybind11: pybind11/2.7.1, pybind11/2.9.2
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice
versa, mainly to create Python bindings of existing C++ code.
python-isal: python-isal/0.11.1
Faster zlib and gzip compatible compression and decompression by providing python bindings
for the isa-l library.
re2c: re2c/2.2
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating
fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead
of using traditional table-driven approach, re2c encodes the generated finite state automata
directly in the form of conditional jumps and comparisons.
scikit-bio: scikit-bio/0.5.7
scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures,
algorithms and educational resources for bioinformatics.
scikit-build: scikit-build/0.11.1, scikit-build/0.15.0
Scikit-Build, or skbuild, is an improved build system generator for CPython
C/C++/Fortran/Cython extensions.
scikit-learn: scikit-learn/1.0.1, scikit-learn/1.0.2, scikit-learn/1.1.2
Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python
world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides
versatile tools for data mining and analysis in any field of science and engineering. It
strives to be simple and efficient, accessible to everybody, and reusable in various
contexts.
settarg: settarg
The settarg module provides a way to connect the loaded modules with your build system by
setting environment variables.
snakemake: snakemake/6.10.0, snakemake/7.22.0
The Snakemake workflow management system is a tool to create reproducible and scalable data
analyses.
snappy: snappy/1.1.9
Snappy is a compression/decompression library. It does not aim for maximum compression, or
compatibility with any other compression library; instead, it aims for very high speeds and
reasonable compression.
spglib-python: spglib-python/1.16.3, spglib-python/2.0.0
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in
C.
statsmodels: statsmodels/0.13.1
Statsmodels is a Python module that allows users to explore data, estimate statistical
models, and perform statistical tests.
tbb: tbb/2020.3, tbb/2021.5.0
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.
torchsampler: torchsampler/0.1.2
A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high
frequent ones.
torchvision: torchvision/0.13.1
Datasets, Transforms and Models specific to Computer Vision
tqdm: tqdm/4.62.3, tqdm/4.64.0
A fast, extensible progress bar for Python and CLI
typing-extensions: typing-extensions/3.10.0.2, typing-extensions/4.3.0
Typing Extensions – Backported and Experimental Type Hints for Python
utf8proc: utf8proc/2.6.1, utf8proc/2.7.0
utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and
other operations for data in the UTF-8 encoding.
util-linux: util-linux/2.35, util-linux/2.37, util-linux/2.38
Set of Linux utilities
worker: worker/1.6.12, worker/1.6.13
The Worker framework has been developed to help deal with parameter exploration experiments
that would otherwise result in many jobs, forcing the user resort to scripting to retain her
sanity; see also
https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.
x264: x264/20210613, x264/20220620
x264 is a free software library and application for encoding video streams into the
H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
x265: x265/3.5
x265 is a free software library and application for encoding video streams into the H.265 AVC
compression format, and is released under the terms of the GNU GPL.
xarray: xarray/0.20.1, xarray/2022.6.0, xarray/2022.9.0
xarray (formerly xray) is an open source project and Python package that aims to bring the
labeled data power of pandas to the physical sciences, by providing N-dimensional variants of
the core pandas data structures.
xmlf90: xmlf90/1.5.4
xmlf90 is a basic XML parsing library written in Fortran.
xorg-macros: xorg-macros/1.19.2, xorg-macros/1.19.3
X.org macros utilities.
xxd: xxd/8.2.4220
xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from
hexdumps of binary files.
zlib: zlib/1.2.11, zlib/1.2.12
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.
zstd: zstd/1.5.0, zstd/1.5.2
Zstandard is a real-time compression algorithm, providing high compression ratios. It offers
a very wide range of compression/speed trade-off, while being backed by a very fast decoder.
It also offers a special mode for small data, called dictionary compression, and can create
dictionaries from any sample set.