barbora.md

Bio

Module	Description
BLAST	Basic Local Alignment Search Tool, or BLAST, is an algorithm for local_comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
BWA	Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
FastQC	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.
GATK	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.
GROMACS	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. It also contains the gmxapi extension for the single precision MPI build.
picard	A set of tools (in Java) for working with next generation sequencing data in the BAM format.
Salmon	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
snpEff	SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

Cae

Module	Description
DualSPHysics	DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems.
OpenFOAM	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.

Chem

Module	Description
Amber	Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
ASE	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.
BEEF	BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
CheMPS2	CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
CoordgenLibs	Schrodinger-developed 2D Coordinate Generation
CP2K	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.
dftd3-lib	This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.
libcint	libcint is an open source library for analytical Gaussian integrals.
libGridXC	A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC.
Libint	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.
libxc	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.
Molden	Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
Molpro	Molpro is a local_complete system of ab initio programs for molecular electronic structure calculations.
OpenBabel	Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
OpenVDB	OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production.
ORCA	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.
PLUMED	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.
PySCF	PySCF is an open-source collection of electronic structure modules powered by Python.
QuantumESPRESSO	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).
spglib-python	Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
TURBOMOLE	TURBOMOLE is a quantum chemical program package, initially developed in the group of Prof. Dr. Reinhart Ahlrichs at the University of Karlsruhe and at the Forschungszentrum Karlsruhe. Until 2007 the main development of the program was conducted by students and postdoctoral researchers in the group of Ahlrichs, who usually changed their field of work after leaving the group. Therefore, the code was well localized at and, consequently, owned by the University of Karlsruhe. However, since 2007 the situation has changed. Several people, who started their work with TURBOMOLE in Karlsruhe, still make significant contributions and feel responsible for the program, but do no longer reside in Karlsruhe. It was thus necessary to arrange the development of TURBOMOLE in a different manner, namely as a company.
VASP	The Vienna Ab initio Simulation Package (VASP) is a local computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. To use VASP, you need an academic license from University of Vienna. Follow the instructions at https://www.vasp.at/index.php/faqs. Please send us a list of authorized users and their IDs for which you need access (use only http://support.it4i.cz/rt). We are responsible for verifying your licenses.
Wannier90	A tool for obtaining maximally-localised Wannier functions
XCFun	Arbitrary order exchange-correlation functional library

Compiler

Module	Description
Clang	C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
GCC	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	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,...).
Go	Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
icc	Intel C and C++ compilers
iccifort	Intel C, C++ & Fortran compilers
ifort	Intel Fortran compiler
intel-compilers	Intel C, C++ & Fortran compilers (classic and oneAPI)
LLVM	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.
NVHPC	C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

Data

Module	Description
CDO	CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
dill	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.
GDAL	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.
h5py	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.
HDF	HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
HDF5	HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
LAME	LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
libPSML	A library to handle PSML, the pseudopotential markup language.
netCDF	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 (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.
PnetCDF	Parallel netCDF: A Parallel I/O Library for NetCDF File Access
SoX	Sound eXchange, the Swiss Army knife of audio manipulation
xmlf90	xmlf90 is a basic XML parsing library written in Fortran.

Debugger

Module	Description
Forge	Allinea Forge is the local_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 local_complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
TotalView	TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with local_complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.
Valgrind	Valgrind: Debugging and profiling tools

Devel

Module	Description
Autoconf	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: GNU Standards-compliant Makefile generator
Autotools	This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
Bazel	Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
Boost	Boost provides free peer-reviewed portable C++ source libraries.
Boost.MPI	Boost provides free peer-reviewed portable C++ source libraries.
CMake	CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
DBus	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.
Doxygen	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.
GObject-Introspection	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.
gperf	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.
HyperQueue	HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated notes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.
intltool	intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
libdwarf	The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information))
libelf	libelf is a free ELF object file access library
libgit2	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.
libnsl	The libnsl package contains the public client interface for NIS(YP).
M4	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.
make	GNU version of make utility
makeinfo	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.
Mako	A super-fast templating language that borrows the best ideas from the existing templating languages
Maven	Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
ncurses	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.
PCRE	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
pkg-config	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 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 is a Python module to interface with the pkg-config command line tool
protobuf	Google Protocol Buffers
Qt5	Qt is a comprehensive cross-platform C++ application framework.
SQLite	SQLite: SQL Database Engine in a C Library
squashfs-tools	Squashfs is a local_compressed read-only filesystem for Linux.
SWIG	SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
xorg-macros	X.org macros utilities.

Lang

Module	Description
Anaconda3	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.
Bison	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.
flex	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.
FriBidi	The Free Implementation of the Unicode Bidirectional Algorithm.
Guile	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.
Java	Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Julia	Julia is a high-level, high-performance dynamic programming language for numerical computing
Lua	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.
NASM	NASM: General-purpose x86 assembler
nodejs	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.
Perl	Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies.
Python	Python is a programming language that lets you work more quickly and integrate your systems more effectively.
R	R is a free software environment for statistical computing and graphics.
Ruby	Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Rust	Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SciPy-bundle	Bundle of Python packages for scientific software
sqsgenerator	This package is a Special Quasirandom Structure generator written in Python3/Cython. Please note that the programm currently only works with Python 3.
Tcl	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.
Tkinter	Tkinter module, built with the Python buildsystem
Yasm	Yasm: Complete rewrite of the NASM assembler with BSD license

Lib

Module	Description
Brotli	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.
Check	Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.
double-conversion	Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
elfutils	The elfutils project provides libraries and tools for ELF files and DWARF data.
FLAC	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.
Flask	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 is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
gc	The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
GDRCopy	A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
GlobalArrays	Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
graphite2	Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.
ICU	ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
jemalloc	jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
libdrm	Direct Rendering Manager runtime library.
libepoxy	Epoxy is a library for handling OpenGL function pointer management for you
libevent	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 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	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	GD is an open source code library for the dynamic creation of images by programmers.
libgeotiff	Library for reading and writing coordinate system information from/to GeoTIFF files
libglvnd	libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libiconv	Libiconv converts from one character encoding to another through Unicode conversion
libjpeg-turbo	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.
libmad	MAD is a high-quality MPEG audio decoder.
libmatheval	GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
libogg	Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
libpng	libpng is the official PNG reference library
libreadline	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 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.
LibTIFF	tiff: Library and tools for reading and writing TIFF data files
libtirpc	Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
libtool	GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistring	This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwind	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
libvorbis	Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
libxml2	Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxslt	Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
lxml	The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
lz4	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.
NCCL	The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
nettle	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.
NSPR	Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSS	Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
PMIx	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.
pocl	Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard
PROJ	Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
pybind11	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.
RapidJSON	A fast JSON parser/generator for C++ with both SAX/DOM style API
scikit-build	Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
SDL2	SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SIONlib	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.
snappy	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.
tbb	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.
tblite	This project is an effort to create a library implementation of the extended tight binding (xTB) Hamiltonian which can be shared between xtb and dftb+. The current state of this project should be considered as highly experimental.
UCC	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	Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
UCX-CUDA	Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.
zlib	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	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.

Math

Module	Description
Eigen	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
ELPA	Eigenvalue SoLvers for Petaflop-Applications .
ELSI	ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
GEOS	GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GMP	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
libcerf	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.
libxsmm	LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
MATLAB	MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
MCR	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.
METIS	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	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPS	A parallel sparse direct solver
Octave	GNU Octave is a high-level interpreted language, primarily intended for numerical local_computations.
QD	Quad Double computation package
Qhull	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.
SCOTCH	Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.