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Available Barbora Modules

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.

Chem

Module Description
CheMPS2 CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
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.
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 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.
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
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.
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.
PSI4 PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform local_computations with more than 2500 basis functions running serially or in parallel.
QuantumESPRESSO Quantum ESPRESSO is an integrated suite of local_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).
Schrodinger Schrödinger aims to provide integrated software solutions and services that truly meet its customers’ needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced local_computational techniques that transform the way chemists design local_compounds and materials.
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.

Compiler

Module Description
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 local_compiler
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 local_compiler) to use LLVM as an optimizer and code generator.
PGI C, C++ and Fortran local_compilers from The Portland Group - PGI

Data

Module Description
HDF5 HDF5 is a unique technology suite that makes possible the management of extremely large and local_complex data collections.
LAME LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
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.
PostgreSQL PostgreSQL is a powerful, open source object-relational database system. It is fully ACID local_compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.

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
ant 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.
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
Boost 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 local_comparison only.
guile Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
intltool intltool is a set of tools to centralize translation of many different file formats using GNU gettext-local_compatible PO files.
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.
Mako A super-fast templating language that borrows the best ideas from the existing templating languages
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).
pkgconfig pkgconfig is a Python module to interface with the pkg-config command line tool
Qt5 Qt is a local_comprehensive cross-platform C++ application framework.
ReFrame ReFrame is a framework for writing regression tests for HPC systems.
SQLite SQLite: SQL Database Engine in a C Library
squashfs-tools Squashfs is a 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.

Geo

Module Description
PROJ_4 PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.

Lang

Module Description
Anaconda3 Built to local_complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers local_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.
byacc Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular local_compiler.
Cython The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.
dotNET-Core-Runtime .NET is a free, cross-platform, open source developer platform for building many different types of applications.
dotNET-Core-SDK .NET is a free, cross-platform, open source developer platform for building many different types of applications.
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.
Java Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
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
numba 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.
Perl Larry Wall's Practical Extraction and Report Language
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.
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.
Yasm Yasm: Complete rewrite of the NASM assembler with BSD license

Lib

Module Description
ICU ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
libdrm Direct Rendering Manager runtime library.
libepoxy Epoxy is a library for handling OpenGL function pointer management for you
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.
libglvnd libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libjpeg-turbo libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG local_compression and delocal_compression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libmatheval GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
Libmsr Welcome to Libmsr, a friendly (well, friendlier) interface to many of the model-specific registers in Intel processors. Now with PCI configuration register support for some Intel hardware.
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
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
LibUUID Portable uuid C library
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).
libyaml LibYAML is a YAML 1.1 parser and emitter written in C.
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.
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.
phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
PyYAML PyYAML is a YAML parser and emitter for the Python programming language.
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.
SuperLU_DIST SuperLU_DIST contains a set of subroutines to solve a sparse linear system A*X=B. It uses Gaussian elimination with static pivoting (GESP). Static pivoting is a technique that combines the numerical stability of partial pivoting with the scalability of Cholesky (no pivoting), to run accurately and efficiently on large numbers of processors. SuperLU_DIST is a parallel extension to the serial SuperLU library. It is targeted for the distributed memory parallel machines. SuperLU_DIST is implemented in ANSI C, and MPI for communications. Currently, the LU factorization and triangular solution routines, which are the most time-consuming part of the solution process, are parallelized. The other routines, such as static pivoting and column preordering for sparsity are performed sequentially. This "alpha" release contains double-precision real and double-precision complex data types.
tbb Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are local_compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.
UCX Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
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 .
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.
libxsmm LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
magma The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
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.
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.
MUMPS A parallel sparse direct solver
Octave GNU Octave is a high-level interpreted language, primarily intended for numerical local_computations.
ParMETIS ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for local_computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR local_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.
SCOTCH Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

Mpi

Module Description
impi Intel MPI Library, local_compatible with MPICH ABI
OpenMPI The Open MPI Project is an open source MPI-2 implementation.

Numlib

Module Description
cuDNN The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
FFTW FFTW is a C subroutine library for local_computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and local_complex data.
GSL 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.
Hypre 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.
imkl Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
mkl Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
NLopt 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.
OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
PETSc PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SLEPc SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
SuiteSparse SuiteSparse is a collection of libraries manipulate sparse matrices.

Os

Module Description
CentOS The CentOS Project is a community-driven free software effort focused on delivering a robust open source ecosystem. For users, we offer a consistent manageable platform that suits a wide variety of deployments. For open source communities, we offer a solid, predictable base to build upon, along with extensive resources to build, test, release, and maintain their code. We’re also expanding the availability of CentOS images across a number of vendors, providing official images for Amazon, Google, and more. For self-hosted cloud, we also provide a generic cloud-init enabled image. For more information about updates and improvements in CentOS 7, please check out the release notes or the release announcement in the mailing list archive.
Debian Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it.
Fedora Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it.
Ubuntu Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it.

Perf

Module Description
Advisor Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
Cube 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.
CubeGUI 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.
CubeLib 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.
CubeWriter 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.
OPARI2 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.
OTF2 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.
PAPI 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.
PDT 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.
Score-P 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.

Phys

Module Description
Gaussian Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
MedeA Materials Design, Inc. announces the release of MedeA® version 2.22 software environment for atomistic materials modeling and simulation.
mumax GPU accelerated micromagnetic simulator.
phono3py This software calculates phonon-phonon interaction related properties
phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
QMCPACK QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense.
UDUNITS UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
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 academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.

Python

Module Description
ASE ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.
attrs Classes Without Boilerplate
Biopython Biopython is a set of freely available tools for biological local_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.
BoltzTraP2 BoltzTraP2 is a modern implementation of the smoothed Fourier interpolation algorithm for electronic bands that formed the base of the original and widely used BoltzTraP code.
click A simple wrapper around optparse for powerful command line utilities.
decorator Better living through Python with decorators.
deepdiff Python 2 and 3 local_compatibility library.
h5py Test utilities for code working with files and commands
lxml The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
Mako A super-fast templating language that borrows the best ideas from the existing templating languages
MarkupSafe Implements a XML/HTML/XHTML Markup safe string for Python.
matplotlib 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.
mpi4py MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
mpmath Python library for arbitrary-precision floating-point arithmetic.
networkx NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of local_complex networks.
numpy NumPy is the fundamental package needed for scientific local_computing with Python.
packaging Core utilities for Python packages.
pandas Powerful data structures for data analysis, time series,and statistics.
ParmEd Python 2 and 3 local_compatibility library.
phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
Pint Pint is a Python package to define, operate and manipulate physical quantities.
pluggy Plugin and hook calling mechanisms for python.
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.
pydantic Data validation and settings management using Python type hinting.
pyparsing The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.
pytest Simple powerful testing with Python
python-dateutil Useful extensions to the standard Python datetime features.
pytz pytz brings the Olson tz database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher.
scipy SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more.
SIP SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
six Python 2 and 3 local_compatibility library.
slepc4py Python bindings for SLEPc.
spglib Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
toml A Python library for parsing and creating TOML.
wheel A built-package format for Python.

System

Module Description
CUDA CUDA (formerly Compute Unified Device Architecture) is a parallel local_computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel local_computational elements in CUDA GPUs.
hwloc 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 local_computing hardware so as to exploit it accordingly and efficiently.
libgcrypt Libgpg-error is a small library that defines common error values for all GnuPG components.
libgpg-error Libgpg-error is a small library that defines common error values for all GnuPG components.
libpciaccess Generic PCI access library.

Toolchain

Module Description
foss GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
gompi GNU Compiler Collection (GCC) based local_compiler toolchain, including OpenMPI for MPI support.
iccifort Intel C, C++ & Fortran compilers
iimpi Intel C/C++ and Fortran compilers, alongside Intel MPI.
intel Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
intelcuda Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit
Py Python 3.6 toolchain

Tools

Module Description
ANSYS ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
binutils binutils: GNU binary utilities
bzip2 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 libcurl is a free and easy-to-use client-side URL transfer library
EasyBuild EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
expat 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)
fuse-ext2 Fuse-ext2 is an EXT2/EXT3/EXT4 filesystem for FUSE, and is built to work with osxfuse.
gettext 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
Ghostscript 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.
git Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
git-lfs Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
GLPK 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.
gperftools gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
gzip gzip (GNU zip) is a popular data compression program as a replacement for compress
help2man help2man produces simple manual pages from the '--help' and '--version' output of other commands.
Inspector Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications
latex Old module, description not available.
Linda TCP Linda is a parallel execution environment which has been used to create a parallel version of Gaussian for local area network and some distributed memory multiprocessor environments.
Meson Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
Ninja Ninja is a small build system with a focus on speed.
numactl 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.
petsc4py petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.
rpmrebuild rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use
SDE Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.
Singularity Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way.
Singularity-wrappers Wrappers for Singularity containers (mailto:easybuild@vsb.cz).
Szip Szip local_compression software, providing lossless local_compression of scientific data
util-linux Set of Linux utilities
VirtualGL VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.
VSCode Visual Studio Code is a distribution of the Code - OSS repository with Microsoft specific customizations released under a traditional Microsoft product license. Visual Studio Code combines the simplicity of a code editor with what developers need for their core edit-build-debug cycle. It provides local_comprehensive code editing, navigation, and understanding support along with lightweight debugging, a rich extensibility model, and lightweight integration with existing tools.
VTune Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
XZ xz: XZ utilities

Vis

Module Description
at-spi2-atk AT-SPI 2 toolkit bridge
at-spi2-core Assistive Technology Service Provider Interface.
ATK 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.
cairo 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
FFmpeg A local_complete, cross-platform solution to record, convert and stream audio and video.
FLTK FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
fontconfig Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
freetype 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.
Gdk-Pixbuf 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.
gettext 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
GLib GLib is one of the base libraries of the GTK+ project
gnuplot Portable interactive, function plotting utility
GST-plugins-base 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 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.
GTK+ 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.
HarfBuzz HarfBuzz is an OpenType text shaping engine.
ImageMagick ImageMagick is a software suite to create, edit, compose, or convert bitmap images
JasPer 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.
jbigkit Old module, description not available.
libGLU The OpenGL Utility Library (GLU) is a local_computer graphics library for OpenGL.
LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
OpenCV 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.
OVITO OVITO is a scientific visualization and analysis software for atomistic and particle simulation data.
Pango 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.
pixman 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.
PyQt5 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.
Tk 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.
VTK 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.
wxWidgets wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.
X11 The X Window System (X11) is a windowing system for bitmap displays
x264 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 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.

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