From 5440cd50bd2ced9e553a2f05789cdf97053d74c2 Mon Sep 17 00:00:00 2001
From: Lukas Krupcik <lukas.krupcik@vsb.cz>
Date: Thu, 31 Mar 2022 08:56:21 +0200
Subject: [PATCH] Thu, 31 Mar 2022 08:56:21 +0200

---
 barbora.md | 143 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 143 insertions(+)

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 | [GEOS](https://trac.osgeo.org/geos) | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
 | [GMP](https://gmplib.org/) | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. |
 | [libxsmm](https://github.com/hfp/libxsmm) | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). |
+| [MATLAB](http://www.mathworks.com/products/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](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview) | 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](https://www.mpfr.org) | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
+| [MUMPS](https://graal.ens-lyon.fr/MUMPS/) | A parallel sparse direct solver |
+| [Octave](http://www.gnu.org/software/octave/) | GNU Octave is a high-level interpreted language, primarily intended for numerical local_computations. |
+| [SCOTCH](https://gforge.inria.fr/projects/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](https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html) | Intel MPI Library, compatible with MPICH ABI |
+| [OpenMPI](https://www.open-mpi.org/) | The Open MPI Project is an open source MPI-3 implementation. |
+
+## Numlib
+
+| Module | Description |
+| ------ | ----------- |
+| [arpack-ng](https://github.com/opencollab/arpack-ng) | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
+| [BLIS](https://github.com/flame/blis/) | BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. |
+| [FFTW](http://www.fftw.org) | 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. |
+| [GSL](https://www.gnu.org/software/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](https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods) | 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](https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html) | Intel oneAPI Math Kernel Library |
+| [OpenBLAS](https://xianyi.github.com/OpenBLAS/) | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
+| [PETSc](https://www.mcs.anl.gov/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](https://www.netlib.org/scalapack/) | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
+| [SuiteSparse](https://faculty.cse.tamu.edu/davis/suitesparse.html) | SuiteSparse is a collection of libraries manipulate sparse matrices. |
+
+## Perf
+
+| Module | Description |
+| ------ | ----------- |
+| [Advisor](https://software.intel.com/intel-advisor-xe) | Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain |
+| [Vampir](http://www.vampir.eu) | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very local_complex performance monitoring data. |
+
+## Phys
+
+| Module | Description |
+| ------ | ----------- |
+| [BerkeleyGW](https://www.berkeleygw.org) | The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. |
+| [COMSOL](https://www.comsol.com) | COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. |
+| [DFTB+](https://www.dftb-plus.info) | DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. |
+| [Elk](http://elk.sourceforge.net/) | An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. |
+| [Gaussian](https://gaussian.com/) | 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. |
+| [QMCPACK](https://qmcpack.org/) | 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. |
+| [Siesta](http://departments.icmab.es/leem/siesta) | 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. |
+| [TB2J](https://python.org/) | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| [VASP](http://www.vasp.at) | 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 |
+| ------ | ----------- |
+| [BoltzTraP2](https://www.imc.tuwien.ac.at/index.php?id=21094) | 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. |
+
+## System
+
+| Module | Description |
+| ------ | ----------- |
+| [CUDA](https://developer.nvidia.com/cuda-toolkit) | CUDA (formerly Compute Unified Device Architecture) is a parallel 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 computational elements in CUDA GPUs. |
+| [CUDAcore](https://developer.nvidia.com/cuda-toolkit) | CUDA (formerly Compute Unified Device Architecture) is a parallel 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 computational elements in CUDA GPUs. |
+| [hwloc](http://www.open-mpi.org/projects/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. |
+| [libpciaccess](https://cgit.freedesktop.org/xorg/lib/libpciaccess/) | Generic PCI access library. |
+| [OpenSSL](https://www.openssl.org/) | 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. |
+
+## Toolchain
+
+| Module | Description |
+| ------ | ----------- |
+| [foss](https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain) | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
+| fosscuda | GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
+| gcccuda | GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. |
+| gompi | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. |
+| gompic | GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. |
+| [iimpi](https://software.intel.com/parallel-studio-xe) | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
+| [intel](https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain) | Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). |
+
+## Tools
+
+| Module | Description |
+| ------ | ----------- |
+| [ANSYS](http://www.ansys.com) | 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](https://directory.fsf.org/project/binutils/) | binutils: GNU binary utilities |
+| [bzip2](https://sourceware.org/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](http://curl.haxx.se) | libcurl is a free and easy-to-use client-side URL transfer library |
+| [DB](https://www.oracle.com/technetwork/products/berkeleydb) | Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. |
+| [EasyBuild](https://easybuilders.github.io/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](https://libexpat.github.io) | 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) |
+| [gettext](https://www.gnu.org/software/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 |
+| [git](https://git-scm.com/) | 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. |
+| [groff](https://www.gnu.org/software/groff) | Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. |
+| [gzip](https://www.gnu.org/software/gzip/) | gzip (GNU zip) is a popular data compression program as a replacement for compress |
+| [help2man](https://www.gnu.org/software/help2man/) | help2man produces simple manual pages from the '--help' and '--version' output of other commands. |
+| [hypothesis](https://github.com/HypothesisWorks/hypothesis) | 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. |
+| [libarchive](https://www.libarchive.org/) | Multi-format archive and compression library |
+| [Linda](https://gaussian.com/lindaprod//) | 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](https://mesonbuild.com) | Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. |
+| [MIKE](http://www.mikepoweredbydhi.com/) | MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide. |
+| NetKet | Old module, description not available. |
+| [networkx](https://pypi.python.org/pypi/networkx) | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. |
+| [Ninja](https://ninja-build.org/) | Ninja is a small build system with a focus on speed. |
+| [numactl](https://github.com/numactl/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. |
+| [OS7](support.it4i.cz) | This module activates the installed modules from RHEL7 or CentOS7. Old modules may be incompatible with the new RHEL8 OS. Users using these modules use them at their own risk without warranty from IT4Innovations. |
+| [OS8](support.it4i.cz) | This module activates the installed modules on RHEL8. |
+| [parallel](https://savannah.gnu.org/projects/parallel/) | parallel: Build and execute shell commands in parallel |
+| [pigz](http://zlib.net/pigz/) | 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 local_compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. |
+| [re2c](https://re2c.org/) | 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. |
+| [Singularity](https://github.com/sylabs/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. |
+| [Szip](https://www.hdfgroup.org/doc_resource/SZIP/) | Szip compression software, providing lossless compression of scientific data |
+| [UnZip](http://www.info-zip.org/UnZip.html) | 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. |
+| [util-linux](https://www.kernel.org/pub/linux/utils/util-linux) | Set of Linux utilities |
+| [VirtualGL](http://www.virtualgl.org) | 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. |
+| [XZ](https://tukaani.org/xz/) | xz: XZ utilities |
+
+## Vis
+
+| Module | Description |
+| ------ | ----------- |
+| [at-spi2-atk](https://wiki.gnome.org/Accessibility) | AT-SPI 2 toolkit bridge |
+| [at-spi2-core](https://wiki.gnome.org/Accessibility) | Assistive Technology Service Provider Interface. |
+| [ATK](https://developer.gnome.org/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. |
+| [Blender](https://www.blender.org/) | Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. |
+| [cairo](https://cairographics.org) | 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 |
+| [fontconfig](https://www.freedesktop.org/wiki/Software/fontconfig/) | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. |
+| [freetype](https://www.freetype.org) | 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](https://developer.gnome.org/gdk-pixbuf/stable/) | 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](http://www.gnu.org/software/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](https://www.gtk.org/) | GLib is one of the base libraries of the GTK+ project |
+| [gnuplot](http://gnuplot.sourceforge.net/) | Portable interactive, function plotting utility |
+| [HarfBuzz](https://www.freedesktop.org/wiki/Software/HarfBuzz) | HarfBuzz is an OpenType text shaping engine. |
+| [JasPer](https://www.ece.uvic.ca/~frodo/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](https://www.cl.cam.ac.uk/~mgk25/jbigkit/) | 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. |
+| [libGLU](https://mesa.freedesktop.org/archive/glu/) | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
+| [matplotlib](https://matplotlib.org) | 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. |
+| [Mesa](https://www.mesa3d.org/) | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
+| [OVITO](https://www.ovito.org/) | OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. |
+| [Pango](https://www.pango.org/) | 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. |
+| [Pillow](https://pillow.readthedocs.org/) | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
+| [pixman](http://www.pixman.org/) | 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. |
+| [Tk](https://www.tcl.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](https://www.vtk.org) | 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. |
+| [X11](https://www.x.org) | The X Window System (X11) is a windowing system for bitmap displays |
-- 
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