Available Barbora Modules
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. |
| 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. |
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. |
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 |
| 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. |
| 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. |
| 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. |
| 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). |
| 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. |
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. |
| 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. |
| Java | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| NASM | NASM: General-purpose x86 assembler |
| 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. |
| 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. |
Lib¶
| Module | Description |
|---|---|
| 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. |
| 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. |
| libtool | GNU libtool is a generic library support script. Libtool hides the local_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). |
| libyaml | LibYAML is a YAML 1.1 parser and emitter written in C. |
| 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. |
| 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. |
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 . |
| 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). |
| 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. |
| Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical local_computations. |
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. |
| 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. |
| OpenBLAS | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| ScaLAPACK | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
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. |
| 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 |
Phys¶
| Module | Description |
|---|---|
| phono3py | This software calculates phonon-phonon interaction related properties |
| phonopy | Phonopy is an open source package of phonon calculations based on the supercell approach. |
| 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 |
|---|---|
| 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. |
| decorator | Better living through Python with decorators. |
| deepdiff | Python 2 and 3 local_compatibility library. |
| 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. |
| 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. |
| pluggy | Plugin and hook calling mechanisms for python. |
| 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. |
| 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. |
| six | Python 2 and 3 local_compatibility library. |
| 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 local_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). |
| 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) |
| 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 | 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. |
| 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. |
| 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 |
| 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. |
| 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 |
| 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 |
|---|---|
| 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 |
| 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. |
| 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 |
| pixman | Pixman is a low-level software library for pixel manipulation, providing features such as image local_compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. |
| 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. |
| X11 | The X Window System (X11) is a windowing system for bitmap displays |