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. |
| GROMACS | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| RELION | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
Cae¶
| Module | Description |
|---|---|
| OpenFOAM | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
Chem¶
| Module | Description |
|---|---|
| ABINIT | ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. |
| ASE | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. |
| BEEF | BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. |
| CheMPS2 | CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
| CP2K | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
| dftd3-lib | This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. |
| GPAW | GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. |
| GPAW-setups | PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. |
| 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. |
| libvdwxc | libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. |
| libxc | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
| Molden | Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac |
| Molpro | Molpro is a local_complete system of ab initio programs for molecular electronic structure calculations. |
| NWChem | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. |
| 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. |
| spglib-python | Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. |
| TURBOMOLE | TURBOMOLE is a quantum chemical program package, initially developed in the group of Prof. Dr. Reinhart Ahlrichs at the University of Karlsruhe and at the Forschungszentrum Karlsruhe. Until 2007 the main development of the program was conducted by students and postdoctoral researchers in the group of Ahlrichs, who usually changed their field of work after leaving the group. Therefore, the code was well localized at and, consequently, owned by the University of Karlsruhe. However, since 2007 the situation has changed. Several people, who started their work with TURBOMOLE in Karlsruhe, still make significant contributions and feel responsible for the program, but do no longer reside in Karlsruhe. It was thus necessary to arrange the development of TURBOMOLE in a different manner, namely as a company. |
Compiler¶
| Module | Description |
|---|---|
| Clang | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. |
| GCC | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| GCCcore | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| Go | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. |
| icc | Intel C and C++ compilers |
| iccifort | Intel C, C++ & Fortran compilers |
| ifort | Intel Fortran 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 compiler) to use LLVM as an optimizer and code generator. |
| NVHPC | C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) |
| PGI | C, C++ and Fortran local_compilers from The Portland Group - PGI |
Data¶
| Module | Description |
|---|---|
| h5py | Test utilities for code working with files and commands |
| 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. |
| netCDF-Fortran | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
| 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 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-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 |
| Maven | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
| ncurses | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
| PCRE | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| PCRE2 | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| pkg-config | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries). |
| 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. |
| renderproto | Xrender protocol and ancillary headers |
| 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. |
| xcb-proto | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| xorg-macros | X.org macros utilities. |
| xproto | X protocol and ancillary headers |
| xtrans | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. |
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. |
| Guile | Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. |
| Java | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
| Julia | Julia is a high-level, high-performance dynamic programming language for numerical computing |
| Lua | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
| NASM | NASM: General-purpose x86 assembler |
| 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. |
| SciPy-bundle | Bundle of Python packages for scientific software |
| Tcl | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
| Tkinter | Tkinter module, built with the Python buildsystem |
| Yasm | Yasm: Complete rewrite of the NASM assembler with BSD license |
Lib¶
| Module | Description |
|---|---|
| AtsPy | Phonopy is an open source package of phonon calculations based on the supercell approach. |
| Check | Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. |
| Clang-Python-bindings | Python bindings for libclang |
| double-conversion | Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. |
| gc | The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. |
| GDRCopy | A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. |
| GlobalArrays | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model |
| ICU | ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. |
| IOTK | The input/output tool kit (IOTK) is a Fortran90 library intended to provide a simplified access to tagged files formatted using some specific rule. |
| libdrm | Direct Rendering Manager runtime library. |
| libepoxy | Epoxy is a library for handling OpenGL function pointer management for you |
| libevent | The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. |
| libfabric | Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. |
| libffi | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
| libgd | GD is an open source code library for the dynamic creation of images by programmers. |
| libglvnd | libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. |
| libiconv | Libiconv converts from one character encoding to another through Unicode conversion |
| libjpeg-turbo | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
| 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 |
| libpthread-stubs | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| 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 |
| libxcb | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
| 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. |
| NFFT | The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data. |
| NSPR | Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. |
| NSS | Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. |
| PMIx | Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. |
| PROJ | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
| pybind11 | pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. |
| 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. |
| snappy | Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. |
| 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. |
| MPFR | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
| MUMPS | A parallel sparse direct solver |
| numpy | NumPy is the fundamental package needed for scientific local_computing with Python. |
| 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 |
|---|---|
| Armadillo | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. |
| arpack-ng | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
| CGAL | The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. |
| 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. |
| Vampir | 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 |
|---|---|
| DFTB+ | 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 | 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 | 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. |
| TRIQS | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. |
| TRIQS-cthyb | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. cthyb = continuous-time hybridisation-expansion quantum Monte Carlo The TRIQS-based hybridization-expansion solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath for an arbitrary local interaction vertex. The “impurity” can be any set of orbitals, on one or several atoms. |
| TRIQS-dft_tools | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculation with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided. |
| TRIQS-hubbardI | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. hubbardI = An application using TRIQS to implement a Hubbard-I solver. |
| TRIQS-tprf | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. TPRF is a TRIQS-based two-particle response function tool box that implements basic operations for higher order response functions such as inversion, products, the random phase approximation, the bethe salpeter equation (in the local vertex approximation), etc.. The aim is to provide efficient (C++/OpenMP/MPI) implementations of the basic operations needed to compute the two-particle response in the different two-particle channels (particle-hole, particle-particle). |
| 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. |
| Yambo | Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. |
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. |
| CUDAcore | 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 | 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. |
| 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 local_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. |
| 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. |
| AtsPy | Phonopy is an open source package of phonon calculations based on the supercell approach. |
| 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 |
| DB | Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. |
| deepdiff | Python 2 and 3 local_compatibility library. |
| dos2unix | dos2unix includes utilities to convert text files with DOS or MAC line breaks to Unix line breaks and vice versa. It also includes conversion of UTF-16 to UTF-8. |
| 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. |
| espreso | Espreso is a set of several highly-scalable solvers based on the methods of domain decomposition designed to take full advantage of today's most powerful petascale supercomputers (pdf). It contains in-house developed FETI based algorithms including the Hybrid Total FETI method suitable for parallel machines with tens or hundreds of thousands of cores. The solver also contains a general API for usage in a third party software. The API has been successfully used to connect ESPRESO with the Elmer (pdf). Even though ESPRESO is C++ library, the API uses plain C only. Hence, it is easy to use it with various other languages such as Fortran. Both mesio and espreso can be configured by ecf files. In addition, espreso can be also configured by a simple GUI. |
| 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. |
| 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. |
| 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. |
| libarchive | Multi-format archive and compression library |
| LicenseChecker | Tools for Dr. Sevcik (mailto:dr.sevcik@vsb.cz)- checking license files |
| 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. |
| MIKE | MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide. |
| networkx | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of local_complex networks. |
| 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. |
| parallel | parallel: Build and execute shell commands in parallel |
| petsc4py | petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. |
| 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. |
| QEMU | QEMU is a generic and open source machine emulator and virtualizer. |
| re2c | 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. |
| 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 compression software, providing lossless compression of scientific data |
| UnZip | 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 | Set of Linux utilities |
| VDE2 | VDE is an ethernet local_compliant virtual network that can be spawned over a set of physical local_computer over the Internet. VDE is part of virtualsquare project. |
| 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 |
| grace | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
| Graphviz | Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. |
| 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. |
| GTS | GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. |
| 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. |
| kbproto | X.org KBProto protocol headers. |
| libGLU | The OpenGL Utility Library (GLU) is a local_computer graphics library for OpenGL. |
| libX11 | X11 client-side library |
| libXau | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. |
| libXdmcp | The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. |
| libXrender | X11 client-side library |
| LittleCMS | Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. |
| 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. |
| 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. |
| ParaView | ParaView is a scientific parallel visualizer. |
| Pillow | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
| 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. |
| VisIt | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool |
| 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. |