karolina.md 139.66 KiB
Ai
| Module | Description |
|---|---|
| PyTorch | Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. |
Base
| Module | Description |
|---|---|
| Python | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| sysbench | sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server. |
Bio
| Module | Description |
|---|---|
| AlphaFold | AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known |
| Biopython | Biopython is a set of freely available tools for biological 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. |
| BWA | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| Cgicc | GNU Cgicc is an ANSI C++ compliant class library that greatly simplifies the creation of CGI applications for the World Wide Web |
| Cordax | CORDAX is an aggregation propensity predictor based on predicted packing energies. |
| ctffind | Program for finding CTFs of electron micrographs. |
| FastCGI | A High-Performance Web Server Interface |
| FoldX | FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. |
| GATK | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
| GROMACS | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| HH-suite | The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). |
| HMMER | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. |
| Kalign | Kalign is a fast multiple sequence alignment program for biological sequences. |
| mrcfile | mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. |
| OpenMM | OpenMM is a toolkit for molecular simulation. |
| picard | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| 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). |
| Salmon | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. |
| snpEff | SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). |
| Tango | N/A |
| Waltz | N/A |
Cae
| Module | Description |
|---|---|
| DualSPHysics | DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems. |
| OpenFOAM | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
| STAR-CCM+ | STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products operating under real-world conditions. |
Chem
| Module | Description |
|---|---|
| ABCluster | ABCluster a program for the global optimization of chemical cluster structures. |
| 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. |
| Amber | Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. |
| ASE | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed. |
| BEEF | BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. |
| CheMPS2 | CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
| CoordgenLibs | Schrodinger-developed 2D Coordinate Generation |
| CP2K | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
| CPPE | CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available. |
| cppe | CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available. |
| DFT-D3 | DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. |
| DFT-D4 | Generally Applicable Atomic-Charge Dependent London Dispersion Correction. |
| 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. |
| Dice | Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems. |
| dkh | Wolf, Reiher, and Hess's Douglas-Kroll-Hess relativistic correction at 2nd–4th order (http://www.reiher.ethz.ch/software/dkh-x2c.html) wrapped in CMake for Psi4 (https://github.com/psi4/psi4) |
| gau2grid | A collocation code for computing gaussians on a grid of the form: out_Lp = x^l y^m z^n \sum_i coeff_i e^(exponent_i * ( |
| gdma | Anthony Stone's GDMA (http://www-stone.ch.cam.ac.uk/programs.html) wrapped in CMake for Psi4 (https://github.com/psi4/psi4) |
| JANPA | JANPA package of programs Overview The aim of the package is to make Natural Population Analysis even more popular by providing a cross-platform open-source tool for performing this analysis. NEW! A new version 2.01 of the janpa program is available. This version features implementation of a newly developed localized property-optimized orbitals (LPOs) and 'the Chemist's LPOs' (CLPOs) orbital localization methods. The package consists of three programs: Janpa - takes MOLDEN-fompatible file as an input and performs NAO/NPA analysis molden2molden - converts MOLDEN-semi-compatible files produced by particular quantum chemistry packages into MOLDEN-compatible files (in an 'extended' MOLDEN format) nwchem2molden - prepares MOLDEN-compatible files from the results of electronic structure calculation done with NwChem Note: As indicated at the NwChem web-site starting from release 6.6 it should be capable of producing the molden files which are readily suitable for JANPA and invoking additional conversion with nwchem2molden should not be necessary |
| kim-api | Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. |
| 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. |
| libcint | libcint is an open source library for analytical Gaussian integrals. |
| libecpint | Libecpint is a C++ library for the efficient evaluation of integrals over ab initio effective core potentials, using a mixture of generated, recursive code and Gauss-Chebyshev quadrature. It is designed to be standalone and generic, and is now in its first stable release. If you experience any problems please raise an issue here; contributions and suggestions are also welcome. |
| libGridXC | A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. |
| Libint | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| Libint2 | Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions. This is the version used in PSI4! |
| 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. |
| mctc-lib | Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats. |
| 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. |
| mstore | Molecular structure store for testing |
| NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| NECI | Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemistry methods. |
| Newton-X | ACTC converts independent triangles into triangle strips or fans. |
| 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. |
| Octopus | Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. |
| 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. |
| OpenMolcas | OpenMolcas is a quantum chemistry software package |
| OpenVDB | OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. |
| ORCA | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. |
| PLUMED | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| 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. |
| PyBerny | PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information. |
| PyCheMPS2 | PyCheMPS2 is a python interface to CheMPS2, for compilation without MPI. CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
| pymatgen | Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. |
| PySCF | PySCF is an open-source collection of electronic structure modules powered by Python. |
| QuantumESPRESSO | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). |
| Schrodinger | Schrödinger aims to provide integrated software solutions and services that truly meet its customers▒~@~Y 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. |
| simint | Simint is a vectorized implementation of the Obara-Saika (OS) method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler. |
| Simple-DFTD3 | Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to provide a user-friendly and uniform interface to the D3 dispersion model and for the calculation of DFT-D3 dispersion corrections. |
| spglib-python | Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. |
| TURBOMOLE | TURBOMOLE is a quantum chemical program package, initially developed in the group of Prof. Dr. Reinhart Ahlrichs at the University of Karlsruhe and at the Forschungszentrum Karlsruhe. Until 2007 the main development of the program was conducted by students and postdoctoral researchers in the group of Ahlrichs, who usually changed their field of work after leaving the group. Therefore, the code was well localized at and, consequently, owned by the University of Karlsruhe. However, since 2007 the situation has changed. Several people, who started their work with TURBOMOLE in Karlsruhe, still make significant contributions and feel responsible for the program, but do no longer reside in Karlsruhe. It was thus necessary to arrange the development of TURBOMOLE in a different manner, namely as a company. |
| VASP | The Vienna Ab initio Simulation Package (VASP) is a local_computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. To use VASP, You need 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. |
| Wannier90 | A tool for obtaining maximally-localised Wannier functions |
| WIEN2k | The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features. |
| XCFun | Arbitrary order exchange-correlation functional library |
| xtb | xtb - An extended tight-binding semi-empirical program package. |
Compiler
| Module | Description |
|---|---|
| AOCC | AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0 |
| AOMP | AMD fork of LLVM, setup for OpenMP offloading to Accelerators |
| 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. |
| hipSYCL | hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP |
| icc | Intel C and C++ compilers |
| iccifort | Intel C, C++ & Fortran compilers |
| ifort | Intel Fortran compiler |
| intel-compilers | Intel C, C++ & Fortran compilers (classic and oneAPI) |
| LLVM | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing local_compiler) to use LLVM as an optimizer and code generator. |
| NVHPC | C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) |
Data
| Module | Description |
|---|---|
| AlphaPulldown | AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer |
| CDO | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. |
| dill | dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. |
| FLAC | Programs and libraries for working with Free Lossless Audio Codec (FLAC) files. |
| GDAL | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
| h5py | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
| HDF | HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. |
| HDF5 | HDF5 is a 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. |
| libPSML | A library to handle PSML, the pseudopotential markup language. |
| MEDCoupling | The MEDCoupling tool gathers several powerful functionalities around the input and output data of simulation codes (meshes and fields mainly). |
| medfile | The MED file format is a specialization of the HDF5 standard. |
| mkl-service | Python hooks for Intel(R) Math Kernel Library runtime control settings. |
| 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. |
| NodeODM | Request is designed to be the simplest way possible to make http calls. It supports HTTPS and follows redirects by default. |
| PnetCDF | Parallel netCDF: A Parallel I/O Library for NetCDF File Access |
| PostgreSQL | PostgreSQL is a powerful, open source object-relational database system. It is fully ACID 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. |
| pyproj | Python interface to PROJ4 library for cartographic transformations |
| scikit-learn | Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
| SoX | Sound eXchange, the Swiss Army knife of audio manipulation |
| xmlf90 | xmlf90 is a basic XML parsing library written in Fortran. |
Debugger
| Module | Description |
|---|---|
| Forge | Allinea Forge is the local_complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to local_complex parallel HPC codes with MPI, OpenMP, threads or CUDA. |
| GDB | The GNU Project Debugger |
| 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 |
| Bazel | Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. |
| Boost | Boost provides free peer-reviewed portable C++ source libraries. |
| Boost.MPI | Boost provides free peer-reviewed portable C++ source libraries. |
| CMake | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
| DBus | D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. |
| Doxygen | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
| flatbuffers | FlatBuffers: Memory Efficient Serialization Library |
| flatbuffers-python | Python Flatbuffers runtime library. |
| 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. |
| hipify-clang | Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced. |
| HyperQueue | HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated notes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs. |
| intltool | intltool is a set of tools to centralize translation of many different file formats using GNU gettext-local_compatible PO files. |
| JUnit | A programmer-oriented testing framework for Java. |
| libdwarf | The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) |
| libelf | libelf is a free ELF object file access library |
| libgit2 | libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. |
| libnsl | The libnsl package contains the public client interface for NIS(YP). |
| M4 | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
| make | GNU version of make utility |
| makeinfo | makeinfo is part of the Texinfo project, the official documentation format of the GNU project. |
| Mako | A super-fast templating language that borrows the best ideas from the existing templating languages |
| ncurses | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
| nsync | nsync is a C library that exports various synchronization primitives, such as mutexes |
| NVSHMEM | NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams. |
| PCRE | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| PCRE2 | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| pkg-config | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries). |
| pkgconf | pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. |
| pkgconfig | pkgconfig is a Python module to interface with the pkg-config command line tool |
| protobuf | Google Protocol Buffers |
| protobuf-python | Python Protocol Buffers runtime library. |
| pydantic | Data validation and settings management using Python type hinting. |
| PyTorch | Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. |
| Qt5 | Qt is a comprehensive cross-platform C++ application framework. |
| Qt6 | Qt is a comprehensive cross-platform C++ application framework. |
| rocm-cuda2hip | ROCm-HIPIFY : Tools to translate CUDA source code into portable HIP C++ automatically. |
| Spack | Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. |
| SQLite | SQLite: SQL Database Engine in a C Library |
| squashfs-tools | Squashfs is a local_compressed read-only filesystem for Linux. |
| SWIG | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
| texinfo | Texinfo is the official documentation format of the GNU project. |
| texlive | TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated. |
| typing-extensions | Typing Extensions – Backported and Experimental Type Hints for Python |
| xorg-macros | X.org macros utilities. |
| ZeroMQ | ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. |
Geo
| Module | Description |
|---|---|
| geopy | geopy is a Python client for several popular geocoding web services. geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, and landmarks across the globe using third-party geocoders and other data sources. |
| PROJ_4 | PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS. |